Novel nucleic acids and polypeptides

1. TECHNICAL FIELD

[0001] The present invention provides novel polynucleotides and proteins encoded by such polo nucleotides, along with uses for these polynucleotides and proteins, for example in therapeutic, diagnostic and research methods.

2. BACKGROUND

[0002] Technology aimed at the discovery of protein factors (including e.g., cytokines, such as lymphokines, interferons, circulating soluble factors, chemokines, and interleukins) has matured rapidly over the past decade. The now routine hybridization cloning and expression cloning techniques clone novel polynucleotides “directly” in the sense that they rely on information directly related to the discovered protein (i.e., partial DNA/amino acid sequence of the protein in the case of hybridization cloning; activity of the protein in the case of expression cloning). More recent “indirect” cloning techniques such as signal sequence cloning, which isolates DNA sequences based on the presence of a now well-recognized secretory leader sequence motif, as well as various PCR-based or low stringency hybridization-based cloning techniques, have advanced the state of the art by making available large numbers of DNA/amino acid sequences for proteins that are known to have biological activity, for example, by virtue of their secreted nature in the case of leader sequence cloning, by virtue of their cell or tissue source in the case of PCR-based techniques, or by virtue of structural similarity to other genes of known biological activity.

[0003] Identified polynucleotide and polypeptide sequences have numerous applications in, for example, diagnostics, forensics, gene mapping; identification of mutations responsible for genetic disorders or other traits, to assess biodiversity, and to produce many other types of data and products dependent on DNA and amino acid sequences.

3. SUMMARY OF THE INVENTION

[0004] The compositions of the present invention include novel isolated polypeptides, novel isolated polynucleotides encoding such polypeptides, including recombinant DNA molecules, cloned genes or degenerate variants thereof, especially naturally occurring variants such as allelic variants, antisense polynucleotide molecules, and antibodies that specifically recognize one or more epitopes present on such polypeptides, as well as hybridomas producing such antibodies.

[0005] The compositions of the present invention additionally include vectors, including expression vectors, containing the polynucleotides of the invention, cells genetically engineered to contain such polynucleotides and cells genetically engineered to express such polynucleotides.

[0006] The present invention relates to a collection or library of at least one novel nucleic acid sequence assembled from expressed sequence tags (ESTs) isolated mainly by sequencing by hybridization (SBH), and in some cases, sequences obtained from one or more public databases. The invention relates also to the proteins encoded by such polynucleotides, along with therapeutic, diagnostic and research utilities for these polynucleotides and proteins. These nucleic acid sequences are designated as SEQ ID NO: 1-245. The polypeptides sequences are designated SEQ ID NO: 246-490. The nucleic acids and polypeptides are provided in the Sequence Listing. In the nucleic acids provided in the Sequence Listing, A is adenosine; C is cytosine; G is guanine; T is thymine; and N is unknown or any of the four bases.

[0007] The nucleic acid sequences of the present invention also include, nucleic acid sequences that hybridize to the complement of SEQ ID NO: 1-245 under stringent hybridization conditions; nucleic acid sequences which are allelic variants or species homologues of any of the nucleic acid sequences recited above, or nucleic acid sequences that encode a peptide comprising a specific domain or truncation of the peptides encoded by SEQ ID NO: 1-245. A polynucleotide comprising a nucleotide sequence having at least 90% identity to an identifying sequence of SEQ ID NO: 1-245 or a degenerate variant or fragment thereof. The identifying sequence can be 100 base pairs in length.

[0008] The nucleic acid sequences of the present invention also include the sequence information from the nucleic acid sequences of SEQ ID NO: 1-245. The sequence information can be a segment of any one of SEQ ID NO: 1-245 that uniquely identifies or represents the sequence information of SEQ ID NO: 1-245.

[0009] A collection as used in this application can be a collection of only one polynucleotide. The collection of sequence information or identifying information of each sequence can be provided on a nucleic acid array. In one embodiment, segments of sequence information are provided on a nucleic acid array to detect the polynucleotide that contains the segment. The array can be designed to detect full-match or mismatch to the polynucleotide that contains the segment. The collection can also be provided in a computer-readable format.

[0010] This invention also includes the reverse or direct complement of any of the nucleic acid sequences recited above; cloning or expression vectors containing the nucleic acid sequences; and host cells or organisms transformed with these expression vectors. Nucleic acid sequences (or their reverse or direct complements) according to the invention have numerous applications in a variety of techniques known to those skilled in the art of molecular biology, such as use as hybridization probes, use as primers for PCR, use in an array, use in computer-readable media, use in sequencing full-length genes, use for chromosome and gene mapping, use in the recombinant production of protein, and use in the generation of anti-sense DNA or RNA, their chemical analogs and the like.

[0011] In a preferred embodiment, the nucleic acid sequences of SEQ ID NO: 1-245 or novel segments or parts of the nucleic acids of the invention are used as primers in expression assays that are well known in the art. In a particularly preferred embodiment, the nucleic acid sequences of SEQ ID NO: 1-245 or novel segments or parts of the nucleic acids provided herein are used in diagnostics for identifying expressed genes or, as well known in the art and exemplified by Vollrath et al., Science 258:52-59 (1992), as expressed sequence tags for physical mapping of the human genome.

[0012] The isolated polynucleotides of the invention include, but are not limited to, a polynucleotide comprising any one of the nucleotide sequences set forth in SEQ ID NO: 1-245; a polynucleotide comprising any of the full length protein coding sequences of SEQ ID NO: 1-245; and a polynucleotide comprising any of the nucleotide sequences of the mature protein coding sequences of SEQ ID NO: 1-245. The polynucleotides of the present invention also include, but are not limited to, a polynucleotide that hybridizes under stringent hybridization conditions to (a) the complement of any one of the nucleotide sequences set forth in SEQ ID NO: 1-245; (b) a nucleotide sequence encoding any one of the amino acid sequences set forth in the Sequence Listing; (c) a polynucleotide which is an allelic variant of any polynucleotides recited above; (d) a polynucleotide which encodes a species homolog (e.g. orthologs) of any of the proteins recited above; or (e) a polynucleotide that encodes a polypeptide comprising a specific domain or truncation of any of the polypeptides comprising an amino acid sequence set forth in the Sequence Listing.

[0013] The isolated polypeptides of the invention include, but are not limited to, a polypeptide comprising any of the amino acid sequences set forth in SEQ ID NO: 246-490; or the corresponding full length or mature protein. Polypeptides of the invention also include polypeptides with biological activity that are encoded by (a) any of the polynucleotides having a nucleotide sequence set forth in SEQ ID NO: 1-245; or (b) polynucleotides that hybridize to the complement of the polynucleotides of (a) under stringent hybridization conditions. Biologically or immunologically active variants of any of the polypeptide sequences in the Sequence Listing, and “substantial equivalents” thereof (e.g., with at least about 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98% or 99% amino acid sequence identity) that preferably retain biological activity are also contemplated. The polypeptides of the invention may be wholly or partially chemically synthesized but are preferably produced by recombinant means using the genetically engineered cells (e.g. host cells) of the invention.

[0014] The invention also provides compositions comprising a polypeptide of the invention. Polypeptide compositions of the invention may further comprise an acceptable carrier, such as a hydrophilic, e.g., pharmaceutically acceptable, carrier.

[0015] The invention also provides host cells transformed or transfected with a polynucleotide of the invention.

[0016] The invention also relates to methods for producing a polypeptide of the invention comprising growing a culture of the host cells of the invention in a suitable culture medium under conditions permitting expression of the desired polypeptide, and purifying the polypeptide from the culture or from the host cells. Preferred embodiments include those in which the protein produced by such process is a mature form of the protein.

[0017] Polynucleotides according to the invention have numerous applications in a variety of techniques known to those skilled in the art of molecular biology. These techniques include use as hybridization probes, use as oligomers, or primers, for PCR, use for chromosome and gene mapping, use in the recombinant production of protein, and use in generation of anti-sense DNA or RNA, their chemical analogs and the like. For example, when the expression of an mRNA is largely restricted to a particular cell or tissue type, polynucleotides of the invention can be used as hybridization probes to detect the presence of the particular cell or tissue mRNA in a sample using, e.g., in situ hybridization.

[0018] In other exemplary embodiments, the polynucleotides are used in diagnostics as expressed sequence tags for identifying expressed genes or, as well known in the art and exemplified by Vollrath et al., Science 258:52-59 (1992), as expressed sequence tags for physical mapping of the human genome.

[0019] The polypeptides according to the invention can be used in a variety of conventional procedures and methods that are currently applied to other proteins. For example, a polypeptide of the invention can be used to generate an antibody that specifically binds the polypeptide. Such antibodies, particularly monoclonal antibodies, are useful for detecting or quantitating the polypeptide in tissue. The polypeptides of the invention can also be used as molecular weight markers, and as a food supplement.

[0020] Methods are also provided for preventing, treating, or ameliorating a medical condition which comprises the step of administering to a mammalian subject a therapeutically effective amount of a composition comprising a polypeptide of the present invention and a pharmaceutically acceptable carrier.

[0021] In particular, the polypeptides and polynucleotides of the invention can be utilized, for example, in methods for the prevention and/or treatment of disorders involving aberrant protein expression or biological activity.

[0022] The present invention further relates to methods for detecting the presence of the polynucleotides or polypeptides of the invention in a sample. Such methods can, for example, be utilized as part of prognostic and diagnostic evaluation of disorders as recited herein and for the identification of subjects exhibiting a predisposition to such conditions. The invention provides a method for detecting the polynucleotides of the invention in a sample, comprising contacting the sample with a compound that binds to and forms a complex with the polynucleotide of interest for a period sufficient to form the complex and under conditions sufficient to form a complex and detecting the complex such that if a complex is detected, the polynucleotide of interest is detected. The invention also provides a method for detecting the polypeptides of the invention in a sample comprising contacting the sample with a compound that binds to and forms a complex with the polypeptide under conditions and for a period sufficient to form the complex and detecting the formation of the complex such that if a complex is formed, the polypeptide is detected.

[0023] The invention also provides kits comprising polynucleotide probes and/or monoclonal antibodies, and optionally quantitative standards, for carrying out methods of the invention. Furthermore, the invention provides methods for evaluating the efficacy of drugs, and monitoring the progress of patients, involved in clinical trials for the treatment of disorders as recited above.

[0024] The invention also provides methods for the identification of compounds that modulate (i.e., increase or decrease) the expression or activity of the polynucleotides and/or polypeptides of the invention. Such methods can be utilized, for example, for the identification of compounds that can ameliorate symptoms of disorders as recited herein. Such methods can include, but are not limited to, assays for identifying compounds and other substances that interact with (e.g., bind to) the polypeptides of the invention. The invention provides a method for identifying a compound that binds to the polypeptides of the invention comprising contacting the compound with a polypeptide of the invention in a cell for a time sufficient to form a polypeptide/compound complex, wherein the complex drives expression of a reporter gene sequence in the cell; and detecting the complex by detecting the reporter gene sequence expression such that if expression of the reporter gene is detected the compound the binds to a polypeptide of the invention is identified.

[0025] The methods of the invention also provide methods for treatment which involve the administration of the polynucleotides or polypeptides of the invention to individuals exhibiting symptoms or tendencies. In addition, the invention encompasses methods for treating diseases or disorders as recited herein comprising administering compounds and other substances that modulate the overall activity of the target genie products. Compounds and other substances can effect such modulation either on the level of target gene/protein expression or target protein activity.

[0026] The polypeptides of the present invention and the polynucleotides encoding them are also useful for the same functions known to one of skill in the art as the polypeptides and polynucleotides to which they have homology (set forth in Table 2); for which they have a signature region (as set forth in Table 3); or for which they have homology to a gene family (as set forth in Table 4). If no homology is set forth for a sequence, then the polypeptides and polynucleotides of the present invention are useful for a variety of applications, as described herein, including use in arrays for detection.

4. DETAILED DESCRIPTION OF THE INVENTION

[0027] 4.1 Definitions

[0028] It must be noted that as used herein and in the appended claims, the singular forms a “an” and “the” include plural references unless the context clearly dictates otherwise.

[0029] The term “active” refers to those forms of the polypeptide which retain the biologic and/or immunologic activities of any naturally occurring polypeptide. According to the invention, the terms “biologically active” or “biological activity” refer to a protein or peptide having structural, regulatory or biochemical functions of a naturally occurring molecule. Likewise “immunologically active” or “immunological activity” refers to the capability of the natural, recombinant or synthetic polypeptide to induce a specific immune response in appropriate animals or cells and to bind with specific antibodies.

[0030] The term “activated cells” as used in this application are those cells which are engaged in extracellular or intracellular membrane trafficking, including the export of secretory or enzymatic molecules as part of a normal or disease process.

[0031] The terms “complementary” or “complementarity” refer to the natural binding of polynucleotides by base pairing. For example, the sequence 5′-AGT-3′ binds to the complementary sequence 3′-TCA-5′. Complementarity between two single-stranded molecules may be “partial” such that only some of the nucleic acids bind or it may be “complete” such that total complementarity exists between the single stranded molecules. The degree of complementarity between the nucleic acid strands has significant effects on the efficiency and strength of the hybridization between the nucleic acid strands.

[0032] The term “embryonic stem cells (ES)” refers to a cell that can give rise to many differentiated cell types in an embryo or an adult, including the germ cells. The term “germ line stem cells (GSCs)” refers to stem cells derived from primordial stem cells that provide a steady and continuous source of germ cells for the production of gametes. The term “primordial germ cells (PGCs)” refers to a small population of cells set aside from other cell lineages particularly from the yolk sac, mesenteries, or gonadal ridges during embryogenesis that have the potential to differentiate into germ cells and other cells. PGCs are the source from which GSCs and ES cells are derived. The PGCs, the GSCs and the ES cells are capable of self-renewal. Thus these cells not only populate the germ line and give rise to a plurality of terminally differentiated cells that comprise the adult specialized organs, but are able to regenerate themselves.

[0033] The term “expression modulating fragment,” EMF, means a series of nucleotides which modulates the expression of an operably linked ORF or another EMF.

[0034] As used herein, a sequence is said to “modulate the expression of an operably linked sequence” when the expression of the sequence is altered by the presence of the EMF. EMFs include, but are not limited to, promoters, and promoter modulating sequences (inducible elements). One class of EMFs are nucleic acid fragments which induce the expression of an operably linked ORF in response to a specific regulatory factor or physiological event.

[0035] The terms “nucleotide sequence” or “nucleic acid” or “polynucleotide” or “oligonculeotide” are used interchangeably and refer to a heteropolymer of nucleotides or the sequence of these nucleotides. These phrases also refer to DNA or RNA of genomic or synthetic origin which may be single-stranded or double-stranded and may represent the sense or the antisense strand, to peptide nucleic acid (PNA) or to any DNA-like or RNA-like material. In the sequences herein A is adenine, C is cytosine, T is thymine, G is guanine and N is A, C, G or T (U). It is contemplated that where the polynucleotide is RNA, the T (thymine) in the sequences provided herein is substituted with U (uracil). Generally, nucleic acid segments provided by this invention may be assembled from fragments of the genome and short oligonucleotide linkers, or from a series of oligonucleotides, or from individual nucleotides, to provide a synthetic nucleic acid which is capable of being expressed in a recombinant transcriptional unit comprising regulatory elements derived from a microbial or viral operon, or a eukaryotic gene.

[0036] The terms “oligonucleotide fragment” or a “polynucleotide fragment”. “portion,” or “segment” or “probe” or “primer” are used interchangeably and refer to a sequence of nucleotide residues which are at least about 5 nucleotides, more preferably at least about 7 nucleotides, more preferably at least about 9 nucleotides, more preferably at least about 11 nucleotides and most preferably at least about 17 nucleotides. The fragment is preferably less than about 500 nucleotides, preferably less than about 200 nucleotides, more preferably less than about 100 nucleotides, more preferably less than about 50 nucleotides and most preferably less than 30 nucleotides. Preferably the probe is from about 6 nucleotides to about 200 nucleotides, preferably from about 15 to about 50 nucleotides, more preferably from about 17 to 30 nucleotides and most preferably from about 20 to 25 nucleotides. Preferably the fragments can be used in polymerase chain reaction (PCR), various hybridization procedures or microarray procedures to identify or amplify identical or related parts of mRNA or DNA molecules. A fragment or segment may uniquely identify each polynucleotide sequence of the present invention. Preferably the fragment comprises a sequence substantially similar to any one of SEQ ID NO: 1-245.

[0037] Probes may, for example, be used to determine whether specific mRNA molecules are present in a cell or tissue or to isolate similar nucleic acid sequences from chromosomal DNA as described by Walsh et al. (Walsh, P. S. et al., 1992, PCR Methods Appl 1:241-250). They may be labeled by nick translation, Klenow fill-in reaction, PCR, or other methods well known in the art. Probes of the present invention, their preparation and/or labeling are elaborated in Sambrook, J. et al., 1989, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, NY; or Ausubel, F. M. et al., 1989, Current Protocols in Molecular Biology, John Wiley & Sons. New York N.Y. both of which are incorporated herein by reference in their entirety.

[0038] The nucleic acid sequences of the present invention also include the sequence information from the nucleic acid sequences of SEQ ID NO: 1-245. The sequence information can be a segment of any one of SEQ ID NO: 1-245 that uniquely identifies or represents the sequence information of that sequence of SEQ ID NO: 1-245. One such segment can be a twenty-mer nucleic acid sequence because the probability that a twenty-mer is fully matched in the human genome is 1 in 300. In the human genome, there are three billion base pairs in one set of chromosomes. Because 420 possible twenty-mers exist, there are 300 times more twenty-mers than there are base pairs in a set of human chromosomes. Using the same analysis, the probability for a seventeen-mer to be fully matched in the human genome is approximately 1 in 5. When these segments are used in arrays for expression studies, fifteen-mer segments can be used. The probability that the fifteen-mer is fully matched in the expressed sequences is also approximately one in five because expressed sequences comprise less than approximately 5% of the entire genome sequence.

[0039] Similarly, when using sequence information for detecting a single mismatch, a segment can be a twenty-five mer. The probability that the twenty-five mer would appear in a human genome with a single mismatch is calculated by multiplying the probability for a full match (1÷425) times the increased probability for mismatch at each nucleotide position (3×25). The probability that an eighteen mer with a single mismatch can be detected in an array for expression studies is approximately one in five. The probability that a twenty-mer with a single mismatch can be detected in a human genome is approximately one in five.

[0040] The term “open reading frame,” ORF, means a series of nucleotide triplets coding for amino acids without any termination codons and is a sequence translatable into protein.

[0041] The terms “operably linked” or “operably associated” refer to functionally related nucleic acid sequences. For example, a promoter is operably associated or operably linked with a coding sequence if the promoter controls the transcription of the coding sequence. While operably linked nucleic acid sequences can be contiguous and in the same reading frame, certain genetic elements e.g. repressor genes are not contiguously linked to the coding sequence but still control transcription/translation of the coding sequence.

[0042] The term “pluripotent” refers to the capability of a cell to differentiate into a number of differentiated cell types that are present in an adult organism. A pluripotent cell is restricted in its differentiation capability in comparison to a totipotent cell.

[0043] The terms “polypeptide” or “peptide” or “amino acid sequence” refer to an oligopeptide, peptide, polypeptide or protein sequence or fragment thereof and to naturally occurring or synthetic molecules. A polypeptide “fragment,” “portion,” or “segment” is a stretch of amino acid residues of at least about 5 amino acids, preferably at least about 7 amino acids, more preferably at least about 9 amino acids and most preferably at least about 17 or more amino acids. The peptide preferably is not greater than about 500 amino acids, more preferably less than 200 amino acids more preferably less than 150 amino acids and most preferably less than 100 amino acids. Preferably the peptide is from about 5 to about 200 amino acids. To be active, any polypeptide must have sufficient length to display biological and/or immunological activity.

[0044] The term “naturally occurring polypeptide” refers to polypeptides produced by cells that have not been genetically engineered and specifically contemplates various polypeptides arising from post-translational modifications of the polypeptide including, but not limited to, acetylation, carboxylation, glycosylation, phosphorylation, lipidation and acylation.

[0045] The term “translated protein coding portion” means a sequence which encodes for the full length protein which may include any leader sequence or any processing sequence.

[0046] The term “mature protein coding sequence” means a sequence which encodes a peptide or protein without a signal or leader sequence. The “mature protein portion” means that portion of the protein which does not include a signal or leader sequence. The peptide may have been produced by processing in the cell which removes any leader/signal sequence. The mature protein portion may or may not include an initial methionine residue. The methionine residue may be removed from the protein during processing in the cell. The peptide may be produced synthetically or the protein may have been produced using a polynucleotide only encoding for the mature protein coding sequence.

[0047] The term “derivative” refers to polypeptides chemically modified by such techniques as ubiquitination, labeling (e.g., with radionuclides or various enzymes), covalent polymer attachment such as pegylation (derivatization with polyethylene glycol) and insertion or substitution by chemical synthesis of amino acids such as ornithine, which do not normally occur in human proteins.

[0048] The term “variant” (or “analog”) refers to any polypeptide differing from naturally occurring polypeptides by amino acid insertions, deletions, and substitutions, created using, e g., recombinant DNA techniques. Guidance in determining which amino acid residues may be replaced, added or deleted without abolishing activities of interest, may be found by comparing the sequence of the particular polypeptide with that of homologous peptides and minimizing the number of amino acid sequence changes made in regions of high homology (conserved regions) or by replacing amino acids with consensus sequence.

[0049] Alternatively, recombinant variants encoding these same or similar polypeptides may be synthesized or selected by making use of the “redundancy” in the genetic code. Various codon substitutions, such as the silent changes which produce various restriction sites, may be introduced to optimize cloning into a plasmid or viral vector or expression in a particular prokaryotic or eukaryotic system. Mutations in the polynucleotide sequence may be reflected in the polypeptide or domains of other peptides added to the polypeptide to modify the properties of any part of the polypeptide, to change characteristics such as ligand-binding affinities, interchain affinities, or degradation/turnover rate.

[0050] Preferably, amino acid “substitutions” are the result of replacing one amino acid with another amino acid having similar structural and/or chemical properties, i.e., conservative amino acid replacements. “Conservative” amino acid substitutions may be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the residues involved. For example, nonpolar (hydrophobic) amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, and methionine; polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine; positively charged (basic) amino acids include arginine, lysine, and histidine; and negatively charged (acidic) amino acids include aspartic acid and glutamic acid. “Insertions” or “deletions” are preferably in the range of about 1 to 20 amino acids, more preferably 1 to 10 amino acids. The variation allowed may be experimentally determined by systematically making insertions, deletions, or substitutions of amino acids in a polypeptide molecule using recombinant DNA techniques and assaying the resulting recombinant variants for activity.

[0051] Alternatively, where alteration of function is desired, insertions, deletions or non-conservative alterations can be engineered to produce altered polypeptides. Such alterations can, for example, alter one or more of the biological functions or biochemical characteristics of the polypeptides of the invention. For example, such alterations may change polypeptide characteristics such as ligand-binding affinities, interchain affinities, or degradation/turnover rate. Further, such alterations can be selected so as to generate polypeptides that are better suited for expression, scale up and the like in the host cells chosen for expression. For example, cysteine residues can be deleted or substituted with another amino acid residue in order to eliminate disulfide bridges.

[0052] The terms “purified” or “substantially purified” as used herein denotes that the indicated nucleic acid or polypeptide is present in the substantial absence of other biological macromolecules, e.g., polynucleotides, proteins, and the like. In one embodiment, the polynucleotide or polypeptide is purified such that it constitutes at least 95% by weight, more preferably at least 99% by weight, of the indicated biological macromolecules present (but water, buffers, and other small molecules, especially molecules having a molecular weight of less than 1000 daltons, can be present).

[0053] The term “isolated” as used herein refers to a nucleic acid or polypeptide separated from at least one other component (e.g., nucleic acid or polypeptide) present with the nucleic acid or polypeptide in its natural source. In one embodiment, the nucleic acid or polypeptide is found in the presence of (if anything) only a solvent, buffer, ion, or other component normally present in a solution of the same. The terms “isolated” and “purified” do not encompass nucleic acids or polypeptides present in their natural source.

[0054] The term “recombinant,” when used herein to refer to a polypeptide or protein, means that a polypeptide or protein is derived from recombinant (e.g., microbial, insect, or mammalian) expression systems. “Microbial” refers to recombinant polypeptides or proteins made in bacterial or fungal (e.g., yeast) expression systems. As a product, “recombinant microbial” defines a polypeptide or protein essentially free of native endogenous substances and unaccompanied by associated native glycosylation. Polypeptides or proteins expressed in most bacterial cultures, e.g., E. coli will be free of glycosylation modifications; polypeptides or proteins expressed in yeast will have a glycosylation pattern in general different from those expressed in mammalian cells.

[0055] The term “recombinant expression vehicle or vector” refers to a plasmid or phage or virus or vector, for expressing a polypeptide from a DNA (RNA) sequence. An expression vehicle can comprise a transcriptional unit comprising an assembly of (1) a genetic element or elements having a regulatory role in gene expression, for example, promoters or enhancers. (2) a structural or coding sequence which is transcribed into mRNA and translated into protein, and (3) appropriate transcription initiation and termination sequences. Structural units intended for use in yeast or eukaryotic expression systems preferably include a leader sequence enabling extracellular secretion of translated protein by a host cell. Alternatively, where recombinant protein is expressed without a leader or transport sequence, it may include an amino terminal methionine residue. This residue may or may not be subsequently cleaved from the expressed recombinant protein to provide a final product.

[0056] The term “recombinant expression system” means host cells which have stably integrated a recombinant transcriptional unit into chromosomal DNA or carry the recombinant transcriptional unit extrachromosomally. Recombinant expression systems as defined herein will express heterologous polypeptides or proteins upon induction of the regulatory elements linked to the DNA segment or synthetic gene to be expressed. This term also means host cells which have stably integrated a recombinant genetic element or elements having a regulatory role in gene expression, for example, promoters or enhancers. Recombinant expression systems as defined herein will express polypeptides or proteins endogenous to the cell upon induction of the regulatory elements linked to the endogenous DNA segment or gene to be expressed. The cells can be prokaryotic or eukaryotic.

[0057] The term “secreted” includes a protein that is transported across or through a membrane, including transport as a result of signal sequences in its amino acid sequence when it is expressed in a suitable host cell. “Secreted” proteins include without limitation proteins secreted wholly (e.g., soluble proteins) or partially (e.g., receptors) from the cell in which they are expressed. “Secreted” proteins also include without limitation proteins that are transported across the membrane of the endoplasmic reticulum. “Secreted” proteins are also intended to include proteins containing non-typical signal sequences (e.g. Interleukin-1 Beta, see Krasney, P. A. and Young, P. R. (1992) Cytokine 4(2): 134-143) and factors released from damaged cells (e.g. Interleukin-1 Receptor Antagonist, see Arend, W. P. et. al. (1998) Annu. Rev. Immunol. 16:27-55)

[0058] Where desired, an expression vector may be designed to contain a “signal or leader sequence” which will direct the polypeptide through the membrane of a cell. Such a sequence may be naturally present on the polypeptides of the present invention or provided from heterologous protein sources by recombinant DNA techniques.

[0059] The term “stringent” is used to refer to conditions that are commonly understood in the art as stringent. Stringent conditions can include highly stringent conditions (i.e., hybridization to filter-bound DNA in 0.5 M NaHPO4. 7% sodium dodecyl sulfate (SDS), 1 mM EDTA at 65° C. and washing in 0. 1×SSC/0.1% SDS at 68° C.), and moderately stringent conditions (i.e., washing in 0.2×SSC/0.1% SDS at 42° C.). Other exemplary hybridization conditions are described herein in the examples.

[0060] In instances of hybridization of deoxyoligonucleotides, additional exemplary stringent hybridization conditions include washing in 6×SSC/0.05% sodium pyrophosphate at 37° C. (for 14-base oligonucleotides), 48° C. (for 17-base oligos), 55° C. (for 20-base oligonucleotides), and 60° C. (for 23-base oligonucleotides).

[0061] As used herein, “substantially equivalent” can refer both to nucleotide and amino acid sequences, for example a mutant sequence, that varies from a reference sequence by one or more substitutions, deletions, or additions, the net effect of which does not result in an adverse functional dissimilarity between the reference and subject sequences. Typically, such a substantially equivalent sequence varies from one of those listed herein by no more than about 35% (i.e., the number of individual residue substitutions, additions, and/or deletions in a substantially equivalent sequence, as compared to the corresponding reference sequence, divided by the total number of residues in the substantially equivalent sequence is about 0.35 or less). Such a sequence is said to have 65% sequence identity to the listed sequence. In one embodiment, a substantially equivalent, e.g., mutant, sequence of the invention varies from a listed sequence by no more than 30% (70% sequence identity); in a variation of this embodiment, by no more than 25% (75% sequence identity); and in a further variation of this embodiment, by no more than 20% (80% sequence identity) and in a further variation of this embodiment, by no more than 10% (90% sequence identity) and in a further variation of this embodiment, by no more that 5% (95% sequence identity). Substantially equivalent, e.g., mutant, amino acid sequences according to the invention preferably have at least 80% sequence identity with a listed amino acid sequence, more preferably at least 85% sequence identity, more preferably at least 90% sequence identity, more preferably at least 95% identity, more preferably at least 98% identity, and most preferably at least 99% identity. Substantially equivalent nucleotide sequences of the invention can have lower percent sequence identities, taking into account, for example, the redundancy or degeneracy of the genetic code. Preferably, nucleotide sequence has at least about 65% identity, more preferably at least about 75% identity, more preferably at least about 80% sequence identity, more preferably at least about 85% sequence identity, more preferably at least about 90% sequence identity, and most preferably at least about 95% identity, more preferably at least about 98% sequence identity, and most preferably at least about 99% sequence identity. For the purposes of the present invention, sequences having substantially equivalent biological activity and substantially equivalent expression characteristics are considered substantially equivalent. For the purposes of determining equivalence, truncation of the mature sequence (e.g. via a mutation which creates a spurious stop codon) should be disregarded. Sequence identity may be determined, e.g. using the Jotun Hein method (Hein. J. (1990) Methods Enzymol. 183 :626-645). Identity between sequences can also be determined by other methods known in the art, e.g. by varying hybridization conditions.

[0062] The term “totipotent” refers to the capability of a cell to differentiate into all of the cell types of an adult organism.

[0063] The term “transformation” means introducing DNA into a suitable host cell so that the DNA is replicable, either as an extrachromosomal element, or by chromosomal integration. The term “transfection” refers to the taking up of an expression vector by a suitable host cell, whether or not any coding sequences are in fact expressed. The term “infection” refers to the introduction of nucleic acids into a suitable host cell by use of a virus or viral vector.

[0064] As used herein, an “uptake modulating fragment,” UMF, means a series of nucleotides which mediate the uptake of a linked DNA fragment into a cell. UMFs can be readily identified using known UMFs as a target sequence or target motif with the computer-based systems described below. The presence and activity of a UMF can be confirmed by attaching the suspected UMF to a marker sequence. The resulting nucleic acid molecule is then incubated with an appropriate host under appropriate conditions and the uptake of the marker sequence is determined. As described above, a UMF will increase the frequency of uptake of a linked marker sequence.

[0065] Each of the above terms is meant to encompass all that is described for each, unless the context dictates otherwise.

[0066] 4.2 Nucleic Acids of the Invention

[0067] Nucleotide sequences of the invention are set forth in the Sequence Listing.

[0068] The isolated polynucleotides of the invention include a polynucleotide comprising the nucleotide sequences of SEQ ID NO: 1-245; a polynucleotide encoding any one of the peptide sequences of SEQ ID NO: 246-490; and a polynucleotide comprising the nucleotide sequence encoding the mature protein coding sequence of the polypeptides of any one of SEQ ID NO: 246-490. The polynucleotides of the present invention also include, but are not limited to, a polynucleotide that hybridizes under stringent conditions to (a) the complement of any of the nucleotides sequences of SEQ ID NO: 1-245; (b) nucleotide sequences encoding any one of the amino acid sequences set forth in the Sequence Listing as SEQ ID NO: 246-490; (c) a polynucleotide which is an allelic variant of any polynucleotide recited above: (d) a polynucleotide which encodes a species homolog of any of the proteins recited above; or (e) a polynucleotide that encodes a polypeptide comprising a specific domain or truncation of the polypeptides of SEQ ID NO: 246-490. Domains of interest may depend on the nature of the encoded polypeptide; e.g. domains in receptor-like polypeptides include ligand-binding, extracellular, transmembrane, or cytoplasmic domains, or combinations thereof; domains in immunoglobulin-like proteins include the variable immunoglobulin-like domains; domains in enzyme-like polypeptides include catalytic and substrate binding domains; and domains in ligand polypeptides include receptor-binding domains.

[0069] The polynucleotides of the invention include naturally occurring or wholly or partially synthetic DNA, e.g., cDNA and genomic DNA, and RNA, e.g., mRNA. The polynucleotides may include all of the coding region of the cDNA or may represent a portion of the coding region of the cDNA.

[0070] The present invention also provides genes corresponding to the cDNA sequences disclosed herein. The corresponding genes can be isolated in accordance with known methods using the sequence information disclosed herein. Such methods include the preparation of probes or primers from the disclosed sequence information for identification and/or amplification of genes in appropriate genomic libraries or other sources of genomic materials. Further 5′ and 3′ sequence can be obtained using methods known in the art. For example, full length cDNA or genomic DNA that corresponds to any of the polynucleotides of SEQ ID NO: 1-245 can be obtained by screening appropriate cDNA or genomic DNA libraries under suitable hybridization conditions using any of the polynucleotides of SEQ ID NO: 1-245 or a portion thereof as a probe. Alternatively, the polynucleotides of SEQ ID NO: 1-245 may be used as the basis for suitable primer(s) that allow identification and/or amplification of genes in appropriate genomic DNA or cDNA libraries.

[0071] The nucleic acid sequences of the invention can be assembled from ESTs and sequences (including cDNA and genomic sequences) obtained from one or more public databases, such as dbEST, gbpri, and UniGene. The EST sequences can provide identifying sequence information, representative fragment or segment information, or novel segment information for the full-length gene.

[0072] The polynucleotides of the invention also provide polynucleotides including nucleotide sequences that are substantially equivalent to the polynucleotides recited above. Polynucleotides according to the invention can have, e.g., at least about 65%, at least about 70%, at least about 75%, at least about 80%, 81%, 82%, 83%, 84%, more typically at least about 85%, 86%, 87%, 88%, 89%, more typically at least about 90%, 91%, 92%, 93%, 94%, and even more typically at least about 95%, 96%, 97%, 98%, 99%, sequence identity to a polynucleotide recited above.

[0073] Included within the scope of the nucleic acid sequences of the invention are nucleic acid sequence fragments that hybridize under stringent conditions to any of the nucleotide sequences of SEQ ID NO: 1-245, or complements thereof, which fragment is greater than about 5 nucleotides, preferably 7 nucleotides, more preferably greater than 9 nucleotides and most preferably greater than 17 nucleotides. Fragments of, e.g. 15, 17, or 20 nucleotides or more that are selective for (i.e. specifically hybridize to) any one of the polynucleotides of the invention are contemplated. Probes capable of specifically hybridizing to a polynucleotide can differentiate polynucleotide sequences of the invention from other polynucleotide sequences in the same family of genes or can differentiate human genes from genes of other species, and are preferably based on unique nucleotide sequences.

[0074] The sequences falling within the scope of the present invention are not limited to these specific sequences, but also include allelic and species variations thereof. Allelic and species variations can be routinely determined by comparing the sequence provided in SEQ ID NO: 1-245, a representative fragment thereof, or a nucleotide sequence at least 90% identical, preferably 95% identical, to SEQ ID NO: 1-245 with a sequence from another isolate of the same species. Furthermore, to accommodate codon variability, the invention includes nucleic acid molecules coding for the same amino acid sequences as do the specific ORFs disclosed herein. In other words, in the coding region of an ORF, substitution of one codon for another codon that encodes the same amino acid is expressly contemplated.

[0075] The nearest neighbor or homology result for the nucleic acids of the present invention, including SEQ ID NO: 1-245, can be obtained by searching a database using an algorithm or a program. Preferably, a BLAST which stands for Basic Local Alignment Search Tool is used to search for local sequence alignments (Altshul, S. F. J Mol. Evol. 36 290-300 (1993) and Altschul S. F. et al. J. Mol. Biol. 21:403-410 (1990)). Alternatively a FASTA version 3 search against Genpept, using Fastxy algorithm.

[0076] Species homologs (or orthologs) of the disclosed polynucleotides and proteins are also provided by the present invention. Species homologs may be isolated and identified by making suitable probes or primers from the sequences provided herein and screening a suitable nucleic acid source from the desired species.

[0077] The invention also encompasses allelic variants of the disclosed polynucleotides or proteins; that is, naturally-occurring alternative forms of the isolated polynucleotide which also encode proteins which are identical, homologous or related to that encoded by the polynucleotides.

[0078] The nucleic acid sequences of the invention are further directed to sequences which encode variants of the described nucleic acids. These amino acid sequence variants may be prepared by methods known in the art by introducing appropriate nucleotide changes into a native or variant polynucleotide. There are two variables in the construction of amino acid sequence variants: the location of the mutation and the nature of the mutation. Nucleic acids encoding the amino acid sequence variants are preferably constructed by mutating the polynucleotide to encode an amino acid sequence that does not occur in nature. These nucleic acid alterations can be made at sites that differ in the nucleic acids from different species (variable positions) or in highly conserved regions (constant regions). Sites at such locations will typically be modified in series, e.g. by substituting first with conservative choices (e.g., hydrophobic amino acid to a different hydrophobic amino acid) and then with more distant choices (e.g., hydrophobic amino acid to a charged amino acid), and then deletions or insertions may be made at the target site. Amino acid sequence deletions generally range from about 1 to 30 residues, preferably about 1 to 10 residues, and are typically contiguous. Amino acid insertions include amino- and/or carboxyl-terminal fusions ranging in length from one to one hundred or more residues, as well as intrasequence insertions of single or multiple amino acid residues. Intrasequence insertions may range generally from about 1 to 10 amino residues, preferably from 1 to 5 residues. Examples of terminal insertions include the heterologous signal sequences necessary for secretion or for intracellular targeting in different host cells and sequences such as FLAG or poly-histidine sequences useful for purifying the expressed protein.

[0079] In a preferred method, polynucleotides encoding the novel amino acid sequences are changed via site-directed mutagenesis. This method uses oligonucleotide sequences to alter a polynucleotide to encode the desired amino acid variant, as well as sufficient adjacent nucleotides on both sides of the changed amino acid to form a stable duplex on either side of the site of being changed. In general, the techniques of site-directed mutagenesis are well known to those of skill in the art and this technique is exemplified by publications such as, Edelman et al., DNA 2:183 (1983). A versatile and efficient method for producing site-specific changes in a polynucleotide sequence was published by Zoller and Smith, Nucleic Acids Res. 10:6487-6500 (1982). PCR may also be used to create amino acid sequence variants of the novel nucleic acids. When small amounts of template DNA are used as starting material, primer(s) that differs slightly in sequence from the corresponding region in the template DNA can generate the desired amino acid variant. PCR amplification results in a population of product DNA fragments that differ from the polynucleotide template encoding the polypeptide at the position specified by the primer. The product DNA fragments replace the corresponding region in the plasmid and this gives a polynucleotide encoding the desired amino acid variant.

[0080] A further technique for generating amino acid variants is the cassette mutagenesis technique described in Wells et al. Gene 34:315 (1985); and other mutagenesis techniques well known in the art, such as, for example, the techniques in Sambrook et al. supra, and Current Protocols in Molecular Biology. Ausubel et al. Due to the inherent degeneracy of the genetic code, other DNA sequences Which encode substantially the same or a functionally equivalent amino acid sequence may be used in the practice of the invention for the cloning and expression of these novel nucleic acids. Such DNA sequences include those which are capable of hybridizing to the appropriate novel nucleic acid sequence under stringent conditions.

[0081] Polynucleotides encoding preferred polypeptide truncations of the invention can be used to generate polynucleotides encoding chimeric or fusion proteins comprising one or more domains of the invention and heterologous protein sequences.

[0082] The polynucleotides of the invention additionally include the complement of any of the polynucleotides recited above. The polynucleotide can be DNA (genomic, cDNA, amplified, or synthetic) or RNA. Methods and algorithms for obtaining such polynucleotides are well known to those of skill in the art and can include, for example, methods for determining hybridization conditions that can routinely isolate polynucleotides of the desired sequence identities.

[0083] In accordance with the invention, polynucleotide sequences comprising the mature protein coding sequences corresponding to any one of SEQ ID NO: 1-245, or functional equivalents thereof, may be used to generate recombinant DNA molecules that direct the expression of that nucleic acid, or a functional equivalent thereof, in appropriate host cells. Also included are the cDNA inserts of any of the clones identified herein.

[0084] A polynucleotide according to the invention can be joined to any of a variety of other nucleotide sequences by well-established recombinant DNA techniques (see Sambrook J et al. (1989) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, NY). Useful nucleotide sequences for joining to polynucleotides include an assortment of vectors, e.g., plasmids, cosmids, lambda phage derivatives, phagemids, and the like, that are well known in the art. Accordingly, the invention also provides a vector including a polynucleotide of the invention and a host cell containing the polynucleotide. In general, the vector contains an origin of replication functional in at least one organism, convenient restriction endonuclease sites, and a selectable marker for the host cell. Vectors according to the invention include expression vectors, replication vectors, probe generation vectors, and sequencing vectors. A host cell according to the invention can be a prokaryotic or eukaryotic cell and can be a unicellular organism or part of a multicellular organism.

[0085] The present invention further provides recombinant constructs comprising a nucleic acid having any of the nucleotide sequences of SEQ ID NO: 1-245 or a fragment thereof or any other polynucleotides of the invention. In one embodiment, the recombinant constructs of the present invention comprise a vector, such as a plasmid or viral vector, into which a nucleic acid having any of the nucleotide sequences of SEQ ID NO: 1-245 or a fragment thereof is inserted, in a forward or reverse orientation. In the case of a vector comprising one of the ORFs of the present invention, the vector ma! further comprise regulatory sequences, including for example, a promoter, operably linked to the ORF. Large numbers of suitable vectors and promoters are known to those of skill in the art and are commercially available for generating the recombinant constructs of the present invention. The following vectors are provided by way of example. Bacterial: pBs, phagescript. PsiX174, pBluescript SK, pBs KS, pNH8a, pNH16a, pNH18a, pNH46a (Stratagene); pTrc99A, pKK223-3, pKK233-3, pDR540, pRIT5 (Pharmacia). Eukaryotic: pWLneo, pSV2cat, pOG44, PXTI, pSG (Stratagene) pSVK3, pBPV, pMSG, pSVL (Pharmacia).

[0086] The isolated polynucleotide of the invention may be operably linked to an expression control sequence such as the pMT2 or pED expression vectors disclosed in Kaufman et al., Nucleic Acids Res. 19, 4485-4490 (1991), in order to produce the protein recombinantly. Many suitable expression control sequences are known in the art. General methods of expressing recombinant proteins are also known and are exemplified in R. Kaufman, Methods in Enzymology 185, 537-566 (1990). As defined herein “operably linked” means that the isolated polynucleotide of the invention and an expression control sequence are situated within a vector or cell in such a way that the protein is expressed by a host cell which has been transformed (transfected) with the ligated polynucleotide/expression control sequence.

[0087] Promoter regions can be selected from any desired gene using CAT (chloramphenicol transferase) vectors or other vectors with selectable markers. Two appropriate vectors are pKK232-8 and pCM7. Particular named bacterial promoters include lac, lacZ, T3, T7, gpt, lambda PR, and trc. Eukaryotic promoters include CMV immediate early, HSV thymidine kinase, early and late SV40, LTRs from retrovirus, and mouse metallothionein-1. Selection of the appropriate vector and promoter is well within the level of ordinary skill in the art. Generally, recombinant expression vectors will include origins of replication and selectable markers permitting transformation of the host cell, e.g., the ampicillin resistance gene of E. coli and S. cerevisiae TRPI gene, and a promoter derived from a highly-expressed gene to direct transcription of a downstream structural sequence. Such promoters can be derived from operons encoding glycolytic enzymes such as 3-phosphoglycerate kinase (PGK), a-factor, acid phosphatase, or heat shock proteins, among others. The heterologous structural sequence is assembled in appropriate phase with translation initiation and termination sequences, and preferably, a leader sequence capable of directing secretion of translated protein into the periplasmic space or extracellular medium. Optionally, the heterologous sequence can encode a fusion protein including an amino terminal identification peptide imparting desired characteristics, e.g. stabilization or simplified purification of expressed recombinant product. Useful expression vectors for bacterial use are constructed by inserting a structural DNA sequence encoding a desired protein together With suitable translation initiation and termination signals in operable reading phase with a functional promoter. The vector will comprise one or more phenotypic selectable markers and an origin of replication to ensure maintenance of the vector and to, if desirable, provide amplification within the host. Suitable prokaryotic hosts for transformation include E. coli, Bacillus subtilis, Salmonella typhimurium and various species within the genera Pseudomonas, Streptomyces, and Staphylococcus, although others may also be employed as a matter of choice.

[0088] As a representative but non-limiting example, useful expression vectors for bacterial use can comprise a selectable marker and bacterial origin of replication derived from commercially available plasmids comprising genetic elements of the well known cloning vector pBR322 (ATCC 37017). Such commercial vectors include, for example, pKK223-3 (Pharmacia Fine Chemicals, Uppsala, Sweden) and GEM 1 (Promega Biotech, Madison, Wis., USA). These pBR322 “backbone” sections are combined with an appropriate promoter and the structural sequence to be expressed. Following transformation of a suitable host strain and growth of the host strain to an appropriate cell density, the selected promoter is induced or derepressed by appropriate means (e.g. temperature shift or chemical induction) and cells are cultured for an additional period. Cells are typically harvested by centrifugation, disrupted by physical or chemical means, and the resulting crude extract retained for further purification.

[0089] Polynucleotides of the invention can also be used to induce immune responses. For example, as described in Fan et al., Nat. Biotech. 17:870-872 (1999), incorporated herein by reference, nucleic acid sequences encoding a polypeptide may be used to generate antibodies against the encoded polypeptide following topical administration of naked plasmid DNA or following injection, and preferably intramuscular injection of the DNA. The nucleic acid sequences are preferably inserted in a recombinant expression vector and may be in the form of naked DNA.

[0090] 4.3 Antisense Nucleic Acids

[0091] Another aspect of the invention pertains to isolated antisense nucleic acid molecules that are hybridizable to or complementary to the nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO: 1-245, or fragments, analogs or derivatives thereof. An “antisense” nucleic acid comprises a nucleotide sequence that is complementary to a “sense” nucleic acid encoding a protein, e.g., complementary to the coding strand of a double-stranded cDNA molecule or complementary to an mRNA sequence. In specific aspects, antisense nucleic acid molecules are provided that comprise a sequence complementary to at least about 10, 25, 50, 100, 250 or 500 nucleotides or an entire coding strand, or to only a portion thereof. Nucleic acid molecules encoding fragments, homologs, derivatives and analogs of a protein of any of SEQ ID NO: 246-490 or antisense nucleic acids complementary to a nucleic acid sequence of SEQ ID NO: 1-245 are additionally provided.

[0092] In one embodiment, an antisense nucleic acid molecule is antisense to a “coding region” of the coding strand of a nucleotide sequence of the invention. The term “coding region” refers to the region of the nucleotide sequence comprising codons which are translated into amino acid residues. In another embodiment, the antisense nucleic acid molecule is antisense to a “noncoding region” of the coding strand of a nucleotide sequence of the invention. The term “noncoding region” refers to 5′ and 3′ sequences which flank the coding region that are not translated into amino acids (i.e., also referred to as 5′ and 3′ untranslated regions).

[0093] Given the coding strand sequences encoding a nucleic acid disclosed herein (e.g., SEQ ID NO: 1-245), antisense nucleic acids of the invention can be designed according to the rules of Watson and Crick or Hoogsteen base pairing. The antisense nucleic acid molecule can be complementary to the entire coding region of an mRNA, but more preferably is an oligonucleotide that is antisense to only a portion of the coding or noncoding region of a mRNA. For example, the antisense oligonucleotide can be complementary to the region surrounding the translation start site of a mRNA. An antisense oligonucleotide can be, for example, about 5, 10, 15, 20, 25, 30, 35, 40, 45 or 50 nucleotides in length. An antisense nucleic acid of the invention can be constructed using chemical synthesis or enzymatic ligation reactions using procedures known in the art. For example, an antisense nucleic acid (e.g., an antisense oligonucleotide) can be chemically synthesized using naturally occurring nucleotides or variously modified nucleotides designed to increase the biological stability of the molecules or to increase the (D physical stability of the duplex formed between the antisense and sense nucleic acids, e.g., phosphorothioate derivatives and acridine substituted nucleotides can be used.

[0094] Examples of modified nucleotides that can be used to generate the antisense nucleic acid include: 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine. 4-acetylcytosine, 5-(carboxyhydroxylmethyl) uracil 5-carboxymethylaminomethyl-2-thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine, 7-methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine, 5′-methoxycarboxymethyluracil, 5-methoxyuracil, 2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid (v), wybutoxosine, pseudouracil, queosine, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid (v), 5-methyl-2-thiouracil, 3-(3-amino-3-N-2-carboxypropyl) uracil, (acp3)w, and 2,6-diaminopurine. Alternatively, the antisense nucleic acid can be produced biologically using an expression vector into which a nucleic acid has been subcloned in an antisense orientation (i.e., RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest, described further in the following subsection).

[0095] The antisense nucleic acid molecules of the invention are typically administered to a subject or generated in situ such that they hybridize with or bind to cellular mRNA and/or genomic DNA encoding a protein according to the invention to thereby inhibit expression of the protein, e.g., by inhibiting transcription and/or translation. The hybridization can be by conventional nucleotide complementarity to form a stable duplex, or, for example, in the case of an antisense nucleic acid molecule that binds to DNA duplexes, through specific interactions in the major groove of the double helix. An example of a route of administration of antisense nucleic acid molecules of the invention includes direct injection at a tissue site. Alternatively, antisense nucleic acid molecules can be modified to target selected cells and then administered systemically. For example, for systemic administration, antisense molecules can be modified such that they specifically bind to receptors or antigens expressed on a selected cell surface, e.g., by linking the antisense nucleic acid molecules to peptides or antibodies that bind to cell surface receptors or antigens. The antisense nucleic acid molecules can also be delivered to cells using the vectors described herein. To achieve sufficient intracellular concentrations of antisense molecules, vector constructs in which the anti sense nucleic acid molecule is placed under the control of a strong pol II or pol III promoter are preferred.

[0096] In yet another embodiment, the antisense nucleic acid molecule of the invention is an α-anomeric nucleic acid molecule. An α-anomeric nucleic acid molecule forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual β-units, the strands run parallel to each other (Gaultier el al. (1987) Nucleic Acids Res 15: 6625-6641). The antisense nucleic acid molecule can also comprise a 2′-o-methylribonucleotide (Inoue et al. (1987) Nucleic Acids Res 15: 6131-6148) or a chimeric RNA-DNA analogue (Inoue et al. (1987) FEBS Lett 215: 327-330).

[0097] 4.4 Ribozymes and PNA Moieties

[0098] In still another embodiment, an antisense nucleic acid of the invention is a ribozyme. Ribozymes are catalytic RNA molecules with ribonuclease activity that are capable of cleaving a single-stranded nucleic acid, such as an mRNA, to which they have a complementary region. Thus, ribozymes (e.g. hammerhead ribozymes (described in Haselhoff and Gerlach (1988) Nature 334:585-591)) can be used to catalytically cleave a mRNA transcripts to thereby inhibit translation of a mRNA. A ribozyme having specificity for a nucleic acid of the invention can be designed based upon the nucleotide sequence of a DNA disclosed herein (i.e. SEQ ID NO: 1-245). For example, a derivative of a Tetrahymena L-19 IVS RNA can be constructed in which the nucleotide sequence of the active site is complementary to the nucleotide sequence to be cleaved in an mRNA of SEQ ID NO: 1-245 (see, e.g., Cech et al. U.S. Pat. No. 4,987,071; and Cech et al. U.S. Pat. No. 5,116,742). Alternatively, polynucleotides of the invention can be used to select a catalytic RNA having a specific ribonuclease activity from a pool of RNA molecules. See, e.g., Bartel et al., (1993) Science 261:1411-1418.

[0099] Alternatively, gene expression can be inhibited by targeting nucleotide sequences complementary to the regulatory region (e.g., promoter and/or enhancers) to form triple helical structures that prevent transcription of the gene in target cells. See generally, Helene. (1991) Anticancer Drug Des. 6: 569-84; Helene, et al. (1992) Ann. N.Y. Acad Sci. 660:27-36; and Maher (1992) Bioassays 14: 807-15.

[0100] In various embodiments, the nucleic acids of the invention can be modified at the base moiety, sugar moiety or phosphate backbone to improve, e.g., the stability, hybridization, or solubility of the molecule. For example, the deoxyribose phosphate backbone of the nucleic acids can be modified to generate peptide nucleic acids (see Hyrup et al. (1996) Bioorg Med Chem 4: 5-23). As used herein, the terms “peptide nucleic acids” or “PNAs” refer to nucleic acid mimics, e.g., DNA mimics, in which the deoxyribose phosphate backbone is replaced by a pseudopeptide backbone and only the four natural nucleobases are retained. The neutral backbone of PNAs has been shown to allow for specific hybridization to DNA and RNA under conditions of low ionic strength. The synthesis of PNA oligomers can be performed using standard solid phase peptide synthesis protocols as described in Hyrup et al. (1996) above; Perry-O'Keefe el al. (1996) PNAS 93: 14670-675.

[0101] PNAs of the invention can be used in therapeutic and diagnostic applications. For example, PNAs can be used as antisense or antigene agents for sequence-specific modulation of gene expression by, e.g., inducing transcription or translation arrest or inhibiting replication. PNAs of the invention can also be used, e.g., in the analysis of single base pair mutations in a gene by, e.g., PNA directed PCR clamping; as artificial restriction enzymes when used in combination with other enzymes, e.g., S1 nucleases (Hyrup B. (1996) above); or as probes or primers for DNA sequence and hybridization (Hyrup et al. (1996), above; Perry-O'Keefe (1996), above).

[0102] In another embodiment. PNAs of the invention can be modified, e.g., to enhance their stability or cellular uptake, by attaching lipophilic or other helper groups to PNA, by the formation of PNA-DNA chimeras, or by the use of liposomes or other techniques of drug delivery known in the art. For example. PNA-DNA chimeras can be generated that may combine the advantageous properties of PNA and DNA. Such chimeras allow DNA recognition enzymes, e.g., RNase H and DNA polymerases, to interact with the DNA portion while the PNA portion would provide high binding affinity and specificity. PNA-DNA chimeras can be linked using linkers of appropriate lengths selected in terms of base stacking, number of bonds between the nucleobases, and orientation (Hyrup (1996) above). The synthesis of PNA-DNA chimeras can be performed as described in Hyrup (1996) above and Finn et al. (1996) Nucl Acids Res 24: 3357-63. For example, a DNA chain can be synthesized on a solid support using standard phosphoramidite coupling chemistry, and modified nucleoside analogs, e.g., 5′-(4-methoxytrityl)amino-5′-deoxy-thymidine phosphoramidite, can be used between the PNA and the 5′ end of DNA (Mag et al. (1989) Nucl Acid Res 17: 5973-88). PNA monomers are then coupled in a stepwise manner to produce a chimeric molecule with a 5′ PNA segment and a 3′ DNA segment (Finn et al. (1996) above). Alternatively, chimeric molecules can be synthesized with a 5′ DNA segment and a 3′ PNA segment. See, Petersen et al. (1975) Bioorg Med Chem Lett 5: 1119-11124.

[0103] In other embodiments, the oligonucleotide may include other appended groups such as peptides (e.g., for targeting host cell receptors in vivo), or agents facilitating transport across the cell membrane (see, e.g., Letsinger et al., 1989, Proc. Natl. Acad. Sci. U.S.A. 86:6553-6556; Lemaitre et al., 1987, Proc. Natl. Acad. Sci. 84:648-652; PCT Publication No. WO88/09810) or the blood-brain barrier (see, e.g., PCT Publication No. WO89/10134). In addition, oligonucleotides can be modified with hybridization triggered cleavage agents (See, e.g., Krol et al., 1988, BioTechniques 6:958-976) or intercalating agents. (See, e.g., Zon, 1988, Pharm. Res. 5: 539-549). To this end, the oligonucleotide may be conjugated to another molecule, e.g., a peptide, a hybridization triggered cross-linking agent, a transport agent, a hybridization-triggered cleavage agent, etc.

[0104] 4.5 Hosts

[0105] The present invention further provides host cells genetically engineered to contain the polynucleotides of the invention. For example, such host cells may contain nucleic acids of the invention introduced into the host cell using known transformation, transfection or infection methods. The present invention still further provides host cells genetically engineered to express the polynucleotides of the invention, wherein such polynucleotides are in operative association with a regulatory sequence heterologous to the host cell which drives expression of the polynucleotides in the cell.

[0106] Knowledge of nucleic acid sequences allows for modification of cells to permit, or increase, expression of endogenous polypeptide. Cells can be modified (e.g. by homologous recombination) to provide increased polypeptide expression by replacing, in whole or in part, the naturally occurring promoter with all or part of a heterologous promoter so that the cells express the polypeptide at higher levels. The heterologous promoter is inserted in such a manner that it is operatively linked to the encoding sequences. See, for example, PCT International Publication No. WO94/12650, PCT International Publication No. WO92/20808, and PCT International Publication No. WO91/09955. It is also contemplated that, in addition to heterologous promoter DNA, amplifiable marker DNA (e.g., ada, dhfr, and the multifunctional CAD gene which encodes carbamyl phosphate synthase, aspartate transcarbamylase, and dihydroorotase) and/or intron DNA may be inserted along with the heterologous promoter DNA. If linked to the coding sequence, amplification of the marker DNA by standard selection methods results in co-amplification of the desired protein coding sequences in the cells.

[0107] The host cell can be a higher eukaryotic host cell, such as a mammalian cell, a lower eukaryotic host cell, such as a yeast cell, or the host cell can be a prokaryotic cell, such as a bacterial cell. Introduction of the recombinant construct into the host cell can be effected by calcium phosphate transfection, DEAE-dextran mediated transfection, or electroporation (Davis, L. et al., Basic Methods in Molecular Biology (1986)). The host cells containing one of the polynucleotides of the invention, can be used in conventional manners to produce the gene product encoded by the isolated fragment (in the case of an ORF) or can be used to produce a heterologous protein under the control of the EMF.

[0108] Any host/vector system can be used to express one or more of the ORFs of the present invention. These include, but are not limited to, eukaryotic hosts such as HeLa cells, Cv-1 cell, COS cells, 293 cells, and Sf9 cells, as well as prokaryotic host such as E. coli and B. subtilis. The most preferred cells are those which do not normally express the particular polypeptide or protein or which expresses the polypeptide or protein at low natural level. Mature proteins can be expressed in mammalian cells, yeast, bacteria, or other cells under the control of appropriate promoters. Cell-free translation systems can also be employed to produce such proteins using RNAs derived from the DNA constructs of the present invention. Appropriate cloning and expression vectors for use with prokaryotic and eukaryotic hosts are described by Sambrook, et al., in Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor, N.Y. (1989), the disclosure of which is hereby incorporated by reference.

[0109] Various mammalian cell culture systems can also be employed to express recombinant protein. Examples of mammalian expression systems include the COS-7 lines of monkey kidney fibroblasts, described by Gluzman, Cell 23:175 (1981). Other cell lines capable of expressing a compatible vector are, for example, the C127, monkey COS cells, Chinese Hamster Ovary (CHO) cells, human kidney 293 cells, human epidermal A431 cells, human Colo205 cells, 3T3 cells, CV-1 cells, other transformed primate cell lines, normal diploid cells, cell strains derived from in vitro culture of primary tissue, primary explants, HeLa cells, mouse L cells, BHK, HL-60, U937, HaK or Jurkat cells. Mammalian expression vectors will comprise an origin of replication, a suitable promoter and also any necessary ribosome binding sites, polyadenylation site, splice donor and acceptor sites, transcriptional termination sequences, and 5′ flanking nontranscribed sequences. DNA sequences derived from the SV40 viral genome, for example, SV40 origin, early promoter, enhancer, splice, and polyadenylation sites may be used to provide the required nontranscribed genetic elements. Recombinant polypeptides and proteins produced in bacterial culture are usually isolated by initial extraction from cell pellets, followed by one or more salting-out, aqueous ion exchange or size exclusion chromatography steps. Protein refolding steps can be used, as necessary, in completing configuration of the mature protein. Finally, high performance liquid chromatography (HPLC) can be employed for final purification steps. Microbial cells employed in expression of proteins can be disrupted by any convenient method, including freeze-thaw cycling, sonication, mechanical disruption, or use of cell lysing agents.

[0110] Alternatively, it may be possible to produce the protein in lower eukaryotes such as yeast or insects or in prokaryotes such as bacteria. Potentially suitable yeast strains include Saccharomyces cerevisiae, Schizosaccharomyces pombe, Kluyveromyces strains, Candida, or any yeast strain capable of expressing heterologous proteins. Potentially suitable bacterial strains include Escherichia coli, Bacillus subtilis, Salmonella typhimurium, or any bacterial strain capable of expressing heterologous proteins. If the protein is made in yeast or bacteria, it may be necessary to modify the protein produced therein, for example by phosphorylation or glycosylation of the appropriate sites, in order to obtain the functional protein. Such covalent attachments may be accomplished using known chemical or enzymatic methods.

[0111] In another embodiment of the present invention, cells and tissues may be engineered to express an endogenous gene comprising the polynucleotides of the invention under the control of inducible regulatory elements, in which case the regulatory sequences of the endogenous gene may be replaced by homologous recombination. As described herein, gene targeting can be used to replace a gene's existing regulatory region with a regulatory sequence isolated from a different gene or a novel regulatory sequence synthesized by genetic engineering methods. Such regulatory sequences may be comprised of promoters, enhancers, scaffold-attachment regions, negative regulatory elements, transcriptional initiation sites, regulatory protein binding sites or combinations of said sequences. Alternatively, sequences which affect the structure or stability of the RNA or protein produced may be replaced, removed, added, or otherwise modified by targeting. These sequence include polyadenylation signals, mRNA stability elements, splice sites, leader sequences for enhancing or modifying transport or secretion properties of the protein, or other sequences which alter or improve the function or stability of protein or RNA molecules.

[0112] The targeting event may be a simple insertion of the regulatory sequence, placing the gene under the control of the new regulatory sequence, e.g., inserting a new promoter or enhancer or both upstream of a gene. Alternatively, the targeting event may be a simple deletion of a regulatory element, such as the deletion of a tissue-specific negative regulatory element. Alternatively, the targeting event may replace an existing element; for example, a tissue-specific enhancer can be replaced by an enhancer that has broader or different cell-type specificity than the naturally occurring elements. Here, the naturally occurring sequences are deleted and new sequences are added. In all cases, the identification of the targeting event may be facilitated by the use of one or more selectable marker genes that are contiguous with the targeting DNA, allowing for the selection of cells in which the exogenous DNA has integrated into the host cell genome. The identification of the targeting event may also be facilitated by the use of one or more marker genes exhibiting the property of negative selection, such that the negatively selectable marker is linked to the exogenous DNA, but configured such that the negatively selectable marker flanks the targeting sequence, and such that a correct homologous recombination event with sequences in the host cell genome does not result in the stable integration of the negatively selectable marker. Markers useful for this purpose include the Herpes Simplex Virus thymidine kinase (TK) gene or the bacterial xanthine-guanine phosphoribosyl-transferase (gpt) gene.

[0113] The gene targeting or gene activation techniques which can be used in accordance with this aspect of the invention are more particularly described in U.S. Pat. No. 5,272,071 to Chappel; U.S. Pat. No. 5,578,461 to Sherwin et al.; International Application No. PCT/US92/09627 (WO93/09222) by Selden et al.; and International Application No. PCT/US90/06436 (WO91/06667) by Skoultchi et al., each of which is incorporated by reference herein in its entirety.

[0114] 4.6 Polypeptides of the Invention

[0115] The isolated polypeptides of the invention include, but are not limited to, a polypeptide comprising: the amino acid sequences set forth as any one of SEQ ID NO: 246-490 or an amino acid sequence encoded by any one of the nucleotide sequences SEQ ID NO: 1-245 or the corresponding full length or mature protein. Polypeptides of the invention also include polypeptides preferably with biological or immunological activity that are encoded by: (a) a polynucleotide having and one of the nucleotide sequences set forth in SEQ ID NO: 1-245 or (b) polynucleotides encoding any one of the amino acid sequences set forth as SEQ ID NO: 246-490 or (c) polynucleotides that hybridize to the complement of the polynucleotides of either (a) or (b) under stringent hybridization conditions. The invention also provides biologically active or immunologically active variants of any of the amino acid sequences set forth as SEQ ID NO: 246-490 or the corresponding full length or mature protein; and “substantial equivalents” thereof (e.g., with at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, 86%, 87%, 88%, 89%, at least about 90%, 91%, 92%, 93%, 94%, typically at least about 95%, 96%, 97%, more typically at least about 98%, or most typically at least about 99% amino acid identity) that retain biological activity. Polypeptides encoded by allelic variants may have a similar, increased, or decreased activity compared to polypeptides comprising SEQ ID NO: 246-490.

[0116] Fragments of the proteins of the present invention which are capable of exhibiting biological activity are also encompassed by the present invention. Fragments of the protein may be in linear form or they may be cyclized using known methods, for example, as described in H. U. Saragovi, et al., Bio/Technology 10, 773-778 (1992) and in R. S. McDowell, et al., J. Amer. Chem. Soc. 114, 9245-9253 (1992), both of which are incorporated herein by reference. Such fragments may be fused to carrier molecules such as immunoglobulins for many purposes, including increasing the valency of protein binding sites.

[0117] The present invention also provides both full-length and mature forms (for example, without a signal sequence or precursor sequence) of the disclosed proteins. The protein coding sequence is identified in the sequence listing by translation of the disclosed nucleotide sequences. The mature form of such protein may be obtained by expression of a full-length polynucleotide in a suitable mammalian cell or other host cell. The sequence of the mature form of the protein is also determinable from the amino acid sequence of the full-length form. Where proteins of the present invention are membrane bound, soluble forms of the proteins are also provided. In such forms, part or all of the regions causing the proteins to be membrane bound are deleted so that the proteins are fully secreted from the cell in which they are expressed.

[0118] Protein compositions of the present invention may further comprise an acceptable carrier, such as a hydrophilic, e.g., pharmaceutically acceptable, carrier.

[0119] The present invention further provides isolated polypeptides encoded by the nucleic acid fragments of the present invention or by degenerate variants of the nucleic acid fragments of the present invention. By “degenerate variant” is intended nucleotide fragments which differ from a nucleic acid fragment of the present invention (e.g. an ORF) by nucleotide sequence but, due to the degeneracy of the genetic code, encode an identical polypeptide sequence. Preferred nucleic acid fragments of the present invention are the ORFs that encode proteins.

[0120] A variety of methodologies known in the art can be utilized to obtain any one of the isolated polypeptides or proteins of the present invention. At the simplest level, the amino acid sequence can be synthesized using commercially available peptide synthesizers. The synthetically-constructed protein sequences, by virtue of sharing primary, secondary or tertiary structural and/or conformational characteristics with proteins may possess biological properties in common therewith, including protein activity. This technique is particularly useful in producing small peptides and fragments of larger polypeptides. Fragments are useful, for example, in generating antibodies against the native polypeptide. Thus, they may be employed as biologically active or immunological substitutes for natural, purified proteins in screening of therapeutic compounds and in immunological processes for the development of antibodies.

[0121] The polypeptides and proteins of the present invention can alternatively be purified from cells which have been altered to express the desired polypeptide or protein. As used herein, a cell is said to be altered to express a desired polypeptide or protein when the cell, through genetic manipulation, is made to produce a polypeptide or protein which it normally does not produce or which the cell normally produces at a lower level. One skilled in the art can readily adapt procedures for introducing and expressing either recombinant or synthetic sequences into eukaryotic or prokaryotic cells in order to generate a cell which produces one of the polypeptides or proteins of the present invention.

[0122] The invention also relates to methods for producing a polypeptide comprising growing a culture of host cells of the invention in a suitable culture medium, and purifying the protein from the cells or the culture in which the cells are grown. For example, the methods of the invention include a process for producing a polypeptide in which a host cell containing a suitable expression vector that includes a polynucleotide of the invention is cultured under conditions that allow expression of the encoded polypeptide. The polypeptide can be recovered from the culture, conveniently from the culture medium, or from a lysate prepared from the host cells and further purified. Preferred embodiments include those in which the protein produced by such process is a full length or mature form of the protein.

[0123] In an alternative method, the polypeptide or protein is purified from bacterial cells which naturally produce the polypeptide or protein. One skilled in the art can readily follow known methods for isolating polypeptides and proteins in order to obtain one of the isolated polypeptides or proteins of the present invention. These include, but are not limited to, immunochromatography, HPLC, size-exclusion chromatography, ion-exchange chromatography, and immuno-affinity chromatography. See, e.g. Scopes. Protein Purification. Principles and Practice, Springer-Verlag (1994): Sambrook, et al. in Molecular Cloning: A Laboratory Manual; Ausubel et al., Current Protocols in Molecular Biology. Polypeptide fragments that retain biological/immunological activity include fragments comprising greater than about 100 amino acids, or greater than about 200 amino acids, and fragments that encode specific protein domains.

[0124] The purified polypeptides can be used in in vitro binding assays which are well known in the art to identify molecules which bind to the polypeptides. These molecules include but are not limited to, for e.g., small molecules, molecules from combinatorial libraries, antibodies or other proteins. The molecules identified in the binding assay are then tested for antagonist or agonist activity in in vivo tissue culture or animal models that are well known in the art. In brief, the molecules are titrated into a plurality of cell cultures or animals and then tested for either cell/animal death or prolonged survival of the animal/cells.

[0125] In addition, the peptides of the invention or molecules capable of binding to the peptides may be complexed with toxins, e.g., ricin or cholera, or with other compounds that are toxic to cells. The toxin-binding molecule complex is then targeted to a tumor or other cell by the specificity of the binding molecule for SEQ ID NO: 246-490.

[0126] The protein of the invention may also be expressed as a product of transgenic animals, e.g., as a component of the milk of transgenic cows, goats, pigs, or sheep which are characterized by somatic or germ cells containing a nucleotide sequence encoding the protein.

[0127] The proteins provided herein also include proteins characterized by amino acid sequences similar to those of purified proteins but into which modification are naturally provided or deliberately engineered. For example, modifications, in the peptide or DNA sequence, can be made by those skilled in the art using known techniques. Modifications of interest in the protein sequences may include the alteration, substitution., replacement, insertion or deletion of a selected amino acid residue in the coding sequence. For example, one or more of the cysteine residues may be deleted or replaced with another amino acid to alter the conformation of the molecule. Techniques for such alteration, substitution, replacement, insertion or deletion are well known to those skilled in the art (see, e.g., U.S. Pat. No. 4,518,584). Preferably, such alteration, substitution, replacement, insertion or deletion retains the desired activity of the protein. Regions of the protein that are important for the protein function can be determined by various methods known in the art including the alanine-scanning method which involved systematic substitution of single or strings of amino acids with alanine, followed by testing the resulting alanine-containing variant for biological activity. This type of analysis determines the importance of the substituted amino acid(s) in biological activity. Regions of the protein that are important for protein function may be determined by the eMATRIX program.

[0128] Other fragments and derivatives of the sequences of proteins which would be expected to retain protein activity in whole or in part and are useful for screening or other immunological methodologies may also be easily made by those skilled in the art given the disclosures herein. Such modifications are encompassed by the present invention.

[0129] The protein may also be produced by operably linking the isolated polynucleotide of the invention to suitable control sequences in one or more insect expression vectors, and employing an insect expression system. Materials and methods for baculovirus/insect cell expression systems are commercially available in kit form from, e.g., Invitrogen, San Diego, Calif., U.S.A. (the MaxBat™ kit), and such methods are well known in the art, as described in Summers and Smith, Texas Agricultural Experiment Station Bulletin No. 1555 (1987), incorporated herein by reference. As used herein, an insect cell capable of expressing a polynucleotide of the present invention is “transformed.”

[0130] The protein of the invention may be prepared by culturing transformed host cells under culture conditions suitable to express the recombinant protein. The resulting expressed protein may then be purified from such culture (i.e., from culture medium or cell extracts) using known purification processes, such as gel filtration and ion exchange chromatography. The purification of the protein may also include an affinity column containing agents which will bind to the protein; one or more column steps over such affinity resins as concanavalin A-agarose, heparin-toyopearl™ or Cibacrom blue 3GA Sepharose™; one or more steps involving hydrophobic interaction chromatography using such resins as phenyl ether, butyl ether, or propyl ether; or immunoaffinity chromatography.

[0131] Alternatively, the protein of the invention may also be expressed in a form which will facilitate purification. For example, it may be expressed as a fusion protein, such as those of maltose binding protein (MBP), glutathione-S-transferase (GST) or thioredoxin (TRX), or as a His tag. Kits for expression and purification of such fusion proteins are commercially available from New England BioLab (Beverly, Mass.), Pharmacia (Piscataway, N.J.) and Invitrogen, respectively. The protein can also be tagged with an epitope and subsequently purified by using a specific antibody directed to such epitope. One such epitope (“FLAG®”) is commercially available from Kodak (New Haven, Conn.).

[0132] Finally, one or more reverse-phase high performance liquid chromatography (RP-HPLC) steps employing hydrophobic RP-HPLC media, e.g., silica gel having pendant methyl or other aliphatic groups, can be employed to further purify the protein. Some or all of the foregoing purification steps, in various combinations, can also be employed to provide a substantially homogeneous isolated recombinant protein. The protein thus purified is substantially free of other mammalian proteins and is defined in accordance With the present invention as an “isolated protein.”

[0133] The polypeptides of the invention include analogs (variants). This embraces fragments, as well as peptides in which one or more amino acids has been deleted, inserted, or substituted. Also, analogs of the polypeptides of the invention embrace fusions of the polypeptides or modifications of the polypeptides of the invention, wherein the polypeptide or analog is fused to another moiety or moieties, e.g., targeting moiety or another therapeutic agent. Such analogs may exhibit improved properties such as activity and/or stability. Examples of moieties which may be fused to the polypeptide or an analog include, for example, targeting moieties which provide for the delivery of polypeptide to pancreatic cells, e.g., antibodies to pancreatic cells, antibodies to immune cells such as T-cells, monocytes, dendritic cells, granulocytes, etc., as well as receptor and ligands expressed on pancreatic or immune cells. Other moieties which may be fused to the polypeptide include therapeutic agents which are used for treatment, for example, immunosuppressive drugs such as cyclosporin, SK506, azathioprine, CD3 antibodies and steroids. Also, polypeptides may be fused to immune modulators, and other cytokines such as alpha or beta interferon.

[0134] 4.6.1 Determining Polypeptide and Polynucleotide Identity and Similarity

[0135] Preferred identity and/or similarity are designed to give the largest match between the sequences tested. Methods to determine identity and similarity are codified in computer programs including, but are not limited to, the GCG program package, including GAP (Devereux, J., et al., Nucleic Acids Research 12(1):387 (1984); Genetics Computer Group, University of Wisconsin, Madison, Wis.). BLASTP, BLASTN, BLASTX, FASTA (Altschul, S. F. et al., J. Molec. Biol. 215:403-410 (1990). PSI-BLAST (Altschul S. F. et al., Nucleic Acids Res, vol. 25, pp. 3389-3402, herein incorporated by reference), eMatrix software (Wu et al., J. Comp. Biol., Vol. 6, pp. 219-235 (1999), herein incorporated by reference), eMotif software (Nevill-Manning et al, ISMB-97, Vol. 4, pp. 202-209, herein incorporated by reference), pFam software (Sonnhammer et al., Nucleic Acids Res. Vol. 26(1), pp. 320-322 (1998), herein incorporated by reference) and the Kyte-Doolittle hydrophobocity prediction algorithm (J. Mol Biol, 157, pp. 105-31 (1982), incorporated herein by reference). The BLAST programs are publicly available from the National Center for Biotechnology Information (NCBI) and other sources (BLAST Manual, Altschul. S., et al. NCB NLM NIH Bethesda. MD 20894; Altschul, S., et al., J. Mol. Biol. 215:403-410 (1990).

[0136] 4.7 Chimeric and Fusion Proteins

[0137] The invention also provides chimeric or fusion proteins. As used herein, a “chimeric protein” or “fusion protein” comprises a polypeptide of the invention operatively linked to another polypeptide. Within a fusion protein the polypeptide according to the invention can correspond to all or a portion of a protein according to the invention. In one embodiment, a fusion protein comprises at least one biologically active portion of a protein according to the invention. In another embodiment, a fusion protein comprises at least two biologically active portions of a protein according to the invention. Within the fusion protein, the term “operatively linked” is intended to indicate that the polypeptide according to the invention and the other polypeptide are fused in-frame to each other. The polypeptide can be fused to the N-terminus or C-terminus.

[0138] For example, in one embodiment a fusion protein comprises a polypeptide according to the invention operably linked to the extracellular domain of a second protein. In another embodiment, the fusion protein is a GST-fusion protein in which the polypeptide sequences of the invention are fused to the C-terminus of the GST (i.e., glutathione S-transferase) sequences.

[0139] In another embodiment, the fusion protein is an immunoglobulin fusion protein in which the polypeptide sequences according to the invention comprise one or more domains fused to sequences derived from a member of the immunoglobulin protein family. The immunoglobulin fusion proteins of the invention can be incorporated into pharmaceutical compositions and administered to a subject to inhibit an interaction between a ligand and a protein of the invention on the surface of a cell, to thereby suppress signal transduction in vivo. The immunoglobulin fusion proteins can be used to affect the bioavailability of a cognate ligand. Inhibition of the ligand/protein interaction may be useful therapeutically for both the treatment of proliferative and differentiative disorders, e.g., cancer as well as modulating (e.g., promoting or inhibiting) cell survival. Moreover, the immunoglobulin fusion proteins of the invention can be used as immunogens to produce antibodies in a subject, to purify ligands, and in screening assays to identify molecules that inhibit the interaction of a polypeptide of the invention with a ligand.

[0140] A chimeric or fusion protein of the invention can b, produced by standard recombinant DNA techniques. For example, DNA fragments coding for the different polypeptide sequences are ligated together in-frame in accordance with conventional techniques, e.g., by employing blunt-ended or stagger-ended termini for ligation, restriction enzyme digestion to provide for appropriate termini, filling-in of cohesive ends as appropriate, alkaline phosphatase treatment to avoid undesirable joining, and enzymatic ligation. In another embodiment, the fusion gene can be synthesized by conventional techniques including automated DNA synthesizers. Alternatively, PCR amplification of gene fragments can be carried out using anchor primers that give rise to complementary overhangs between two consecutive gene fragments that can subsequently be annealed and reamplified to generate a chimeric gene sequence (see, for example, Ausubel et al. (eds.) CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, 1992). Moreover, many expression vectors are commercially available that already encode a fusion moiety (e.g., a GST polypeptide). A nucleic acid encoding a polypeptide of the invention can be cloned into such an expression vector such that the fusion moiety is linked in-frame to the protein of the invention.

[0141] 4.8 Gene Therapy

[0142] Mutations in the polynucleotides of the invention may result in loss of normal function of the encoded protein. The invention thus provides gene therapy to restore normal activity of the polypeptides of the invention; or to treat disease states involving polypeptides of the invention. Delivery of a functional gene encoding polypeptides of the invention to appropriate cells is effected ex vivo, in situ, or in vivo by use of vectors, and more particularly viral vectors (e.g., adenovirus, adeno-associated virus, or a retrovirus), or ex vivo by use of physical DNA transfer methods (e.g., liposomes or chemical treatments). See, for example, Anderson, Nature, supplement to vol. 392, no. 6679, pp.25-20 (1998). For additional reviews of gene therapy technology see Friedmann, Science, 244: 1275-1281(1989); Verma, Scientific American: 68-84 (1990); and Miller, Nature, 357: 455-460 (1992). Introduction of any one of the nucleotides of the present invention or a gene encoding the polypeptides of the present invention can also be accomplished with extrachromosomal substrates (transient expression) or artificial chromosomes (stable expression). Cells may also be cultured ex vivo in the presence of proteins of the present invention in order to proliferate or to produce a desired effect on or activity in such cells. Treated cells can then be introduced in vivo for therapeutic purposes. Alternatively, it is contemplated that in other human disease states, preventing the expression of or inhibiting the activity of polypeptides of the invention will be useful in treating the disease states. It is contemplated that antisense therapy or gene therapy could be applied to negatively regulate the expression of polypeptides of the invention.

[0143] Other methods inhibiting expression of a protein include the introduction of antisense molecules to the nucleic acids of the present invention, their complements, or their translated RNA sequences, by methods known in the art. Further, the polypeptides of the present invention can be inhibited by using targeted deletion methods, or the insertion of a negative regulatory element such as a silencer, which is tissue specific.

[0144] The present invention still further provides cells genetically engineered in vivo to express the polynucleotides of the invention, wherein such polynucleotides are in operative association with a regulatory sequence heterologous to the host cell which drives expression of the polynucleotides in the cell. These methods can be used to increase or decrease the expression of the polynucleotides of the present invention.

[0145] Knowledge of DNA sequences provided by the invention allows for modification of cells to permit, increase, or decrease, expression of endogenous polypeptide. Cells can be modified (e.g., by homologous recombination) to provide increased polypeptide expression by replacing, in whole or in part, the naturally occurring promoter with all or part of a heterologous promoter so that the cells express the protein at higher levels. The heterologous promoter is inserted in such a manner that it is operatively linked to the desired protein encoding sequences. See, for example, PCT International Publication No. WO 94/12650, PCT International Publication No. WO 92/20808, and PCT International Publication No. WO 91/09955. It is also contemplated that, in addition to heterologous promoter DNA, amplifiable marker DNA (e.g., ada, dhfr, and the multifunctional CAD gene which encodes carbamyl phosphate synthase, aspartate transcarbamylase, and dihydroorotase) and/or intron DNA may be inserted along with the heterologous promoter DNA. If linked to the desired protein coding sequence, amplification of the marker DNA by standard selection methods results in co-amplification of the desired protein coding sequences in the cells.

[0146] In another embodiment of the present invention, cells and tissues may be engineered to express an endogenous gene comprising the polynucleotides of the invention under the control of inducible regulatory elements, in which case the regulatory sequences of the endogenous gene may be replaced by homologous recombination. As described herein, gene targeting can be used to replace a gene's existing regulatory region with a regulatory sequence isolated from a different gene or a novel regulatory sequence synthesized by genetic engineering methods. Such regulatory sequences may be comprised of promoters, enhancers, scaffold-attachment regions, negative regulatory elements, transcriptional initiation sites, regulatory protein binding sites or combinations of said sequences. Alternatively, sequences which affect the structure or stability of the RNA or protein produced may be replaced, removed, added, or otherwise modified by targeting. These sequences include polyadenylation signals, MRNA stability elements, splice sites, leader sequences for enhancing or modifying transport or secretion properties of the protein, or other sequences which alter or improve the function or stability of protein or RNA molecules.

[0147] The targeting event may be a simple insertion of the regulatory sequence, placing the gene under the control of the new regulatory sequence, e.g., inserting a new promoter or enhancer or both upstream of a gene. Alternatively, the targeting event may be a simple deletion of a regulatory element, such as the deletion of a tissue-specific negative regulatory element. Alternatively, the targeting event may replace an existing element; for example, a tissue-specific enhancer can be replaced by an enhancer that has broader or different cell-type specificity than the naturally occurring elements. Here, the naturally occurring sequences are deleted and new sequences are added. In all cases, the identification of the targeting event may be facilitated by the use of one or more selectable marker genes that are contiguous with the targeting DNA, allowing for the selection of cells in which the exogenous DNA has integrated into the cell genome. The identification of the targeting event may also be facilitated by the use of one or more marker genes exhibiting the property of negative selection, such that the negatively selectable marker is linked to the exogenous DNA, but configured such that the negatively selectable marker flanks the targeting sequence, and such that a correct homologous recombination event with sequences in the host cell genome does not result in the stable integration of the negatively selectable marker. Markers useful for this purpose include the Herpes Simplex Virus thymidine kinase (TK) gene or the bacterial xanthine-guanine phosphoribosyl-transferase (gpt) gene.

[0148] The gene targeting or gene activation techniques which can be used in accordance with this aspect of the invention are more particularly described in U.S. Pat. No. 5,272,071 to Chappel; U.S. Pat. No. 5,578,461 to Sherwin et al.; International Application No. PCT/US92/09627 (WO93/09222) by Selden et al.; and International Application No. PCT/US90/06436 (WO91/06667) by Skoultchi et al., each of which is incorporated by reference herein in its entirety.

[0149] 4.9 Transgenic Animals

[0150] In preferred methods to determine biological functions of the polypeptides of the invention in vivo, one or more genes provided by the invention are either over expressed or inactivated in the germ line of animals using homologous recombination [Capecchi, Science 244:1288-1292 (1989)]. Animals in which the gene is over expressed, under the regulatory control of exogenous or endogenous promoter elements, are known as transgenic animals. Animals in which an endogenous gene has been inactivated by homologous recombination are referred to as “knockout” animals. Knockout animals, preferably non-human mammals, can be prepared as described in U.S. Pat. No. 5,557,032, incorporated herein by reference. Transgenic animals are useful to determine the roles polypeptides of the invention play in biological processes, and preferably in disease states. Transgenic animals are useful as model systems to identify compounds that modulate lipid metabolism. Transgenic animals, preferably non-human mammals, are produced using methods as described in U.S. Pat. No. 5,489,743 and PCT Publication No. WO94/28122, incorporated herein by reference.

[0151] Transgenic animals can be prepared wherein all or part of a promoter of the polynucleotides of the invention is either activated or inactivated to alter the level of expression of the polypeptides of the invention. Inactivation can be carried out using homologous recombination methods described above. Activation can be achieved by supplementing or even replacing the homologous promoter to provide for increased protein expression. The homologous promoter can be supplemented by insertion of one or more heterologous enhancer elements known to confer promoter activation in a particular tissue.

[0152] The polynucleotides of the present invention also make possible the development, through, e.g., homologous recombination or knock out strategies, of animals that fail to express polypeptides of the invention or that express a variant polypeptide. Such animals are useful as models for studying the in vivo activities of polypeptide as well as for studying modulators of the polypeptides of the invention.

[0153] In preferred methods to determine biological functions of the polypeptides of the invention in vivo, one or more genes provided by the invention are either over expressed or inactivated in the germ line of animals using homologous recombination [Capecchi, Science 244:1288-1292 (1989)]. Animals in which the gene is over expressed, under the regulatory control of exogenous or endogenous promoter elements, are known as transgenic animals. Animals in which an endogenous gene has been inactivated by homologous recombination are referred to as “knockout” animals. Knockout animals, preferably non-human mammals, can be prepared as described in U.S. Pat. No. 5,557,032, incorporated herein by reference. Transgenic animals are useful to determine the roles polypeptides of the invention play in biological processes, and preferably in disease states. Transgenic animals are useful as model systems to identify compounds that modulate lipid metabolism. Transgenic animals, preferably non-human mammals, are produced using methods as described in U.S. Pat. No. 5,489,743 and PCT Publication No. WO94/28122, incorporated herein by reference.

[0154] Transgenic animals can be prepared wherein all or part of the polynucleotides of the invention promoter is either activated or inactivated to alter the level of expression of the polypeptides of the invention. Inactivation can be carried out using homologous recombination methods described above. Activation can be achieved by supplementing or even replacing the homologous promoter to provide for increased protein expression. The homologous promoter can be supplemented by insertion of one or more heterologous enhancer elements known to confer promoter activation in a particular tissue.

[0155] 4.10 Uses and Biological Activity

[0156] The polynucleotides and proteins of the present invention are expected to exhibit one or more of the uses or biological activities (including those associated with assays cited herein) identified herein. Uses or activities described for proteins of the present invention may be provided by administration or use of such proteins or of polynucleotides encoding such proteins (such as, for example, in gene therapies or vectors suitable for introduction of DNA). The mechanism underlying the particular condition or pathology will dictate whether the polypeptides of the invention, the polynucleotides of the invention or modulators (activators or inhibitors) thereof would be beneficial to the subject in need of treatment. Thus, “therapeutic compositions of the invention” include compositions comprising isolated polynucleotides (including recombinant DNA molecules, cloned genes and degenerate variants thereof) or polypeptides of the invention (including full length protein, mature protein and truncations or domains thereof), or compounds and other substances that modulate the overall activity of the target gene products, either at the level of target gene/protein expression or target protein activity. Such modulators include polypeptides, analogs, (variants), including fragments and fusion proteins, antibodies and other binding proteins; chemical compounds that directly or indirectly activate or inhibit the polypeptides of the invention (identified, e.g., via drug screening assays as described herein); antisense polynucleotides and polynucleotides suitable for triple helix formation; and in particular antibodies or other binding partners that specifically recognize one or more epitopes of the polypeptides of the invention.

[0157] The polypeptides of the present invention may likewise be involved in cellular activation or in one of the other physiological pathways described herein.

[0158] 4.10.1 Research Uses and Utilities

[0159] The polynucleotides provided by the present invention can be used by the research community for various purposes. The polynucleotides can be used to express recombinant protein for analysis, characterization or therapeutic use; as markers for tissues in which the corresponding protein is preferentially expressed (either constitutively or at a particular stage of tissue differentiation or development or in disease states); as molecular weight markers on gels; as chromosome markers or tags (when labeled) to identify chromosomes or to map related gene positions; to compare with endogenous DNA sequences in patients to identify potential genetic disorders; as probes to hybridize and thus discover novel, related DNA sequences; as a source of information to derive PCR primers for genetic fingerprinting; as a probe to “subtract-out” known sequences in the process of discovering other novel polynucleotides; for selecting and making oligomers for attachment to a “gene chip” or other support, including for examination of expression patterns; to raise anti-protein antibodies using DNA immunization techniques; and as an antigen to raise anti-DNA antibodies or elicit another immune response. Where the polynucleotide encodes a protein which binds or potentially binds to another protein (such as, for example, in a receptor-ligand interaction), the polynucleotide can also be used in interaction trap assays (such as, for example, that described in Gyuris et al. Cell 75:791-803 (1993)) to identify polynucleotides encoding the other protein with which binding occurs or to identify inhibitors of the binding interaction.

[0160] The polypeptides provided by the present invention can similarly be used in assays to determine biological activity, including in a panel of multiple proteins for high-throughput screening; to raise antibodies or to elicit another immune response; as a reagent (including the labeled reagent) in assays designed to quantitatively determine levels of the protein (or its receptor) in biological fluids; as markers for tissues in which the corresponding polypeptide is preferentially expressed (either constitutively or at a particular stage of tissue differentiation or development or in a disease state); and, of course, to isolate correlative receptors or ligands. Proteins involved in these binding interactions can also be used to screen for peptide or small molecule inhibitors or agonists of the binding interaction.

[0161] Any or all of these research utilities are capable of being developed into reagent grade or kit format for commercialization as research products.

[0162] Methods for performing the uses listed above are well known to those skilled in the art. References disclosing such methods include without limitation “Molecular Cloning: A Laboratory Manual”, 2d ed. Cold Spring Harbor Laboratory Press, Sambrook, J., E. F. Fritsch and T. Maniatis eds., 1989, and “Methods in Enzymology: Guide to Molecular Cloning Techniques”, Academic Press, Berger, S. L. and A. R. Kimmel eds., 1987.

[0163] 4.10.2 Nutritional Uses

[0164] Polynucleotides and polypeptides of the present invention can also be used as nutritional sources or supplements. Such uses include without limitation use as a protein or amino acid supplement, use as a carbon source, use as a nitrogen source and use as a source of carbohydrate. In such cases the polypeptide or polynucleotide of the invention can be added to the feed of a particular organism or can be administered as a separate solid or liquid preparation, such as in the form of powder, pills, solutions, suspensions or capsules. In the case of microorganisms, the polypeptide or polynucleotide of the invention can be added to the medium in or on which the microorganism is cultured.

[0165] 4.10.3 Cytokine and Cell Proliferation/Differentiation Activity

[0166] A polypeptide of the present invention may exhibit activity relating to cytokine, cell proliferation (either inducing or inhibiting) or cell differentiation (either inducing or inhibiting) activity or may induce production of other cytokines in certain cell populations. A polynucleotide of the invention can encode a polypeptide exhibiting such attributes. Many protein factors discovered to date, including all known cytokines, have exhibited activity in one or more factor-dependent cell proliferation assays, and hence the assays serve as a convenient confirmation of cytokine activity. The activity of therapeutic compositions of the present invention is evidenced by any one of a number of routine factor dependent cell proliferation assays for cell lines including, without limitation, 32D, DA2, DAIG, T10, B9, B9/11, BaF3, MC9/G, M+(preB M+), 2E8, RB5, DA1, 123, T1165, HT2, CTLL2, TF-1, Mo7e, CMK, HUVEC, and Caco. Therapeutic compositions of the invention can be used in the following:

[0167] Assays for T-cell or thymocyte proliferation include without limitation those described in: Current Protocols in Immunology, Ed by J. E. Coligan, A. M. Kruisbeek, D. H. Margulies, E. M. Shevach, W. Strober, Pub. Greene Publishing Associates and Wiley-Interscience (Chapter 3, In Vitro assays for Mouse Lymphocyte Function 3.1-3.19; Chapter 7, Immunologic studies in Humans); Takai et al., J. Immunol. 137:3494-3500, 1986; Bertagnolli et al., J. Immunol. 145:1706-1712, 1990; Bertagnolli et al., Cellular Immunology 133:327-341, 1991; Bertagnolli, et al., I. Immunol. 149:3778-3783, 1992; Bowman et al., I. Immunol. 152:1756-1761, 1994.

[0168] Assays for cytokine production and/or proliferation of spleen cells, lymph node cells or thymocytes include, without limitation, those described in: Polyclonal T cell stimulation, Kruisbeek, A. M. and Shevach, E. M. In Current Protocols in Immunology. J. E. e.a. Coligan eds. Vol 1 pp. 3.12.1-3.12.14, John Wiley and Sons, Toronto. 1994; and Measurement of mouse and human interleukin-y, Schreiber, R. D. In Current Protocols in Immunology. J. E. e.a. Coligan eds. Vol 1 pp. 6.8.1-6.8.8, John Wiley and Sons, Toronto. 1994.

[0169] Assays for proliferation and differentiation of hematopoietic and lymphopoietic cells include, without limitation, those described in: Measurement of Human and Murine Interleukin 2 and Interleukin 4, Bottomly, K., Davis, L. S. and Lipsky, P. E. In Current Protocols in Immunology. J. E. e.a. Coligan eds. Vol 1 pp. 6.3.1-6.3.12, John Wiley and Sons, Toronto. 1991; deVries et al., J. Exp. Med. 173:1205-1211, 1991. Moreau et al., Nature 336:690-692, 1988; Greenberger et al., Proc. Natl. Acad. Sci. U.S.A. 80:2931-2938, 1983; Measurement of mouse and human interleukin 6—Nordan, R. In Current Protocols in Immunology. J. E. Coligan eds. Vol 1 pp. 6.6.1-6.6.5, John Wiley and Sons. Toronto. 1991, Smith et al., Proc. Natl. Aced. Sci. U.S.A. 83:1857-1861, 1986; Measurement of human Interleukin 11—Bennett, F., Giannotti, J., Clark, S. C. and Turner, K. J. In Current Protocols in Immunology. J. E. Coligan eds. Vol 1 pp. 6.15.1 John Wiley and Sons, Toronto. 1991; Measurement of mouse and human Interleukin 9—Ciarletta, A., Giannotti, J., Clark. S. C. and Turner, K. J. In Current Protocols in Immunology. J. E. Coligan eds. Vol 1 pp. 6.13.1. John Wiley and Sons. Toronto. 1991.

[0170] Assays for T-cell clone responses to antigens (which will identify, among others, proteins that affect APC-T cell interactions as well as direct T-cell effects by measuring proliferation and cytokine production) include, without limitation, those described in: Current Protocols in Immunology, Ed by J. E. Coligan, A. M. Kruisbeek, D. H. Margulies, E. M. Shevach, W Strober. Pub. Greene Publishing Associates and Wiley-Interscience (Chapter 3, In Vitro assays for Mouse Lymphocyte Function; Chapter 6, Cytokines and their cellular receptors; Chapter 7, Immunologic studies in Humans); Weinberger et al., Proc. Natl. Acad. Sci. USA 77:6091-6095, 1980; Weinberger et al., Eur. J. Immun. 11:405-411, 1981; Takai et al., J. Immunol. 137:3494-3500, 1986; Takai et al., J. Immunol. 140:508-512. 1988.

[0171] 4.10.4 Stem Cell Growth Factor Activity

[0172] A polypeptide of the present invention may exhibit stem cell growth factor activity and be involved in the proliferation, differentiation and survival of pluripotent and totipotent stem cells including primordial germ cells, embryonic stem cells, hematopoietic stem cells and/or germ line stem cells. Administration of the polypeptide of the invention to stem cells in vivo or ex vivo is expected to maintain and expand cell populations in a totipotential or pluripotential state which would be useful for re-engineering damaged or diseased tissues, transplantation, manufacture of bio-pharmaceuticals and the development of bio-sensors. The ability to produce large quantities of human cells has important working applications for the production of human proteins which currently must be obtained from non-human sources or donors, implantation of cells to treat diseases such as Parkinson's, Alzheimer's and other neurodegenerative diseases; tissues for grafting such as bone marrow, skin, cartilage, tendons, bone, muscle (including cardiac muscle), blood vessels, cornea, neural cells, gastrointestinal cells and others; and organs for transplantation such as kidney, liver, pancreas (including islet cells), heart and lung.

[0173] It is contemplated that multiple different exogenous growth factors and/or cytokines may be administered in combination with the polypeptide of the invention to achieve the desired effect, including any of the growth factors listed herein, other stem cell maintenance factors, and specifically including stem cell factor (SCF), leukemia inhibitory factor (LIF), Flt-3 ligand (Flt-3L), any of the interleukins, recombinant soluble IL-6 receptor fused to IL-6, macrophage inflammatory protein 1-alpha (MIP-1-alpha), G-CSF, GM-CSF, thrombopoietin (TPO), platelet factor 4 (PF-4), platelet-derived growth factor (PDGF), neural growth factors and basic fibroblast growth factor (bFGF).

[0174] Since totipotent stem cells can give rise to virtually any mature cell type, expansion of these cells in culture will facilitate the production of large quantities of mature cells. Techniques for culturing stem cells are known in the art and administration of polypeptides of the invention, optionally with other growth factors and/or cytokines, is expected to enhance the survival and proliferation of the stem cell populations. This can be accomplished by direct administration of the polypeptide of the invention to the culture medium. Alternatively, stroma cells transfected with a polynucleotide that encodes for the polypeptide of the invention can be used as a feeder layer for the stem cell populations in culture or in vivo. Stromal support cells for feeder layers may include embryonic bone marrow fibroblasts, bone marrow stromal cells, fetal liver cells, or cultured embryonic fibroblasts (see U.S. Pat. No. 5,690,926).

[0175] Stem cells themselves can be transfected with a polynucleotide of the invention to induce autocrine expression of the polypeptide of the invention. This will allow for generation of undifferentiated totipotential/pluripotential stem cell lines that are useful as is or that can then be differentiated into the desired mature cell types. These stable cell lines can also serve as a source of undifferentiated totipotential/pluripotential mRNA to create cDNA libraries and templates for polymerase chain reaction experiments. These studies would allow for the isolation and identification of differentially expressed genes in stem cell populations that regulate stem cell proliferation and/or maintenance.

[0176] Expansion and maintenance of totipotent stem cell populations will be useful in the treatment of many pathological conditions. For example, polypeptides of the present invention may be used to manipulate stem cells in culture to give rise to neuroepithelial cells that can be used to augment or replace cells damaged by illness, autoimmune disease, accidental damage or genetic disorders. The polypeptide of the invention may be useful for inducing the proliferation of neural cells and for the regeneration of nerve and brain tissue, i.e. for the treatment of central and peripheral nervous system diseases and neuropathies, as well as mechanical and traumatic disorders which involve degeneration, death or trauma to neural cells or nerve tissue. In addition, the expanded stem cell populations can also be genetically altered for gene therapy purposes and to decrease host rejection of replacement tissues after grafting or implantation.

[0177] Expression of the polypeptide of the invention and its effect on stem cells can also be manipulated to achieve controlled differentiation of the stem cells into more differentiated cell types. A broadly applicable method of obtaining pure populations of a specific differentiated cell type from undifferentiated stem cell populations involves the use of a cell-type specific promoter driving a selectable marker. The selectable marker allows only cells of the desired type to survive. For example, stem cells can be induced to differentiate into cardiomyocytes (Wobus et al. Differentiation, 48: 173-182, (1991); Klug et al., J. Clin. Invest. 98(1): 216-224, (1998)) or skeletal muscle cells (Browder, L. W. In: Principles of Tissue Engineering eds. Lanza et al., Academic Press (1997)). Alternatively, directed differentiation of stem cells can be accomplished by culturing the stem cells in the presence of a differentiation factor such as retinoic acid and an antagonist of the polypeptide of the invention which would inhibit the effects of endogenous stem cell factor activity and allow differentiation to proceed.

[0178] In vitro cultures of stem cells can be used to determine if the polypeptide of the invention exhibits stem cell growth factor activity. Stem cells are isolated from any one of various cell sources (including hematopoietic stem cells and embryonic stem cells) and cultured on a feeder layer, as described by Thompson et al. Proc. Natl. Acad. Sci, U.S.A., 92: 7844-7848 (1995), in the presence of the polypeptide of the invention alone or in combination with other growth factors or cytokines. The ability of the polypeptide of the invention to induce stem cells proliferation is determined by colony formation on semi-solid support e.g. as described by Bernstein et al., Blood, 77: 2316-2321 (1991).

[0179] 4.10.5 Hematopoiesis Regulating Activity

[0180] A polypeptide of the present invention may be involved in regulation of hematopoiesis and, consequently, in the treatment of myeloid or lymphoid cell disorders. Even marginal biological activity in support of colony forming cells or of factor-dependent cell lines indicates involvement in regulating hematopoiesis, e.g. in supporting the growth and proliferation of erythroid progenitor cells alone or in combination with other cytokines, thereby indicating utility, for example, in treating various anemias or for use in conjunction with irradiation/chemotherapy to stimulate the production of erythroid precursors and/or erythroid cells; in supporting the growth and proliferation of myeloid cells such as granulocytes and monocytes/macrophages (i.e., traditional CSF activity) useful, for example, in conjunction with chemotherapy to prevent or treat consequent myelo-suppression; in supporting the growth and proliferation of megakaryocytes and consequently of platelets thereby allowing prevention or treatment of various platelet disorders such as thrombocytopenia, and generally for use in place of or complimentary to platelet transfusions; and/or in supporting the growth and proliferation of hematopoietic stem cells which are capable of maturing to any and all of the above-mentioned hematopoietic cells and therefore find therapeutic utility in various stem cell disorders (such as those usually treated with transplantation, including, without limitation, aplastic anemia and paroxysmal nocturnal hemoglobinuria), as well as in repopulating the stem cell compartment post irradiation/chemotherapy, either in-vivo or ex-vivo (i.e., in conjunction with bone marrow transplantation or with peripheral progenitor cell transplantation (homologous or heterologous)) as normal cells or genetically manipulated for gene therapy.

[0181] Therapeutic compositions of the invention can be used in the following:

[0182] Suitable assays for proliferation and differentiation of various hematopoietic lines are cited above.

[0183] Assays for embryonic stem cell differentiation (which will identify, among others, proteins that influence embryonic differentiation hematopoiesis) include, without limitation, those described in: Johansson et al. Cellular Biology 15:141-151. 1995: Keller et al., Molecular and Cellular Biology 13:473-486. 1993: McClanahan et al. Blood 81:2903-2915, 1993.

[0184] Assays for stem cell survival and differentiation (which will identify, among others, proteins that regulate lympho-hematopoiesis) include, without limitation, those described in: Methylcellulose colony forming assays. Freshney, M. G. In Culture of Hematopoietic Cells. R. I. Freshney, et al. eds. Vol pp. 265-268, Wiley-Liss, Inc., New York, N.Y. 1994; Hirayama et al., Proc. Natl. Acad. Sci. USA 89:5907-5911. 1992; Primitive hematopoietic colony forming cells with high proliferative potential, McNiece, I. K. and Briddell, R. A. In Culture of Hematopoietic Cells. R. I. Freshney, et al. eds. Vol pp. 23-39, Wiley-Liss, Inc., New York, N.Y. 1994; Neben et al., Experimental Hematology 22:353-359, 1994; Cobblestone area forming cell assay, Ploemacher, R. E. In Culture of Hematopoietic Cells. R. I. Freshney, et al. eds. Vol pp. 1-21, Wiley-Liss, Inc., New York, N.Y. 1994; Long term bone marrow cultures in the presence of stromal cells, Spooncer, E., Dexter, M. and Allen, T. In Culture of Hematopoietic Cells. R. I. Freshney, et al. eds. Vol pp. 163-179, Wiley-Liss, Inc., New York, N.Y. 1994; Long term culture initiating cell assay, Sutherland, H. J. In Culture of Hematopoietic Cells. R. I. Freshney, et al. eds. Vol pp. 139-162, Wiley-Liss, Inc., New York, N.Y. 1994.

[0185] 4.10.6 Tissue Growth Activity

[0186] A polypeptide of the present invention also may be involved in bone, cartilage, tendon, ligament and/or nerve tissue growth or regeneration, as well as in wound healing and tissue repair and replacement, and in healing of burns, incisions and ulcers.

[0187] A polypeptide of the present invention which induces cartilage and/or bone growth in circumstances where bone is not normally formed, has application in the healing of bone fractures and cartilage damage or defects in humans and other animals. Compositions of a polypeptide, antibody, binding partner, or other modulator of the invention may have prophylactic use in closed as well as open fracture reduction and also in the improved fixation of artificial joints. De novo bone formation induced by an osteogenic agent contributes to the repair of congenital, trauma induced, or oncologic resection induced craniofacial defects, and also is useful in cosmetic plastic surgery.

[0188] A polypeptide of this invention may also be involved in attracting bone-forming cells, stimulating growth of bone-forming cells, or inducing differentiation of progenitors of bone-forming cells. Treatment of osteoporosis, osteoarthritis, bone degenerative disorders, or periodontal disease, such as through stimulation of bone and/or cartilage repair or by blocking inflammation or processes of tissue destruction (collagenase activity, osteoclast activity, etc.) mediated by inflammatory processes may also be possible using the composition of the invention.

[0189] Another category of tissue regeneration activity that may involve the polypeptide of the present invention is tendon/ligament formation. Induction of tendon/ligament-like tissue or other tissue formation in circumstances where such tissue is not normally formed, has application in the healing of tendon or ligament tears, deformities and other tendon or ligament defects in humans and other animals. Such a preparation employing a tendon/ligament-like tissue inducing protein may have prophylactic use in preventing damage to tendon or ligament tissue, as well as use in the improved fixation of tendon or ligament to bone or other tissues, and in repairing defects to tendon or ligament tissue. De novo tendon/ligament-like tissue formation induced by a composition of the present invention contributes to the repair of congenital, trauma induced, or other tendon or ligament defects of other origin, and is also useful in cosmetic plastic surgery for attachment or repair of tendons or ligaments. The compositions of the present invention may provide environment to attract tendon- or ligament-forming cells, stimulate growth of tendon- or ligament-forming cells, induce differentiation of progenitors of tendon- or ligament-forming cells, or induce growth of tendon/ligament cells or progenitors ex vivo for return in vivo to effect tissue repair. The compositions of the invention may also be useful in the treatment of tendinitis, carpal tunnel syndrome and other tendon or ligament defects. The compositions may also include an appropriate matrix and/or sequestering agent as a carrier as is well known in the art.

[0190] The compositions of the present invention may also be useful for proliferation of neural cells and for regeneration of nerve and brain tissue, i.e. for the treatment of central and peripheral nervous system diseases and neuropathies, as well as mechanical and traumatic disorders, which involve degeneration, death or trauma to neural cells or nerve tissue. More specifically, a G composition may be used in the treatment of diseases of the peripheral nervous system, such as peripheral nerve injuries, peripheral neuropathy and localized neuropathies, and central nervous system diseases, such as Alzheimer's, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, and Shy-Drager syndrome. Further conditions which may be treated in accordance with the present invention include mechanical and traumatic disorders, such as spinal cord disorders, head trauma and cerebrovascular diseases such as stroke. Peripheral neuropathies resulting from chemotherapy or other medical therapies may also be treatable using a composition of the invention.

[0191] Compositions of the invention may also be useful to promote better or faster closure of non-healing wounds, including without limitation pressure ulcers, ulcers associated with vascular insufficiency, surgical and traumatic wounds, and the like.

[0192] Compositions of the present invention may also be involved in the generation or regeneration of other tissues, such as organs (including, for example, pancreas, liver, intestine, kidney, skin, endothelium), muscle (smooth, skeletal or cardiac) and vascular (including vascular endothelium) tissue, or for promoting the growth of cells comprising such tissues. Part of the desired effects may be by inhibition or modulation of fibrotic scarring may allow normal tissue to regenerate. A polypeptide of the present invention may also exhibit angiogenic activity.

[0193] A composition of the present invention may also be useful for gut protection or regeneration and treatment of lung or liver fibrosis, reperfusion injury in various tissues, and conditions resulting from systemic cytokine damage.

[0194] A composition of the present invention may also be useful for promoting or inhibiting differentiation of tissues described above from precursor tissues or cells; or for inhibiting the growth of tissues described above.

[0195] Therapeutic compositions of the invention can be used in the following:

[0196] Assays for tissue generation activity include, without limitation, those described in: International Patent Publication No. WO95/16035 (bone, cartilage, tendon); International Patent Publication No. WO95/05846 (nerve, neuronal); International Patent Publication No. WO91/07491 (skin, endothelium).

[0197] Assays for wound healing activity include, without limitation, those described in: Winter, Epidermal Wound Healing, pps. 71-112 (Maibach, H. I. and Rovee, D. T., eds.), Year Book Medical Publishers, Inc., Chicago, as modified by Eaglstein and Mertz, J. Invest. Dermatol 71:382-84 (1978).

[0198] 4.10.7 Immune Stimulating or Suppressing Activity

[0199] A polypeptide of the present invention may also exhibit immune stimulating or immune suppressing activity, including without limitation the activities for which assays are described herein. A polynucleotide of the invention can encode a polypeptide exhibiting such activities. A protein may be useful in the treatment of various immune deficiencies and disorders (including severe combined immunodeficiency (SCID)), e.g., in regulating (up or down) growth and proliferation of T and/or B lymphocytes, as well as effecting the cytolytic activity of NK cells and other cell populations. These immune deficiencies may be genetic or be caused by viral (e.g., HIV) as well as bacterial or fungal infections, or may result from autoimmune disorders. More specifically, infectious diseases causes by viral, bacterial, fungal or other infection may be treatable using a protein of the present invention, including infections by HIV, hepatitis viruses, herpes viruses, mycobacteria, Leishmania spp, malaria spp, and various fungal infections such as candidiasis. Of course, in this regard, proteins of the present invention may also be useful where a boost to the immune system generally may be desirable, i.e. in the treatment of cancer.

[0200] Autoimmune disorders which may be treated using a protein of the present invention include, for example, connective tissue disease, multiple sclerosis, systemic lupus erythematosus, rheumatoid arthritis, autoimmune pulmonary inflammation. Guillain-Barre syndrome, autoimmune thyroiditis, insulin dependent diabetes mellitis, myasthenia gravis, graft-versus-host disease and autoimmune inflammatory eye disease. Such a protein (or antagonists thereof, including antibodies) of the present invention may also to be useful in the treatment of allergic reactions and conditions (e.g., anaphylaxis, serum sickness, drug reactions, food allergies, insect venom allergies, mastocytosis, allergic rhinitis, hypersensitivity pneumonitis, urticaria, angioedema, eczema, atopic dermatitis, allergic contact dermatitis, erythema multiforme, Stevens-Johnson syndrome, allergic conjunctivitis, atopic keratoconjunctivitis, venereal keratoconjunctivitis, giant papillary conjunctivitis and contact allergies), such as asthma (particularly allergic asthma) or other respiratory problems. Other conditions, in which immune suppression is desired (including, for example, organ transplantation), may also be treatable using a protein (or antagonists thereof) of the present invention. The therapeutic effects of the polypeptides or antagonists thereof on allergic reactions can be evaluated by in vivo animals models such as the cumulative contact enhancement test (Lastbom et al., Toxicology 125: 59-66, 1998), skin prick test (Hoffmann et al., Allergy 54: 446-54. 1999), guinea pig skin sensitization test (Vohr et al., Arch. Toxocol. 73: 501-9), and murine local lymph node assay (Kimber et al., J. Toxicol. Environ. Health 53: 563-79).

[0201] Using the proteins of the invention it may also be possible to modulate immune responses, in a number of ways. Down regulation may be in the form of inhibiting or blocking an immune response already in progress or may involve preventing the induction of an immune response. The functions of activated T cells may be inhibited by suppressing T cell responses or by inducing specific tolerance in T cells, or both. Immunosuppression of T cell responses is generally an active, non-antigen-specific, process which requires continuous exposure of the T cells to the suppressive agent. Tolerance, which involves inducing non-responsiveness or anergy in T cells, is distinguishable from immunosuppression in that it is generally antigen-specific and persists after exposure to the tolerizing agent has ceased. Operationally, tolerance can be demonstrated by the lack of a T cell response upon reexposure to specific antigen in the absence of the tolerizing agent.

[0202] Down regulating or preventing one or more antigen functions (including without limitation B lymphocyte antigen functions (such as, for example, B7)), e.g., preventing high level lymphokine synthesis by activated T cells, will be useful in situations of tissue, skin and organ transplantation and in graft-versus-host disease (GVHD). For example, blockage of T cell function should result in reduced tissue destruction in tissue transplantation. Typically, in tissue transplants, rejection of the transplant is initiated through its recognition as foreign by T cells, followed by an immune reaction that destroys the transplant. The administration of a therapeutic composition of the invention may prevent cytokine synthesis by immune cells, such as T cells, and thus acts as an immunosuppressant. Moreover, a lack of costimulation may also be sufficient to anergize the T cells, thereby inducing tolerance in a subject. Induction of long-term tolerance by B lymphocyte antigen-blocking reagents may avoid the necessity of repeated administration of these blocking reagents. To achieve sufficient immunosuppression or tolerance in a subject, it may also be necessary to block the function of a combination of B lymphocyte antigens.

[0203] The efficacy of particular therapeutic compositions in preventing organ transplant rejection or GVHD can be assessed using animal models that are predictive of efficacy in humans. Examples of appropriate systems which can be used include allogeneic cardiac grafts in rats and xenogeneic pancreatic islet cell grafts in mice, both of which have been used to examine the immunosuppressive effects of CTLA41 g fusion proteins in vivo as described in Lenschow et al., Science 257:789-792 (1992) and Turka et al., Proc. Natl. Acad. Sci USA, 89:11102-11105 (1992). In addition, murine models of GVHD (see Paul ed., Fundamental Immunology, Raven Press. New York, 1989, pp. 846-847) can be used to determine the effect of therapeutic compositions of the invention on the development of that disease.

[0204] Blocking antigen function may also be therapeutically useful for treating autoimmune diseases. Many autoimmune disorders are the result of inappropriate activation of T cells that are reactive against self tissue and which promote the production of cytokines and autoantibodies involved in the pathology of the diseases. Preventing the activation of autoreactive T cells may reduce or eliminate disease symptoms. Administration of reagents which block stimulation of T cells can be used to inhibit T cell activation and prevent production of autoantibodies or T cell-derived cytokines which may be involved in the disease process. Additionally, blocking reagents may induce antigen-specific tolerance of autoreactive T cells which could lead to long-term relief from the disease. The efficacy of blocking reagents in preventing or alleviating autoimmune disorders can be determined using a number of well-characterized animal models of human autoimmune diseases. Examples include murine experimental autoimmune encephalitis, systemic lupus erythmatosis in MRL/lpr/lpr mice or NZB hybrid mice, murine autoimmune collagen arthritis, diabetes mellitus in NOD mice and BB rats, and murine experimental myasthenia gravis (see Paul ed., Fundamental Immunology. Raven Press, New York, 1989, pp. 840-856).

[0205] Upregulation of an antigen function (e.g. a B lymphocyte antigen function), as a means of up regulating immune responses, may also be useful in therapy. Upregulation of immune responses may be in the form of enhancing an existing immune response or eliciting an initial immune response. For example, enhancing an immune response may be useful in cases of viral infection, including systemic viral diseases such as influenza, the common cold, and encephalitis.

[0206] Alternatively, anti-viral immune responses may be enhanced in an infected patient by removing T cells from the patient, costimulating the T cells in vitro with viral antigen-pulsed APCs either expressing a peptide of the present invention or together with a stimulatory form of a soluble peptide of the present invention and reintroducing the in vitro activated T cells into the patient. Another method of enhancing anti-viral immune responses would be to isolate infected cells from a patient, transfect them with a nucleic acid encoding a protein of the present invention as described herein such that the cells express all or a portion of the protein on their surface, and reintroduce the transfected cells into the patient. The infected cells would now be capable of delivering a costimulatory signal to, and thereby activate, T cells in vivo.

[0207] A polypeptide of the present invention may provide the necessary stimulation signal to T cells to induce a T cell mediated immune response against the transfected tumor cells. In addition, tumor cells which lack MHC class I or MHC class II molecules, or which fail to reexpress sufficient mounts of MHC class I or MHC class II molecules, can be transfected with nucleic acid encoding all or a portion of (e.g., a cytoplasmic-domain truncated portion) of an MHC class I alpha chain protein and P2 microglobulin protein or an MHC class II alpha chain protein and an MHC class II beta chain protein to thereby express MHC class I or MHC class II proteins on the cell surface. Expression of the appropriate class I or class II MHC in conjunction with a peptide having the activity of a B lymphocyte antigen (e.g., B7-1, B7-2, B7-3) induces a T cell mediated immune response against the transfected tumor cell. Optionally, a gene encoding an antisense construct which blocks expression of an MHC class II associated protein, such as the invariant chain, can also be cotransfected with a DNA encoding a peptide having the activity of a B lymphocyte antigen to promote presentation of tumor associated antigens and induce tumor specific immunity. Thus, the induction of a T cell mediated immune response in a human subject may be sufficient to overcome tumor-specific tolerance in the subject.

[0208] The activity of a protein of the invention may, among other means, be measured by the following methods:

[0209] Suitable assays for thymocyte or splenocyte cytotoxicity include, without limitation, those described in: Current Protocols in Immunology, Ed by J. E. Coligan, A. M. Kruisbeek, D. H. Margulies, E. M. Shevach, W. Strober, Pub. Greene Publishing Associates and Wiley-Interscience (Chapter 3. In Vitro assays for Mouse Lymphocyte Function 3.1-3.19; Chapter 7. Immunologic studies in Humans); Herrmann et al. Proc. Natl. Acad. Sci. USA 78:2488-2492. 1981; Herrmann et al. J. Immunol. 128:1968-1974. 1982: Handa et al., J. Immunol. 135:1564-1572, 1985: Takai et al., I. Immunol. 137:3494-3500. 1986: Takai et al., J. Immunol. 140:508-512, 1988; Bowman et al. J. Virology 61:1992-1998: Bertagnolli et al., Cellular Immunology 133:327-341, 1991: Brown et al., J. Immunol. 153:3079-3092, 1994.

[0210] Assays for T-cell-dependent immunoglobulin responses and isotype switching (which will identify, among others, proteins that modulate T-cell dependent antibody responses and that affect Th1/Th2 profiles) include, without limitation, those described in: Maliszewski, J. Immunol. 144:3028-3033, 1990; and Assays for B cell function: In vitro antibody production, Mond, J. J. and Brunswick, M. In Current Protocols in Immunology. J. E. e.a. Coligan eds. Vol 1 pp. 3.8.1-3.8.16, John Wiley and Sons, Toronto. 1994.

[0211] Mixed lymphocyte reaction (MLR) assays (which will identify, among others, proteins that generate predominantly Th1 and CTL responses) include, without limitation, those described in: Current Protocols in Immunology, Ed by J. E. Coligan, A. M. Kruisbeek, D. H. Margulies, E. M. Shevach, W. Strober, Pub. Greene Publishing Associates and Wiley-Interscience (Chapter 3, In Vitro assays for Mouse Lymphocyte Function 3.1-3.19; Chapter 7, Immunologic studies in Humans); Takai et al., J. Immunol. 137:3494-3500, 1986; Takai et al., J. Immunol. 140:508-512, 1988; Bertagnolli et al., J. Immunol. 149:3778-3783, 1992.

[0212] Dendritic cell-dependent assays (which will identify, among others, proteins expressed by dendritic cells that activate naive T-cells) include, without limitation, those described in: Guery et al., J. Immunol. 134:536-544, 1995; Inaba et al., Journal of Experimental Medicine 173:549-559, 1991; Macatonia et al., Journal of Immunology 154:5071-5079, 1995; Porgador et al., Journal of Experimental Medicine 182:255-260, 1995; Nair et al., Journal of Virology 67:4062-4069, 1993; Huang et al., Science 264:961-965, 1994; Macatonia et al., Journal of Experimental Medicine 169:1255-1264, 1989; Bhardwaj et al., Journal of Clinical Investigation 94:797-807, 1994; and Inaba et al., Journal of Experimental Medicine 172:631-640, 1990.

[0213] Assays for lymphocyte survival/apoptosis (which will identify, among others, proteins that prevent apoptosis after superantigen induction and proteins that regulate lymphocyte homeostasis) include, without limitation, those described in: Darzynkiewicz et al., Cytometry 13:795-808, 1992; Gorczyca et al., Leukemia 7:659-670. 1993; Gorczyca et al., Cancer Research 53:1945-1951, 1993; Itoh et al., Cell 66:233-243, 1991: Zacharchuk, Journal of Immunology 145:4037-4045, 1990; Zamai et al., Cytometry 14:891-897. 1993; Gorczyca et al., International Journal of Oncology 1:639-648, 1992.

[0214] Assays for proteins that influence early steps of T-cell commitment and development include, without limitation, those described in: Antica et al. Blood 84:111-117, 1994; Fine et al., Cellular Immunology 155:111-122. 1994; Galy et al. Blood 85:2770-2778, 1995; Toki et al. Proc. Nat. Acad Sci. USA 88:7548-7551, 1991.

[0215] 4.10.8 Activin/Inhibin Activity

[0216] A polypeptide of the present invention may also exhibit activin- or inhibin-related activities. A polynucleotide of the invention may encode a polypeptide exhibiting such characteristics. Inhibins are characterized by their ability to inhibit the release of follicle stimulating hormone (FSH), while activins and are characterized by their ability to stimulate the release of follicle stimulating hormone (FSH). Thus, a polypeptide of the present invention, alone or in heterodimers with a member of the inhibin family, may be useful as a contraceptive based on the ability of inhibins to decrease fertility in female mammals and decrease spermatogenesis in male mammals. Administration of sufficient amounts of other inhibins can induce infertility in these mammals. Alternatively, the polypeptide of the invention, as a homodimer or as a heterodimer with other protein subunits of the inhibin group, may be useful as a fertility inducing therapeutic, based upon the ability of activin molecules in stimulating FSH from cells of the anterior pituitary. See, for example, U.S. Pat. No. 4,798,885. A polypeptide of the invention may also be useful for advancement of the onset of fertility in sexually immature mammals, so as to increase the lifetime reproductive performance of domestic animals such as, but not limited to, cows, sheep and pigs.

[0217] The activity of a polypeptide of the invention may, among other means, be measured by the following methods.

[0218] Assays for activin/inhibin activity include, without limitation, those described in: Vale et al., Endocrinology 91:562-572, 1972; Ling et al. Nature 321:779-782, 1986; Vale et al., Nature 321:776-779, 1986; Mason et al., Nature 318:659-663, 1985; Forage et al., Proc. Natl. Acad. Sci. USA 83:3091-3095, 1986.

[0219] 4.10.9 Chemotactic/Chemokinetic Activity

[0220] A polypeptide of the present invention may be involved in chemotactic or chemokinetic activity for mammalian cells, including, for example, monocytes, fibroblasts, neutrophils, T-cells, mast cells, eosinophils, epithelial and/or endothelial cells. A polynucleotide of the invention can encode a polypeptide exhibiting such attributes. Chemotactic and chemokinetic receptor activation can be used to mobilize or attract a desired cell population to a desired site of action. Chemotactic or chemokinetic compositions (e.g. proteins, antibodies, binding partners, or modulators of the invention) provide particular advantages in treatment of wounds and other trauma to tissues, as well as in treatment of localized infections. For example, attraction of lymphocytes, monocytes or neutrophils to tumors or sites of infection may result in improved immune responses against the tumor or infecting agent.

[0221] A protein or peptide has chemotactic activity for a particular cell population if it can stimulate, directly or indirectly, the directed orientation or movement of such cell population. Preferably, the protein or peptide has the ability to directly stimulate directed movement of cells. Whether a particular protein has chemotactic activity for a population of cells can be readily determined by employing such protein or peptide in any known assay for cell chemotaxis.

[0222] Therapeutic compositions of the invention can be used in the following:

[0223] Assays for chemotactic activity (which will identify proteins that induce or prevent chemotaxis) consist of assays that measure the ability of a protein to induce the migration of cells across a membrane as well as the ability of a protein to induce the adhesion of one cell population to another cell population. Suitable assays for movement and adhesion include, without limitation, those described in: Current Protocols in Immunology, Ed by J. E. Coligan, A. M. Kruisbeek, D. H. Marguiles, E. M. Shevach, W. Strober, Pub. Greene Publishing Associates and Wiley-Interscience (Chapter 6.12, Measurement of alpha and beta Chemokines 6.12.1-6.12.28; Taub et al. J. Clin. Invest. 95:1370-1376, 1995; Lind et al. APMIS 103:140-146, 1995; Muller et al Eur. J. Immunol. 25:1744-1748; Gruber et al. J. of Immunol. 152:5860-5867, 1994; Johnston et al. J. of Immunol. 153:1762-1768, 1994.

[0224] 4.10.10 Hemostatic and Thrombolytic Activity

[0225] A polypeptide of the invention may also be involved in hemostasis or thrombolysis or thrombosis. A polynucleotide of the invention can encode a polypeptide exhibiting such attributes. Compositions may be useful in treatment of various coagulation disorders (including hereditary disorders, such as hemophilias) or to enhance coagulation and other hemostatic events in treating wounds resulting from trauma, surgery or other causes. A composition of the invention may also be useful for dissolving or inhibiting formation of thromboses and for treatment and prevention of conditions resulting therefrom (such as, for example, infarction of cardiac and central nervous system vessels (e.g., stroke).

[0226] Therapeutic compositions of the invention can be used in the following:

[0227] Assay for hemostatic and thrombolytic activity include, without limitation, those described in: Linet et al. J. Clin. Pharmacol. 26:131-140, 1986; Burdick et al., Thrombosis Res. 45:413-419, 1987; Humphrey et al. Fibrinolysis 5:71-79 (1991); Schaub, Prostaglandins 35:467-474. 1988.

[0228] 4.10.11 Cancer Diagnosis and Therapy

[0229] Polypeptides of the invention may be involved in cancer cell generation, proliferation or metastasis. Detection of the presence or amount of polynucleotides or polypeptides of the invention may be useful for the diagnosis and/or prognosis of one or more types of cancer. For example, the presence or increased expression of a polynucleotide/polypeptide of the invention may indicate a hereditary risk of cancer, a precancerous condition, or an ongoing malignancy. Conversely, a defect in the gene or absence of the polypeptide may be associated with a cancer condition. Identification of single nucleotide polymorphisms associated with cancer or a predisposition to cancer may also be useful for diagnosis or prognosis.

[0230] Cancer treatments promote tumor regression by inhibiting tumor cell proliferation, inhibiting angiogenesis (growth of new blood vessels that is necessary to support tumor growth) and/or prohibiting metastasis by reducing tumor cell motility or invasiveness. Therapeutic compositions of the invention may be effective in adult and pediatric oncology including in solid phase tumors/malignancies, locally advanced tumors, human soft tissue sarcomas, metastatic cancer, including lymphatic metastases, blood cell malignancies including multiple myeloma, acute and chronic leukemias, and lymphomas, head and neck cancers including mouth cancer, larynx cancer and thyroid cancer, lung cancers including small cell carcinoma and non-small cell cancers, breast cancers including small cell carcinoma and ductal carcinoma, gastrointestinal cancers including esophageal cancer, stomach cancer, colon cancer, colorectal cancer and polyps associated with colorectal neoplasia, pancreatic cancers, liver cancer, urologic cancers including bladder cancer and prostate cancer, malignancies of the female genital tract including ovarian carcinoma, uterine (including endometrial) cancers, and solid tumor in the ovarian follicle, kidney cancers including renal cell carcinoma, brain cancers including intrinsic brain tumors, neuroblastoma, astrocytic brain tumors, gliomas, metastatic tumor cell invasion in the central nervous system, bone cancers including osteomas, skin cancers including malignant melanoma, tumor progression of human skin keratinocytes, squamous cell carcinoma, basal cell carcinoma, hemangiopericytoma and Karposi's sarcoma.

[0231] Polypeptides, polynucleotides, or modulators of polypeptides of the invention (including inhibitors and stimulators of the biological activity of the polypeptide of the invention) may be administered to treat cancer. Therapeutic compositions can be administered in therapeutically effective dosages alone or in combination with adjuvant cancer therapy such as surgery, chemotherapy, radiotherapy, thermotherapy, and laser therapy, and may provide a beneficial effect, e.g. reducing tumor size, slowing rate of tumor growth, inhibiting metastasis, or otherwise improving overall clinical condition, without necessarily eradicating the cancer.

[0232] The composition can also be administered in therapeutically effective amounts as a portion of an anti-cancer cocktail. An anti-cancer cocktail is a mixture of the polypeptide or modulator of the invention with one or more anti-cancer drugs in addition to a pharmaceutically acceptable carrier for delivery. The use of anti-cancer cocktails as a cancer treatment is routine. Anti-cancer drugs that are well known in the art and can be used as a treatment in combination with the polypeptide or modulator of the invention include: Actinomycin D, Aminoglutethimide. Asparaginase, Bleomycin, Busulfan, Carboplatin, Carmustine, Chlorambucil, Cisplatin (cis-DDP), Cyclophosphamide, Cytarabine HCl (Cytosine arabinoside), Dacarbazine, Dactinomycin, Daunorubicin HCl, Doxorubicin HCl, Estramustine phosphate sodium, Etoposide (V16-213), Floxuridine, 5-Fluorouracil (5-Fu), Flutamide, Hydroxyurea (hydroxycarbamide), Ifosfamide, Interferon Alpha-2a, Interferon Alpha-2b, Leuprolide acetate (LHRH-releasing factor analog), Lomustine, Mechlorethamine HCl (nitrogen mustard), Melphalan, Mercaptopurine, Mesna, Methotrexate (MTX), Mitomycin, Mitoxantrone HCl, Octreotide, Plicamycin, Procarbazine HCl, Streptozocin, Tamoxifen citrate, Thioguanine, Thiotepa, Vinblastine sulfate, Vincristine sulfate, Amsacrine, Azacitidine, Hexamethylmelamine, Interleukin-2, Mitoguazone, Pentostatin, Semustine, Teniposide, and Vindesine sulfate.

[0233] In addition, therapeutic compositions of the invention may be used for prophylactic treatment of cancer. There are hereditary conditions and/or environmental situations (e.g. exposure to carcinogens) known in the art that predispose an individual to developing cancers. Under these circumstances, it may be beneficial to treat these individuals with therapeutically effective doses of the polypeptide of the invention to reduce the risk of developing cancers.

[0234] In vitro models can be used to determine the effective doses of the polypeptide of the invention as a potential cancer treatment. These in vitro models include proliferation assays of cultured tumor cells, growth of cultured tumor cells in soft agar (see Freshney, (1987) Culture of Animal Cells: A Manual of Basic Technique, Wily-Liss, New York, N.Y. Ch 18 and Ch 21), tumor systems in nude mice as described in Giovanella et al., J. Natl. Can. Inst., 52: 921-30 (1974), mobility and invasive potential of tumor cells in Boyden Chamber assays as described in Pilkington et al., Anticancer Res., 17: 4107-9 (1997), and angiogenesis assays such as induction of vascularization of the chick chorioallantoic membrane or induction of vascular endothelial cell migration as described in Ribatta et al., Intl. J. Dev. Biol., 40: 1189-97 (1999) and Li et al., Clin. Exp. Metastasis, 17:423-9 (1999), respectively. Suitable tumor cells lines are available, e.g. from American Type Tissue Culture Collection catalogs.

[0235] 4.10.12 Receptor/Ligand Activity

[0236] A polypeptide of the present invention may also demonstrate activity as receptor, receptor ligand or inhibitor or agonist of receptor/ligand interactions. A polynucleotide of the invention can encode a polypeptide exhibiting such characteristics. Examples of such receptors and ligands include, without limitation, cytokine receptors and their ligands, receptor kinases and their ligands, receptor phosphatases and their ligands, receptors involved in cell-cell interactions and their ligands (including without limitation, cellular adhesion molecules (such as selecting, integrins and their ligands) and receptor/ligand pairs involved in antigen presentation, antigen recognition and development of cellular and humoral immune responses. Receptors and ligands are also useful for screening of potential peptide or small molecule inhibitors of the relevant receptor/ligand interaction. A protein of the present invention (including, without limitation, fragments of receptors and ligands) may themselves be useful as inhibitors of receptor/ligand interactions.

[0237] The activity of a polypeptide of the invention may, among other means, be measured by the following methods:

[0238] Suitable assays for receptor-ligand activity include without limitation those described in: Current Protocols in Immunology, Ed by J. E. Coligan, A. M. Kruisbeek, D. H. Margulies, E. M. Shevach, W. Strober, Pub. Greene Publishing Associates and Wiley-Interscience (Chapter 7.28, Measurement of Cellular Adhesion under static conditions 7.28.1-7.28.22), Takai et al., Proc. Natl. Acad. Sci. USA 84:6864-6868, 1987; Bierer et al., J. Exp. Med. 168:1145-1156, 1988; Rosenstein et al., J. Exp. Med. 169:149-160 1989; Stoltenborg et al., J. Immunol. Methods 175:59-68, 1994; Stitt et al. Cell 80:661-670, 1995.

[0239] By way of example, the polypeptides of the invention may be used as a receptor for a ligand(s) thereby transmitting the biological activity of that ligand(s). Ligands may be identified through binding assays, affinity chromatography, dihybrid screening assays, BIAcore assays, gel overlay assays, or other methods known in the art.

[0240] Studies characterizing drugs or proteins as agonist or antagonist or partial agonists or a partial antagonist require the use of other proteins as competing ligands. The polypeptides of the present invention or ligand(s) thereof may be labeled by being coupled to radioisotopes, colorimetric molecules or a toxin molecules by conventional methods. (“Guide to Protein Purification” Murray P. Deutscher (ed) Methods in Enzymology Vol. 182 (1990) Academic Press, Inc. San Diego). Examples of radioisotopes include, but are not limited to, tritium and carbon-14. Examples of colorimetric molecules include, but are not limited to, fluorescent molecules such as fluorescamine, or rhodamine or other colorimetric molecules. Examples of toxins include, but are not limited, to ricin.

[0241] 4.10.13 Drug Screening

[0242] This invention is particularly useful for screening chemical compounds by using the novel polypeptides or binding fragments thereof in any of a variety of drug screening techniques. The polypeptides or fragments employed in such a test may either be free in solution, affixed to a solid support, borne on a cell surface or located intracellularly. One method of drug screening utilizes eukaryotic or prokaryotic host cells which are stably transformed with recombinant nucleic acids expressing the polypeptide or a fragment thereof. Drugs are screened against such transformed cells in competitive binding assays. Such cells, either in viable or fixed form, can be used for standard binding assays. One may measure, for example, the formation of complexes between polypeptides of the invention or fragments and the agent being tested or examine the diminution in complex formation between the novel polypeptides and an appropriate cell line, which are well known in the art.

[0243] Sources for test compounds that may be screened for ability to bind to or modulate (i.e., increase or decrease) the activity of polypeptides of the invention include (1) inorganic and organic chemical libraries, (2) natural product libraries, and (3) combinatorial libraries comprised of either random or mimetic peptides, oligonucleotides or organic molecules.

[0244] Chemical libraries may be readily synthesized or purchased from a number of commercial sources, and may include structural analogs of known compounds or compounds that are identified as “hits” or “leads” via natural product screening.

[0245] The sources of natural product libraries are microorganisms (including bacteria and fungi), animals, plants or other vegetation, or marine organisms, and libraries of mixtures for screening may be created by: (1) fermentation and extraction of broths from soil, plant or marine microorganisms or (2) extraction of the organisms themselves. Natural product libraries include polyketides, non-ribosomal peptides, and (non-naturally occurring) variants thereof. For a review, see Science 282:63-68 (1998).

[0246] Combinatorial libraries are composed of large numbers of peptides, oligonucleotides or organic compounds and can be readily prepared by traditional automated synthesis methods, PCR, cloning or proprietary synthetic methods. Of particular interest are peptide and oligonucleotide combinatorial libraries. Still other libraries of interest include peptide, protein, peptidomimetic, multiparallel synthetic collection, recombinatorial, and polypeptide libraries. For a review of combinatorial chemistry and libraries created therefrom, see Myers, Curr. Opin. Biotechnol. 8:701-707 (1997). For reviews and examples of peptidomimetic libraries, see Al-Obeidi et al., Mol. Biotechnol, 9(3):205-23 (1998): Hruby et al., Curr Opin Chem Biol, 1(1): 14-19 (1997); Dorner et al., Bioorg Med Chem. 4(5):709-15 (1996) (alkylated dipeptides).

[0247] Identification of modulators through use of the various libraries described herein permits modification of the candidate “hit” (or “lead”) to optimize the capacity of the “hit” to bind a polypeptide of the invention. The molecules identified in the binding assay are then tested for antagonist or agonist activity in in vivo tissue culture or animal models that are well known in the art. In brief, the molecules are titrated into a plurality of cell cultures or animals and then tested for either cell/animal death or prolonged survival of the animal/cells.

[0248] The binding molecules thus identified man be complexed with toxins, e.g. ricin or cholera, or with other compounds that are toxic to cells such as radioisotopes. The toxin-binding molecule complex is then targeted to a tumor or other cell by the specificity of the binding molecule for a polypeptide of the invention. Alternatively, the binding molecules may be complexed with imaging agents for targeting and imaging purposes.

[0249] 4.10.14 Assay for Receptor Activity

[0250] The invention also provides methods to detect specific binding of a polypeptide e.g. a ligand or a receptor. The art provides numerous assays particularly useful for identifying previously unknown binding partners for receptor polypeptides of the invention. For example, expression cloning using mammalian or bacterial cells, or dihybrid screening assays can be used to identify polynucleotides encoding binding partners. As another example, affinity chromatography with the appropriate immobilized polypeptide of the invention can be used to isolate polypeptides that recognize and bind polypeptides of the invention. There are a number of different libraries used for the identification of compounds, and in particular small molecules, that modulate (i.e. increase or decrease) biological activity of a polypeptide of the invention. Ligands for receptor polypeptides of the invention can also be identified by adding exogenous ligands, or cocktails of ligands to two cells populations that are genetically identical except for the expression of the receptor of the invention: one cell population expresses the receptor of the invention whereas the other does not. The response of the two cell populations to the addition of ligands(s) are then compared. Alternatively, an expression library can be co-expressed with the polypeptide of the invention in cells and assayed for an autocrine response to identify potential ligand(s). As still another example. BIAcore assays, gel overlay assays, or other methods known in the art can be used to identify binding partner polypeptides, including, (1) organic and inorganic chemical libraries. (2) natural product libraries, and (3) combinatorial libraries comprised of random peptides, oligonucleotides or organic molecules.

[0251] The role of downstream intracellular signaling molecules in the signaling cascade of the polypeptide of the invention can be determined. For example, a chimeric protein in which the cytoplasmic domain of the polypeptide of the invention is fused to the extracellular portion of a protein, whose ligand has been identified, is produced in a host cell. The cell is then incubated with the ligand specific for the extracellular portion of the chimeric protein, thereby activating the chimeric receptor. Known downstream proteins involved in intracellular signaling can then be assayed for expected modifications i.e. phosphorylation. Other methods known to those in the art can also be used to identify signaling molecules involved in receptor activity.

[0252] 4.10.15 Anti-Inflammatory Activity

[0253] Compositions of the present invention may also exhibit anti-inflammatory activity. The anti-inflammatory activity may be achieved by providing a stimulus to cells involved in the inflammatory response, by inhibiting or promoting cell-cell interactions (such as, for example, cell adhesion), by inhibiting or promoting chemotaxis of cells involved in the inflammatory process, inhibiting or promoting cell extravasation, or by stimulating or suppressing production of other factors which more directly inhibit or promote an inflammatory response. Compositions with such activities can be used to treat inflammatory conditions including chronic or acute conditions), including without limitation intimation associated with infection (such as septic shock, sepsis or systemic inflammatory response syndrome (SIRS)), ischemia-reperfusion injury, endotoxin lethality, arthritis, complement-mediated hyperacute rejection, nephritis, cytokine or chemokine-induced lung injury, inflammatory bowel disease, Crohn's disease or resulting from over production of cytokines such as TNF or IL-1. Compositions of the invention may also be useful to treat anaphylaxis and hypersensitivity to an antigenic substance or material. Compositions of this invention may be utilized to prevent or treat conditions such as, but not limited to, sepsis, acute pancreatitis, endotoxin shock, cytokine induced shock, rheumatoid arthritis, chronic inflammatory arthritis, pancreatic cell damage from diabetes mellitus type 1, graft versus host disease, inflammatory bowel disease, inflamation associated with pulmonary disease, other autoimmune disease or inflammatory disease, an antiproliferative agent such as for acute or chronic mylegenous leukemia or in the prevention of premature labor secondary to intrauterine infections.

[0254] 4.10.16 Leukemias

[0255] Leukemias and related disorders may be treated or prevented by administration of a therapeutic that promotes or inhibits function of the polynucleotides and/or polypeptides of the invention. Such leukemias and related disorders include but are not limited to acute leukemia, acute lymphocytic leukemia, acute myelocytic leukemia, myeloblastic, promyelocytic, myelomonocytic, monocytic, erythroleukemia, chronic leukemia, chronic myelocytic (granulocytic) leukemia and chronic lymphocytic leukemia (for a review of such disorders, see Fishman et al. 1985. Medicine. 2d Ed., J. B. Lippincott Co., Philadelphia).

[0256] 4.10.17 Nervous System Disorders

[0257] Nervous system disorders, involving cell types which can be tested for efficacy of intervention with compounds that modulate the activity of the polynucleotides and/or polypeptides of the invention, and which can be treated upon thus observing an indication of therapeutic utility, include but are not limited to nervous system injuries, and diseases or disorders which result in either a disconnection of axons, a diminution or degeneration of neurons, or demyelination. Nervous system lesions which may be treated in a patient (including human and non-human mammalian patients) according to the invention include but are not limited to the following lesions of either the central (including spinal cord, brain) or peripheral nervous systems:

[0258] (i) traumatic lesions, including lesions caused by physical injury or associated with surgery, for example, lesions which sever a portion of the nervous system, or compression injuries;

[0259] (ii) ischemic lesions, in which a lack of oxygen in a portion of the nervous system results in neuronal injury or death, including cerebral infarction or ischemia, or spinal cord infarction or ischemia;

[0260] (iii) infectious lesions, in which a portion of the nervous system is destroyed or injured as a result of infection, for example, by an abscess or associated with infection by human immunodeficiency virus, herpes zoster or herpes simplex virus or with Lyme disease, tuberculosis, syphilis;

[0261] (iv) degenerative lesions, in which a portion of the nervous system is destroyed or injured as a result of a degenerative process including but not limited to degeneration associated with Parkinson's disease, Alzheimer's disease, Huntington's chorea, or amyotrophic lateral sclerosis;

[0262] (v) lesions associated with nutritional diseases or disorders, in which a portion of the nervous system is destroyed or injured by a nutritional disorder or disorder of metabolism including but not limited to, vitamin B12 deficiency, folic acid deficiency, Wernicke disease, tobacco-alcohol amblyopia, Marchiafava-Bignami disease (primary degeneration of the corpus callosum), and alcoholic cerebellar degeneration;

[0263] (vi) neurological lesions associated with systemic diseases including but not limited to diabetes (diabetic neuropathy, Bell's palsy), systemic lupus erythematosus, carcinoma, or sarcoidosis;

[0264] (vii) lesions caused by toxic substances including alcohol, lead, or particular neurotoxins; and

[0265] (viii) demyelinated lesions in which a portion of the nervous system is destroyed or injured by a demyelinating disease including but not limited to multiple sclerosis, human immunodeficiency virus-associated myelopathy, transverse myelopathy or various etiologies, progressive multi focal leukoencephalopathy, and central pontine myelinolysis.

[0266] Therapeutics which are useful according to the invention for treatment of a nervous system disorder may be selected by testing for biological activity in promoting the survival or differentiation of neurons. For example, and not by way of limitation, therapeutics which elicit any of the following effects may be useful according to the invention:

[0267] (i) increased survival time of neurons in culture;

[0268] (ii) increased sprouting of neurons in culture or in vivo;

[0269] (iii) increased production of a neuron-associated molecule in culture or in vivo, e.g., choline acetyltransferase or acetylcholinesterase with respect to motor neurons; or

[0270] (iv) decreased symptoms of neuron dysfunction in vivo.

[0271] Such effects may be measured by any method known in the art. In preferred, non-limiting embodiments, increased survival of neurons may be measured by the method set forth in Arakawa et al. (1990, J. Neurosci. 10:3507-3515); increased sprouting of neurons may be detected by methods set forth in Pestronk et al. (1980, Exp. Neurol. 70:65-82) or Brown et al. (1981, Ann. Rev. Neurosci. 4:17-42); increased production of neuron-associated molecules may be measured by bioassay, enzymatic assay, antibody binding, Northern blot assay, etc., depending on the molecule to be measured; and motor neuron dysfunction may be measured by assessing the physical manifestation of motor neuron disorder, e.g., weakness, motor neuron conduction velocity, or functional disability.

[0272] In specific embodiments, motor neuron disorders that may be treated according to the invention include but are not limited to disorders such as infarction, infection, exposure to toxin, trauma, surgical damage, degenerative disease or malignancy that may affect motor neurons as well as other components of the nervous system, as well as disorders that selectively affect neurons such as amyotrophic lateral sclerosis, and including but not limited to progressive spinal muscular atrophy, progressive bulbar palsy, primary lateral sclerosis, infantile and juvenile muscular atrophy, progressive bulbar paralysis of childhood (Fazio-Londe syndrome), poliomyelitis and the post polio syndrome, and Hereditary Motorsensory Neuropathy (Charcot-Marie-Tooth Disease).

[0273] 4.10.18 Other Activities

[0274] A polypeptide of the invention may also exhibit one or more of the following additional activities or effects: inhibiting the growth, infection or function of, or killing, infectious agents, including, without limitation, bacteria, viruses, fungi and other parasites; effecting (suppressing or enhancing) bodily characteristics, including, without limitation, height, weight, hair color, eye color, skin, fat to lean ratio or other tissue pigmentation, or organ or body part size or shape (such as, for example, breast augmentation or diminution, change in bone form or shape); effecting biorhythms or circadian cycles or rhythms; effecting the fertility of male or female subjects: effecting the metabolism, catabolism, anabolism, processing, utilization, storage or elimination of dietary fat, lipid, protein, carbohydrate, vitamins, minerals, co-factors or other nutritional factors or component(s); effecting behavioral characteristics, including, without limitation, appetite, libido, stress, cognition (including cognitive disorders), depression (including depressive disorders) and violent behaviors; providing analgesic effects or other pain reducing effects; promoting differentiation and growth of embryonic stem cells in lineages other than hematopoietic lineages; hormonal or endocrine activity; in the case of enzymes, correcting deficiencies of the enzyme and treating deficiency-related diseases; treatment of hyperproliferative disorders (such as, for example, psoriasis); immunoglobulin-like activity (such as, for example, the ability to bind antigens or complement); and the ability to act as an antigen in a vaccine composition to raise an immune response against such protein or another material or entity which is cross-reactive with such protein.

[0275] 4.10.19 Identification of Polymorphisms

[0276] The demonstration of polymorphisms makes possible the identification of such polymorphisms in human subjects and the pharmacogenetic use of this information for diagnosis and treatment. Such polymorphisms may be associated with, e.g., differential predisposition or susceptibility to various disease states (such as disorders involving inflammation or immune response) or a differential response to drug administration, and this genetic information can be used to tailor preventive or therapeutic treatment appropriately. For example, the existence of a polymorphism associated with a predisposition to inflammation or autoimmune disease makes possible the diagnosis of this condition in humans by identifying the presence of the polymorphism.

[0277] Polymorphisms can be identified in a variety of ways known in the art which all generally involve obtaining a sample from a patient, analyzing DNA from the sample, optionally involving isolation or amplification of the DNA, and identifying the presence of the polymorphism in the DNA. For example, PCR may be used to amplify an appropriate fragment of genomic DNA which may then be sequenced. Alternatively, the DNA may be subjected to allele-specific oligonucleotide hybridization (in which appropriate oligonucleotides are hybridized to the DNA under conditions permitting detection of a single base mismatch) or to a single nucleotide extension assay (in which an oligonucleotide that hybridizes immediately adjacent to the position of the polymorphism is extended with one or more labeled nucleotides). In addition, traditional restriction fragment length polymorphism analysis (using restriction enzymes that provide differential digestion of the genomic DNA depending on the presence or absence of the polymorphism) may be performed. Arrays with nucleotide sequences of the present invention can be used to detect polymorphisms. The array can comprise modified nucleotide sequences of the present invention in order to detect the nucleotide sequences of the present invention. In the alternative, any one of the nucleotide sequences of the present invention can be placed on the array to detect changes from those sequences.

[0278] Alternatively a polymorphism resulting in a change in the amino acid sequence could also be detected by detecting a corresponding change in amino acid sequence of the protein, e.g., by an antibody specific to the variant sequence.

[0279] 4.10.20 Arthritis and Inflammation

[0280] The immunosuppressive effects of the compositions of the invention against rheumatoid arthritis is determined in an experimental animal model system. The experimental model system is adjuvant induced arthritis in rats, and the protocol is described by J. Holoshitz, et at., 1983, Science, 219:56, or by B. Waksman et al., 1963. Int. Arch. Allergy Appl. Immunol., 23:129. Induction of the disease can be caused by a single injection, generally intradermally, of a suspension of killed Mycobacterium tuberculosis in complete Freund's adjuvant (CFA). The route of injection can vary, but rats may be injected at the base of the tail with an adjuvant mixture. The polypeptide is administered in phosphate buffered solution (PBS) at a dose of about 1-5 mg/kg. The control consists of administering PBS only.

[0281] The procedure for testing the effects of the test compound would consist of intradermally injecting killed Mycobacterium tuberculosis in CFA followed by immediately administering the test compound and subsequent treatment every other day until day 24. At 14, 15, 18, 20, 22, and 24 days after injection of Mycobacterium CFA., an overall arthritis score may be obtained as described by J. Holoskitz above. An analysis of the data would reveal that the test compound would have a dramatic affect on the swelling of the joints as measured by a decrease of the arthritis score.

[0282] 4.11 Therapeutic Methods

[0283] The compositions (including polypeptide fragments, analogs, variants and antibodies or other binding partners or modulators including antisense polynucleotides) of the invention have numerous applications in a variety of therapeutic methods. Examples of therapeutic applications include, but are not limited to, those exemplified herein.

[0284] 4.11.1 EXAMPLE

[0285] One embodiment of the invention is the administration of an effective amount of the polypeptides or other composition of the invention to individuals affected by a disease or disorder that can be modulated by, regulating the peptides of the invention. While the mode of administration is not particularly important, parenteral administration is preferred. An exemplary mode of administration is to deliver an intravenous bolus. The dosage of the polypeptides or other composition of the invention will normally be determined by the prescribing physician. It is to be expected that the dosage will vary according to the age, weight, condition and response of the individual patient. Typically, the amount of polypeptide administered per dose will be in the range of about 0.01 μg/kg to 100 mg/kg of body weight, with the preferred dose being about 0.1 μg/kg to 10 mg/kg of patient body weight. For parenteral administration, polypeptides of the invention will be formulated in an injectable form combined with a pharmaceutically acceptable parenteral vehicle. Such vehicles are well known in the art and examples include water, saline, Ringer's solution, dextrose solution, and solutions consisting of small amounts of the human serum albumin. The vehicle may contain minor amounts of additives that maintain the isotonicity and stability of the polypeptide or other active ingredient. The preparation of such solutions is within the skill of the art.

[0286] 4.12 Pharmaceutical Formulations and Routes of Administration

[0287] A protein or other composition of the present invention (from whatever source derived, including without limitation from recombinant and non-recombinant sources and including antibodies and other binding partners of the polypeptides of the invention) may be administered to a patient in need, by itself, or in pharmaceutical compositions where it is mixed with suitable carriers or excipient(s) at doses to treat or ameliorate a variety of disorders. Such a composition may optionally contain (in addition to protein or other active ingredient and a carrier) diluents, fillers, salts, buffers, stabilizers, solubilizers, and other materials well known in the art. The term “pharmaceutically acceptable” means a non-toxic material that does not interfere with the effectiveness of the biological activity of the active ingredient(s). The characteristics of the carrier will depend on the route of administration. The pharmaceutical composition of the invention may also contain cytokines, lymphokines, or other hematopoietic factors such as M-CSF. GM-CSF, TNF, IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12, IL-13, IL-14, IL-15, IFN, TNF0, TNF1, TNF2, G-CSF, Meg-CSF, thrombopoietin, stem cell factor, and erythropoietin. In further compositions, proteins of the invention may be combined with other agents beneficial to the treatment of the disease or disorder in question. These agents include various growth factors such as epidermal growth factor (EGF), platelet-derived growth factor (PDGF), transforming growth factors (TGF-α and TGF-β), insulin-like growth factor (IGF), as well as cytokines described herein.

[0288] The pharmaceutical composition may further contain other agents which either enhance the activity of the protein or other active ingredient or complement its activity or use in treatment. Such additional factors and/or agents may be included in the pharmaceutical composition to produce a synergistic effect with protein or other active ingredient of the invention, or to minimize side effects. Conversely, protein or other active ingredient of the present invention may be included in formulations of the particular clotting factor, cytokine, lymphokine, other hematopoietic factor, thrombolytic or anti-thrombotic factor, or anti-inflammatory agent to minimize side effects of the clotting factor, cytokine, lymphokine, other hematopoietic factor, thrombolytic or anti-thrombotic factor, or anti-inflammatory agent (such as IL-1 Ra, IL-1 Hy1, IL-1 Hy2, anti-TNF, corticosteroids, immunosuppressive agents). A protein of the present invention may be active in multimers (e.g., heterodimers or homodimers) or complexes with itself or other proteins. As a result, pharmaceutical compositions of the invention may comprise a protein of the invention in such multimeric or complexed form.

[0289] As an alternative to being included in a pharmaceutical composition of the invention including a first protein, a second protein or a therapeutic agent may be concurrently administered with the first protein (e.g., at the same time, or at differing times provided that therapeutic concentrations of the combination of agents is achieved at the treatment site). Techniques for formulation and administration of the compounds of the instant application may be found in “Remington's Pharmaceutical Sciences.” Mack Publishing Co., Easton, Pa., latest edition. A therapeutically effective dose further refers to that amount of the compound sufficient to result in amelioration of symptoms, e.g., treatment, healing, prevention or amelioration of the relevant medical condition, or an increase in rate of treatment, healing, prevention or amelioration of such conditions. When applied to an individual active ingredient, administered alone, a therapeutically effective dose refers to that ingredient alone. When applied to a combination, a therapeutically effective dose refers to combined amounts of the active ingredients that result in the therapeutic effect, whether administered in combination, serially or simultaneously.

[0290] In practicing the method of treatment or use of the present invention, a therapeutically effective amount of protein or other active ingredient of the present invention is administered to a mammal having a condition to be treated. Protein or other active ingredient of the present invention may be administered in accordance with the method of the invention either alone or in combination with other therapies such as treatments employing cytokines, lymphokines or other hematopoletic factors. When co-administered with one or more cytokines, lymphokines or other hematopoietic factors, protein or other active ingredient of the present invention may be administered either simultaneously with the cytokine(s), lymphokine(s), other hematopoietic factor(s), thrombolytic or anti-thrombotic factors, or sequentially. If administered sequentially, the attending physician will decide on the appropriate sequence of administering protein or other active ingredient of the present invention in combination with cytokine(s), lymphokine(s), other hematopoietic factor(s), thrombolytic or anti-thrombotic factors.

[0291] 4.12.1 Routes of Administration

[0292] Suitable routes of administration may, for example, include oral, rectal, transmucosal, or intestinal administration; parenteral delivery, including intramuscular, subcutaneous, intramedullary injections, as well as intrathecal, direct intraventricular, intravenous, intraperitoneal, intranasal, or intraocular injections. Administration of protein or other active ingredient of the present invention used in the pharmaceutical composition or to practice the method of the present invention can be carried out in a variety of conventional ways, such as oral ingestion, inhalation, topical application or cutaneous, subcutaneous, intraperitoneal, parenteral or intravenous injection. Intravenous administration to the patient is preferred.

[0293] Alternately, one may administer the compound in a local rather than systemic manner, for example, via injection of the compound directly into a arthritic joints or in fibrotic tissue, often in a depot or sustained release formulation. In order to prevent the scarring process frequently occurring as complication of glaucoma surgery, the compounds may be administered topically, for example, as eye drops. Furthermore, one may administer the drug in a targeted drug delivery system, for example, in a liposome coated with a specific antibody, targeting, for example, arthritic or fibrotic tissue. The liposomes will be targeted to and taken up selectively by the afflicted tissue.

[0294] The polypeptides of the invention are administered by any route that delivers an effective dosage to the desired site of action. The determination of a suitable route of administration and an effective dosage for a particular indication is within the level of skill in the art. Preferably for wound treatment, one administers the therapeutic compound directly to the site. Suitable dosage ranges for the polypeptides of the invention can be extrapolated from these dosages or from similar studies in appropriate animal models. Dosages can then be adjusted as necessary by the clinician to provide maximal therapeutic benefit.

[0295] 4.12.2 Compositions/Formulations

[0296] Pharmaceutical compositions for use in accordance with the present invention thus may be formulated in a conventional manner using one or more physiologically acceptable carriers comprising excipients and auxiliaries which facilitate processing of the active compounds into preparations which can be used pharmaceutically. These pharmaceutical compositions may be manufactured in a manner that is itself known, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping or lyophilizing processes. Proper formulation is dependent upon the route of administration chosen. When a therapeutically effective amount of protein or other active ingredient of the present invention is administered orally, protein or other active ingredient of the present invention will be in the form of a tablet, capsule, powder, solution or elixir. When administered in tablet form, the pharmaceutical composition of the invention may additionally contain a solid carrier such as a gelatin or an adjuvant. The tablet, capsule, and powder contain from about 5 to 95% protein or other active ingredient of the present invention, and preferably from about 25 to 90% protein or other active ingredient of the present invention. When administered in liquid form, a liquid carrier such as water, petroleum, oils of animal or plant origin such as peanut oil, mineral oil, soybean oil, or sesame oil, or synthetic oils may be added. The liquid form of the pharmaceutical composition may further contain physiological saline solution, dextrose or other saccharide solution, or glycols such as ethylene glycol, propylene glycol or polyethylene glycol. When administered in liquid form, the pharmaceutical composition contains from about 0.5 to 90% by weight of protein or other active ingredient of the present invention, and preferably from about 1 to 50% protein or other active ingredient of the present invention.

[0297] When a therapeutically effective amount of protein or other active ingredient of the present invention is administered by intravenous, cutaneous or subcutaneous injection, protein or other active ingredient of the present invention will be in the form of a pyrogen-free, parenterally acceptable aqueous solution. The preparation of such parenterally acceptable protein or other active ingredient solutions, having due regard to pH, isotonicity, stability, and the like, is within the skill in the art. A preferred pharmaceutical composition for intravenous, cutaneous, or subcutaneous injection should contain, in addition to protein or other active ingredient of the present invention, an isotonic vehicle such as Sodium Chloride Injection, Ringer's Injection, Dextrose Injection, Dextrose and Sodium Chloride Injection. Lactated Ringer's Injection, or other vehicle as known in the art. The pharmaceutical composition of the present invention may also contain stabilizers, preservatives, buffers, antioxidants, or other additives known to those of skill in the art. For injection, the agents of the invention may be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hanks's solution, Ringer's solution, or physiological saline buffer. For transmucosal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art.

[0298] For oral administration, the compounds can be formulated readily by combining the active compounds with pharmaceutically acceptable carriers ell known in the art. Such carriers enable the compounds of the invention to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions and the like, for oral ingestion by a patient to be treated. Pharmaceutical preparations for oral use can be obtained from a solid excipient, optionally grinding a resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries, if desired, to obtain tablets or dragee cores. Suitable excipients are, in particular, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose preparations such as, for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl-cellulose, sodium carboxymethylcellulose, and/or polyvinylpyrrolidone (PVP). If desired, disintegrating agents may be added, such as the cross-linked polyvinyl pyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate. Dragee cores are provided with suitable coatings. For this purpose, concentrated sugar solutions may be used, which may optionally contain gum arabic, talc, polyvinyl pyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures. Dyestuffs or pigments may be added to the tablets or dragee coatings for identification or to characterize different combinations of active compound doses.

[0299] Pharmaceutical preparations which can be used orally include push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin and a plasticizer, such as glycerol or sorbitol. The push-fit capsules can contain the active ingredients in admixture with filler such as lactose, binders such as starches, and/or lubricants such as talc or magnesium stearate and, optionally, stabilizers. In soft capsules, the active compounds may be dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycols. In addition, stabilizers may be added. All formulations for oral administration should be in dosages suitable for such administration. For buccal administration, the compositions may take the form of tablets or lozenges formulated in conventional manner.

[0300] For administration by inhalation, the compounds for use according to the present invention are conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebuliser, with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In the case of a pressurized aerosol the dosage unit may be determined by providing a real c to deliver a metered amount. Capsules and cartridges of, e.g., gelatin for use in an inhaler or insufflator may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch. The compounds may be formulated for parenteral administration by injection, e.g., by bolus injection or continuous infusion. Formulations for injection may be presented in unit dosage form, e.g., in ampules or in multi-dose containers, with an added preservative. The compositions may take such forms as suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents.

[0301] Pharmaceutical formulations for parenteral administration include aqueous solutions of the active compounds in water-soluble form. Additionally, suspensions of the active compounds may be prepared as appropriate oily injection suspensions. Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acid esters, such as ethyl oleate or triglycerides, or liposomes. Aqueous injection suspensions may contain substances which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran. Optionally, the suspension may also contain suitable stabilizers or agents which increase the solubility of the compounds to allow for the preparation of highly concentrated solutions. Alternatively, the active ingredient may be in powder form for constitution with a suitable vehicle, e.g., sterile pyrogen-free water, before use.

[0302] The compounds may also be formulated in rectal compositions such as suppositories or retention enemas, e.g., containing conventional suppository bases such as cocoa butter or other glycerides. In addition to the formulations described previously, the compounds may also be formulated as a depot preparation. Such long acting formulations may be administered by implantation (for example subcutaneously or intramuscularly) or by intramuscular injection. Thus, for example, the compounds may be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salt.

[0303] A pharmaceutical carrier for the hydrophobic compounds of the invention is a co-solvent system comprising benzyl alcohol, a nonpolar surfactant, a water-miscible organic polymer, and an aqueous phase. The co-solvent system may be the VPD co-solvent system. VPD is a solution of 3% w/v benzyl alcohol, 8% w/v of the nonpolar surfactant polysorbate 80, and 65% w/v polyethylene glycol 300, made up to volume in absolute ethanol. The VPD co-solvent system (VPD:5W) consists of VPD diluted 1:1 with a 5% dextrose in water solution. This co-solvent system dissolves hydrophobic compounds well, and itself produces low toxicity upon systemic administration. Naturally, the proportions of a co-solvent system may be varied considerably without destroying its solubility and toxicity characteristics. Furthermore, the identity of the co-solvent components may be varied: for example, other low-toxicity nonpolar surfactants may be used instead of polysorbate 80: the fraction size of polyethylene glycol may be varied: other biocompatible polymers may replace polyethylene glycol, e.g. polyvinyl pyrrolidone; and other sugars or polysaccharides may substitute for dextrose. Alternatively, other delivery systems for hydrophobic pharmaceutical compounds may be employed. Liposomes and emulsions are well known examples of delivery vehicles or carriers for hydrophobic drugs. Certain organic solvents such as dimethylsulfoxide also may be employed, although usually at the cost of greater toxicity. Additionally, the compounds may be delivered using a sustained-release system, such as semipermeable matrices of solid hydrophobic polymers containing the therapeutic agent. Various types of sustained-release materials have been established and are well known by those skilled in the art. Sustained-release capsules may, depending on their chemical nature, release the compounds for a few weeks up to over 100 days. Depending on the chemical nature and the biological stability of the therapeutic reagent, additional strategies for protein or other active ingredient stabilization may be employed.

[0304] The pharmaceutical compositions also may comprise suitable solid or gel phase carriers or excipients. Examples of such carriers or excipients include but are not limited to calcium carbonate, calcium phosphate, various sugars, starches, cellulose derivatives, gelatin, and polymers such as polyethylene glycols. Many of the active ingredients of the invention may be provided as salts with pharmaceutically compatible counter ions. Such pharmaceutically acceptable base addition salts are those salts which retain the biological effectiveness and properties of the free acids and which are obtained by reaction with inorganic or organic bases such as sodium hydroxide, magnesium hydroxide, ammonia, trialkylamine, dialkylamine, monoalkylamine, dibasic amino acids, sodium acetate, potassium benzoate, triethanol amine and the like.

[0305] The pharmaceutical composition of the invention may be in the form of a complex of the protein(s) or other active ingredient(s) of present invention along with protein or peptide antigens. The protein and/or peptide antigen will deliver a stimulatory signal to both B and T lymphocytes. B lymphocytes will respond to antigen through their surface immunoglobulin receptor. T lymphocytes will respond to antigen through the T cell receptor (TCR) following presentation of the antigen by MHC proteins. MHC and structurally related proteins including those encoded by class I and class II MHC genes on host cells will serve to present the peptide antigen(s) to T lymphocytes. The antigen components could also be supplied as purified MHC-peptide complexes alone or with co-stimulatory molecules that can directly signal T cells. Alternatively antibodies able to bind surface immunoglobulin and other molecules on B cells as well as antibodies able to bind the TCR and other molecules on T cells can be combined with the pharmaceutical composition of the invention.

[0306] The pharmaceutical composition of the invention may be in the form of a liposome in which protein of the present invention is combined, in addition to other pharmaceutically acceptable carriers, with amphipathic agents such as lipids which exist in aggregated form as micelles, insoluble monolayers, liquid crystals, or lamellar layers in aqueous solution. Suitable lipids for liposomal formulation include, without limitation, monoglycerides, diglycerides, sulfatides, lysolecithins, phospholipids, saponin, bile acids, and the like. Preparation of such liposomal formulations is within the level of skill in the art, as disclosed, for example, in U.S. Pat. Nos. 4,235,871; 4,501,728; 4,837,028; and 4,737,323, all of which are incorporated herein by reference.

[0307] The amount of protein or other active ingredient of the present invention in the pharmaceutical composition of the present invention will depend upon the nature and severity of the condition being treated, and on the nature of prior treatments which the patient has undergone. Ultimately, the attending physician will decide the amount of protein or other active ingredient of the present invention with which to treat each individual patient. Initially, the attending physician will administer low doses of protein or other active ingredient of the present invention and observe the patient's response. Larger doses of protein or other active ingredient of the present invention may be administered until the optimal therapeutic effect is obtained for the patient, and at that point the dosage is not increased further. It is contemplated that the various pharmaceutical compositions used to practice the method of the present invention should contain about 0.01 μg to about 100 mg (preferably about 0.1 μg to about 10 mg, more preferably about 0.1 μg to about 1 mg) of protein or other active ingredient of the present invention per kg body weight. For compositions of the present invention which are useful for bone, cartilage, tendon or ligament regeneration, the therapeutic method includes administering the composition topically, systematically, or locally as an implant or device. When administered, the therapeutic composition for use in this invention is, of course, in a pyrogen-free, physiologically acceptable form. Further, the composition may desirably be encapsulated or injected in a viscous form for delivery to the site of bone, cartilage or tissue damage. Topical administration may be suitable for wound healing and tissue repair. Therapeutically useful agents other than a protein or other active ingredient of the invention which may also optionally be included in the composition as described above, may alternatively or additionally, be administered simultaneously or sequentially with the composition in the methods of the invention. Preferably for bone and/or cartilage formation, the composition would include a matrix capable of delivering the protein-containing or other active ingredient-containing composition to the site of bone and/or cartilage damage, providing a structure for the developing bone and cartilage and optimally capable of being resorbed into the body. Such matrices may be formed of materials presently in use for other implanted medical applications.

[0308] The choice of matrix material is based on biocompatibility, biodegradability, mechanical properties, cosmetic appearance and interface properties. The particular application of the compositions will define the appropriate formulation. Potential matrices for the compositions may be biodegradable and chemically defined calcium sulfate, tricalcium phosphate, hydroxyapatite, polylactic acid, polyglycolic acid and polyanhydrides. Other potential materials are biodegradable and biologically well-defined, such as bone or dermal collagen. Further matrices are comprised of pure proteins or extracellular matrix components. Other potential matrices are nonbiodegradable and chemically defined, such as sintered hydroxyapatite, bioglass, aluminates, or other ceramics. Matrices may be comprised of combinations of any of the above mentioned types of material, such as polylactic acid and hydroxyapatite or collagen and tricalcium phosphate. The bioceramics may be altered in composition, such as in calcium-aluminate-phosphate and processing to alter pore size, particle size, particle shape, and biodegradability. Presently preferred is a 50:50 (mole weight) copolymer of lactic acid and glycolic acid in the form of porous particles having diameters ranging from 150 to 800 microns. In some applications, it will be useful to utilize a sequestering agent, such as carboxymethyl cellulose or autologous blood clot, to prevent the protein compositions from disassociating from the matrix.

[0309] A preferred family of sequestering agents is cellulosic materials such as alkylcelluloses (including hydroxyalkylcelluloses), including methylcellulose, ethylcellulose, hydroxyethylcellulose, hydroxypropylcellulose, hydroxypropyl-methylcellulose, and carboxymethylcellulose, the most preferred being cationic salts of carboxymethylcellulose (CMC). Other preferred sequestering agents include hyaluronic acid, sodium alginate, poly(ethylene glycol), polyoxyethylene oxide, carboxyvinyl polymer and poly(vinyl alcohol). The amount of sequestering agent useful herein is 0.5-20 wt %, preferably 1-10 wt % based on total formulation weight, which represents the amount necessary to prevent desorption of the protein from the polymer matrix and to provide appropriate handling of the composition, yet not so much that the progenitor cells are prevented from infiltrating the matrix, thereby providing the protein the opportunity to assist the osteogenic activity of the progenitor cells. In further compositions, proteins or other active ingredients of the invention may be combined with other agents beneficial to the treatment of the bone and/or cartilage defect, wound, or tissue in question. These agents include various growth factors such as epidermal growth factor (EGF), platelet derived growth factor (PDGF), transforming growth factors (TGF-α and TGF-β), and insulin-like growth factor (IGF).

[0310] The therapeutic compositions are also presently valuable for veterinary applications. Particularly domestic animals and thoroughbred horses, in addition to humans, are desired patients for such treatment with proteins or other active ingredients of the present invention. The dosage regimen of a protein-containing, pharmaceutical composition to be used in tissue regeneration will be determined by the attending physician considering various factors which modify the action of the proteins, e.g., amount of tissue weight desired to be formed, the site of damage, the condition of the damaged tissue, the size of a wound, type of damaged tissue (e.g., bone), the patient's age, sex, and diet, the severity of any infection, time of administration and other clinical factors. The dosage may vary with the type of matrix used in the reconstitution and with inclusion of other proteins in the pharmaceutical composition. For example, the addition of other known growth factors, such as IGF 1 (insulin like growth factor 1), to the final composition, may also effect the dosage. Progress can be monitored by periodic assessment of tissue/bone growth and/or repair, for example, X-rays, histomorphometric determinations and tetracycline labeling.

[0311] Polynucleotides of the present invention can also be used for gene therapy. Such polynucleotides can be introduced either in vivo or ex vivo into cells for expression in a mammalian subject. Polynucleotides of the invention may also be administered by other known methods for introduction of nucleic acid into a cell or organism (including, without limitation, in the form of viral vectors or naked DNA). Cells may also be cultured ex vivo in the presence of proteins of the present invention in order to proliferate or to produce a desired effect on or activity in such cells. Treated cells can then be introduced in vivo for therapeutic purposes.

[0312] 4.12.3 Effective Dosage

[0313] Pharmaceutical compositions suitable for use in the present invention include compositions wherein the active ingredients are contained in an effective amount to achieve its intended purpose. More specifically, a therapeutically effective amount means an amount effective to prevent development of or to alleviate the existing symptoms of the subject being treated. Determination of the effective amount is well within the capability of those skilled in the art, especially in light of the detailed disclosure provided herein. For any compound used in the method of the invention, the therapeutically effective dose can be estimated initially from appropriate in vitro assays. For example, a dose can be formulated in animal models to achieve a circulating concentration range that can be used to more accurately determine useful doses in humans. For example, a dose can be formulated in animal models to achieve a circulating concentration range that includes the IC50 as determined in cell culture (i.e., the concentration of the test compound which achieves a half-maximal inhibition of the protein's biological activity). Such information can be used to more accurately determine useful doses in humans.

[0314] A therapeutically effective dose refers to that amount of the compound that results in amelioration of symptoms or a prolongation of survival in a patient. Toxicity and therapeutic efficacy of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio between LD50 and ED50. Compounds which exhibit high therapeutic indices are preferred. The data obtained from these cell culture assays and animal studies can be used in formulating a range of dosage for use in human. The dosage of such compounds lies preferably within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. The exact formulation, route of administration and dosage can be chosen by the individual physician in view of the patient's condition. See, e.g., Fingl et al., 1975, in “The Pharmacological Basis of Therapeutics”, Ch. 1 p.1. Dosage amount and interval may be adjusted individually to provide plasma levels of the active moiety which are sufficient to maintain the desired effects, or minimal effective concentration (MEC). The MEC will vary for each compound but can be estimated from in vitro data. Dosages necessary to achieve the MEC will depend on individual characteristics and route of administration. However, HPLC assays or bioassays can be used to determine plasma concentrations.

[0315] Dosage intervals can also be determined using MEC value. Compounds should be administered using a regimen which maintains plasma levels above the MEC for 10-90% of the time, preferably between 30-90% and most preferably between 50-90%. In cases of local administration or selective uptake, the effective local concentration of the drug may not be related to plasma concentration.

[0316] An exemplary dosage regimen for polypeptides or other compositions of the invention will be in the range of about 0.01 μg/kg to 100 mg/kg of body weight daily, with the preferred dose being about 0.1 μg/kg to 25 mg/kg of patient body weight daily, varying in adults and children. Dosing may be once daily, or equivalent doses may be delivered at longer or shorter intervals.

[0317] The amount of composition administered will, of course, be dependent on the subject being treated, on the subject's age and weight, the severity of the affliction, the manner of administration and the judgment of the prescribing physician.

[0318] 4.12.4 Packaging

[0319] The compositions may, if desired, be presented in a pack or dispenser device which may contain one or more unit dosage forms containing the active ingredient. The pack may, for example, comprise metal or plastic foil, such as a blister pack. The pack or dispenser device may be accompanied by instructions for administration. Compositions comprising a compound of the invention formulated in a compatible pharmaceutical carrier may also be prepared, placed in an appropriate container, and labeled for treatment of an indicated condition.

[0320] 4.13 Antibodies

[0321] Also included in the invention are antibodies to proteins, or fragments of proteins of the invention. The term “antibody” as used herein refers to immunoglobulin molecules and immunologically active portions of immunoglobulin (Ig) molecules, i.e., molecules that contain an antigen binding site that specifically binds (immunoreacts with) an antigen. Such antibodies include, but are not limited to, polyclonal, monoclonal, chimeric, single chain, Fab, Fab and F(ab′)2 fragments, and an Fab expression library. In general, an antibody molecule obtained from humans relates to any of the classes IgG, IgM, IgA, IgE and IgD, which differ from one another by the nature of the heavy chain present in the molecule. Certain classes have subclasses as well, such as IgG1, IgG2, and others. Furthermore, in humans, the light chain may be a kappa chain or a lambda chain. Reference herein to antibodies includes a reference to all such classes, subclasses and types of human antibody species.

[0322] An isolated related protein of the invention may be intended to serve as an antigen, or a portion or fragment thereof, and additionally can be used as an immunogen to generate antibodies that immunospecifically bind the antigen, using standard techniques for polyclonal and monoclonal antibody preparation. The full-length protein can be used or, alternatively, the invention provides antigenic peptide fragments of the antigen for use as immunogens. An antigenic peptide fragment comprises at least 6 amino acid residues of the amino acid sequence of the full length protein, such as the amino acid sequences shown in SEQ ID NO: 246-490, and encompasses an epitope thereof such that an antibody raised against the peptide forms a specific immune complex with the full length protein or with any fragment that contains the epitope. Preferably, the antigenic peptide comprises at least 10 amino acid residues, or at least 15 amino acid residues, or at least 20 amino acid residues, or at least 30 amino acid residues. Preferred epitopes encompassed by the antigenic peptide are regions of the protein that are located on its surface; commonly these are hydrophilic regions.

[0323] In certain embodiments of the invention, at least one epitope encompassed by the antigenic peptide is a region of related protein that is located on the surface of the protein, e.g., a hydrophilic region. A hydrophobicity analysis of the human related protein sequence will indicate which regions of a related protein are particularly hydrophilic and, therefore, are likely to encode surface residues useful for targeting antibody production. As a means for targeting antibody production, hydropathy plots showing regions of hydrophilicity and hydrophobicity may be generated by any method well known in the art, including, for example, the Kyte Doolittle or the Hopp Woods methods, either with or without Fourier transformation. See, e.g., Hopp and Woods, 1981. Proc. Nat. Acad Sci. USA 78: 3824-3828; Kyte and Doolittle 1982, J. Mol. Biol. 157: 105-142, each of which is incorporated herein by reference in its entirety. Antibodies that are specific for one or more domains within an antigenic protein, or derivatives, fragments, analogs or homologs thereof, are also provided herein.

[0324] A protein of the invention, or a derivative, fragment, analog, homolog or ortholog thereof, may be utilized as an immunogen in the generation of antibodies that immunospecifically bind these protein components.

[0325] Various procedures known within the art may be used for the production of polyclonal or monoclonal antibodies directed against a protein of the invention, or against derivatives, fragments, analogs homologs or orthologs thereof (see, for example, Antibodies: A Laboratory Manual, Harlow E. and Lane D, 1988, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., incorporated herein by reference). Some of these antibodies are discussed below.

[0326] 4.13.1 Polyclonal Antibodies

[0327] For the production of polyclonal antibodies, various suitable host animals (e.g., rabbit, goat, mouse or other mammal) may be immunized by one or more injections with the native protein, a synthetic variant thereof, or a derivative of the foregoing. An appropriate immunogenic preparation can contain, for example, the naturally occurring immunogenic protein, a chemically synthesized polypeptide representing the immunogenic protein, or a recombinantly expressed immunogenic protein. Furthermore, the protein may be conjugated to a second protein known to be immunogenic in the mammal being immunized. Examples of such immunogenic proteins include but are not limited to keyhole limpet hemocyanin, serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor. The preparation can further include an adjuvant. Various adjuvants used to increase the immunological response include, but are not limited to, Freund's (complete and incomplete), mineral gels (e.g., aluminum hydroxide), surface active substances (e.g. lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, dinitrophenol, etc.), adjuvants usable in humans such as Bacille Calmette-Guerin and Corynebacterium parvum, or similar immunostimulatory agents. Additional examples of adjuvants which can be employed include MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate).

[0328] The polyclonal antibody molecules directed against the immunogenic protein can be isolated from the mammal (e.g., from the blood) and further purified by well known techniques, such as affinity chromatography using protein A or protein G, which provide primarily the IgG fraction of immune serum. Subsequently, or alternatively, the specific antigen which is the target of the immunoglobulin sought, or an epitope thereof, may be immobilized on a column to purify the immune specific antibody by immunoaffinity chromatography. Purification of immunoglobulins is discussed, for example, by D. Wilkinson (The Scientist, published by The Scientist, Inc., Philadelphia Pa., Vol. 14, No. 8 (Apr. 17, 2000), pp. 25-28).

[0329] 4.13.2 Monoclonal Antibodies

[0330] The term “monoclonal antibody” (MAb) or “monoclonal antibody composition”, as used herein, refers to a population of antibody molecules that contain only one molecular species of antibody molecule consisting of a unique light chain gene product and a unique heavy chain gene product. In particular, the complementarity determining regions (CDRs) of the monoclonal antibody are identical in all the molecules of the population. MAbs thus contain an antigen binding site capable of immunoreacting with a particular epitope of the antigen characterized by a unique binding affinity for it.

[0331] Monoclonal antibodies can be prepared using hybridoma methods, such as those described by Kohler and Milstein, Nature, 256:495 (1975). In a hybridoma method, a mouse, hamster, or other appropriate host animal, is typically immunized with an immunizing agent to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immunizing agent. Alternatively, the lymphocytes can be immunized in vitro. The immunizing agent will typically include the protein antigen, a fragment thereof or a fusion protein thereof. Generally, either peripheral blood lymphocytes are used if cells of human origin are desired, or spleen cells or lymph node cells are used if non-human mammalian sources are desired. The lymphocytes are then fused with an immortalized cell line using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell (Goding, Monoclonal Antibodies: Principles and Practice, Academic Press, (1986) pp. 59-103). Immortalized cell lines are usually transformed mammalian cells, particularly myeloma cells of rodent, bovine and human origin. Usually, rat or mouse myeloma cell lines are employed. The hybridoma cells can be cultured in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused, immortalized cells. For example, if the parental cells lack the enzyme hypoxanthine guanine phosphoribosyl transferase (HGPRT or HPRT), the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine (“HAT medium”), which substances prevent the growth of HGPRT-deficient cells.

[0332] Preferred immortalized cell lines are those that fuse efficiently, support stable high level expression of antibody by the selected antibody-producing cells, and are sensitive to a medium such as HAT medium. More preferred immortalized cell lines are murine myeloma lines, which can be obtained, for instance, from the Salk Institute Cell Distribution Center, San Diego, Calif. and the American Type Culture Collection, Manassas, Va. Human myeloma and mouse-human heteromyeloma cell lines also have been described for the production of human monoclonal antibodies (Kozbor, J. Immunol., 133:3001 (1984); Brodeur et al., Monoclonal Antibody Production Techniques and Applications, Marcel Dekker, Inc., New York, (1987) pp. 51-63).

[0333] The culture medium in which the hybridoma cells are cultured can then be assayed for the presence of monoclonal antibodies directed against the antigen. Preferably, the binding specificity of monoclonal antibodies produced by the hybridoma cells is determined by immunoprecipitation or by an in vitro binding assay, such as radioimmunoassay (RIA) or enzyme-linked immunoabsorbent assay (ELISA). Such techniques and assays are known in the art. The binding affinity of the monoclonal antibody can, for example, be determined by the Scatchard analysis of Munson and Pollard, Anal. Biochem., 107:220 (1980). Preferably, antibodies having a high degree of specificity and a high binding affinity for the target antigen are isolated.

[0334] After the desired hybridoma cells are identified, the clones can be subcloned by limiting dilution procedures and grown by standard methods. Suitable culture media for this purpose include, for example. Dulbecco's Modified Eagle's Medium and RPMI-1640 medium. Alternatively, the hybridoma cells can be grown in vivo as ascites in a mammal.

[0335] The monoclonal antibodies secreted by the subclones can be isolated or purified from the culture medium or ascites fluid by conventional immunoglobulin purification procedures such as, for example, protein A-Sepharose, hydroxylapatite chromatography, gel electrophoresis, dialysis, or affinity chromatography.

[0336] The monoclonal antibodies can also be made by recombinant DNA methods, such as those described in U.S. Pat. No. 4,816,567. DNA encoding the monoclonal antibodies of the invention can be readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of murine antibodies). The hybridoma cells of the invention serve as a preferred source of such DNA. Once isolated, the DNA can be placed into expression vectors, which are then transfected into host cells such as simian COS cells, Chinese hamster ovary (CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin protein, to obtain the synthesis of monoclonal antibodies in the recombinant host cells. The DNA also can be modified, for example, by substituting the coding sequence for human heavy and light chain constant domains in place of the homologous murine sequences (U.S. Pat. No. 4,816,567: Morrison, Nature 368, 812-13 (1994)) or by covalently joining to the immunoglobulin coding sequence all or part of the coding sequence for a non-immunoglobulin polypeptide. Such a non-immunoglobulin polypeptide can be substituted for the constant domains of an antibody of the invention, or can be substituted for the variable domains of one antigen-combining site of an antibody of the invention to create a chimeric bivalent antibody.

[0337] 4.13.3 Humanized Antibodies

[0338] The antibodies directed against the protein antigens of the invention can further comprise humanized antibodies or human antibodies. These antibodies are suitable for administration to humans without engendering an immune response by the human against the administered immunoglobulin. Humanized forms of antibodies are chimeric immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab′, F(ab′)2 or other antigen-binding subsequences of antibodies) that are principally comprised of the sequence of a human immunoglobulin, and contain minimal sequence derived from a non-human immunoglobulin. Humanization can be performed following the method of Winter and co-workers (Jones et al., Nature, 321:522-525 (1986); Riechmann et al., Nature, 332:323-327 (1988); Verhoeyen et al., Science, 239:1534-1536 (1988)), by substituting rodent CDRs or CDR sequences for the corresponding sequences of a human antibody. (See also U.S. Pat. No. 5,225,539.) In some instances, Fv framework residues of the human immunoglobulin are replaced by corresponding non-human residues. Humanized antibodies can also comprise residues which are found neither in the recipient antibody nor in the imported CDR or framework sequences. In general, the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the framework regions are those of a human immunoglobulin consensus sequence. The humanized antibody optimally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin (Jones et al., 1986; Riechmann et al., 1988; and Presta., Curr. Op. Struct. Biol., 2:593-596 (1992)).

[0339] 4.13.4 Human Antibodies

[0340] Fully human antibodies relate to antibody molecules in which essentially the entire sequences of both the light chain and the heavy chain, including the CDRs, arise from human genes. Such antibodies are termed “human antibodies”, or “fully human antibodies” herein. Human monoclonal antibodies can be prepared by the trioma technique: the human B-cell hybridoma technique (see Kozbor, et al. 1983 Immunol Today 4: 72) and the EBV hybridoma technique to produce human monoclonal antibodies (see Cole, et al. 1985 In: MONOCLONAL ANTIBODIES AND CANCER THERAPY. Alan R. Liss, Inc. pp. 77-96). Human monoclonal antibodies may be utilized in the practice of the present invention and may be produced by using human hybridomas (see Cote, et al., 1983. Proc Natl Acad Sci USA 80: 2026-2030) or by transforming human B-cells with Epstein Barr Virus in vitro (see Cole, et al., 1985 In: MONOCLONAL ANTIBODIES AND CANCER THERAPY, Alan R. Liss, Inc., pp. 77-96).

[0341] In addition, human antibodies can also be produced using additional techniques, including phage display libraries (Hoogenboom and Winter, J. Mol. Biol., 227:381 (1991); Marks et al., J. Mol. Biol., 222:581 (1991)). Similarly, human antibodies can be made by introducing human immunoglobulin loci into transgenic animals, e.g., mice in which the endogenous immunoglobulin genes have been partially or completely inactivated. Upon challenge, human antibody production is observed, which closely resembles that seen in humans in all respects, including gene rearrangement, assembly, and antibody repertoire. This approach is described, for example, in U.S. Pat. Nos. 5,545,807; 5,545,806; 5,569,825; 5,625,126; 5,633,425; 5,661,016, and in Marks et al. (Bio/Technology 10 779-783 (1992)); Lonberg et al. (Nature 368 856-859 (1994)); Morrison (Nature 368, 812-13 (1994)); Fishwild et al,(Nature Biotechnology 14, 845-51 (1996)); Neuberger (Nature Biotechnology 14, 826 (1996)); and Lonberg and Huszar (Intern. Rev. Immunol. 13 65-93 (1995)).

[0342] Human antibodies may additionally be produced using transgenic nonhuman animals which are modified so as to produce fully human antibodies rather than the animal's endogenous antibodies in response to challenge by an antigen. (See PCT publication WO94/02602). The endogenous genes encoding the heavy and light immunoglobulin chains in the nonhuman host have been incapacitated, and active loci encoding human heavy and light chain immunoglobulins are inserted into the host's genome. The human genes are incorporated, for example, using yeast artificial chromosomes containing the requisite human DNA segments. An animal which provides all the desired modifications is then obtained as progeny by crossbreeding intermediate transgenic animals containing fewer than the full complement of the modifications. The preferred embodiment of such a nonhuman animal is a mouse, and is termed the Xenomouse™ as disclosed in PCT publications WO 96/33735 and WO 96/34096. This animal produces B cells which secrete fully human immunoglobulins. The antibodies can be obtained directly from the animal after immunization with an immunogen of interest, as, for example, a preparation of a polyclonal antibody, or alternatively from immortalized B cells derived from the animal, such as hybridomas producing monoclonal antibodies. Additionally, the genes encoding the immunoglobulins with human variable regions can be recovered and expressed to obtain the antibodies directly, or can be further modified to obtain analogs of antibodies such as, for example, single chain Fv molecules.

[0343] An example of a method of producing a nonhuman host, exemplified as a mouse, lacking expression of an endogenous immunoglobulin heavy chain is disclosed in U.S. Pat. No. 5,939,598. It can be obtained by a method including deleting the J segment genes from at least one endogenous heavy chain locus in an embryonic stem cell to prevent rearrangement of the locus and to prevent formation of a transcript of a rearranged immunoglobulin heavy chain locus, the deletion being effected by a targeting vector containing a gene encoding a selectable marker; and producing from the embryonic stem cell a transgenic mouse whose somatic and germ cells contain the gene encoding the selectable marker.

[0344] A method for producing an antibody of interest, such as a human antibody, is disclosed in U.S. Pat. No. 5,916,771. It includes introducing an expression vector that contains a nucleotide sequence encoding a heavy chain into one mammalian host cell in culture, introducing an expression vector containing a nucleotide sequence encoding a light chain into another mammalian host cell, and fusing the two cells to form a hybrid cell. The hybrid cell expresses an antibody containing the heavy chain and the light chain.

[0345] In a further improvement on this procedure, a method for identifying a clinically relevant epitope on an immunogen, and a correlative method for selecting an antibody that binds immunospecifically to the relevant epitope with high affinity, are disclosed in PCT publication WO 99/53049.

[0346] 4.13.5 Fab Fragments and Single Chain Antibodies

[0347] According to the invention, techniques can be adapted for the production of single-chain antibodies specific to an antigenic protein of the invention (see e.g., U.S. Pat. No. 4,946,778). In addition, methods can be adapted for the construction of Fab expression libraries (see e.g., Huse, et al., 1989 Science 246: 1275-1281) to allow rapid and effective identification of monoclonal Fab fragments with the desired specificity for a protein or derivatives, fragments, analogs or homologs thereof. Antibody fragments that contain the idiotypes to a protein antigen may be produced by techniques known in the art including, but not limited to: (i) an F(ab′)2 fragment produced by pepsin digestion of an antibody molecule; (ii) an Fab fragment generated by reducing the disulfide bridges of an F(ab′)2 fragment; (iii) an Fab fragment generated by the treatment of the antibody molecule with papain and a reducing agent and (iv) F, fragments.

[0348] 4.13.6 Bispecific Antibodies

[0349] Bispecific antibodies are monoclonal, preferably human or humanized, antibodies that have binding specificities for at least two different antigens. In the present case, one of the binding specificities is for an antigenic protein of the invention. The second binding target is any other antigen, and advantageously is a cell-surface protein or receptor or receptor subunit.

[0350] Methods for making bispecific antibodies are known in the art. Traditionally, the recombinant production of bispecific antibodies is based on the co-expression of two immunoglobulin heavy-chain/light-chain pairs, where the two heavy chains have different specificities (Milstein and Cuello, Nature, 305:537-539 (1983)). Because of the random assortment of immunoglobulin heavy and light chains, these hybridomas (quadromas) produce a potential mixture of ten different antibody molecules, of which only one has the correct bispecific structure. The purification of the correct molecule is usually accomplished by affinity chromatography steps. Similar procedures are disclosed in WO 93/08829, published May 13, 1993, and in Traunecker et al., 1991 EMBO J., 10:3655-3659.

[0351] Antibody variable domains with the desired binding specificities (antibody-antigen combining sites) can be fused to immunoglobulin constant domain sequences. The fusion preferably is with an immunoglobulin heavy-chain constant domain, comprising at least part of the hinge, CH2, and CH3 regions. It is preferred to have the first heavy-chain constant region (CH1) containing the site necessary for light-chain binding present in at least one of the fusions. DNAs encoding the immunoglobulin heavy-chain fusions and, if desired, the immunoglobulin light chain, are inserted into separate expression vectors, and are co-transfected into a suitable host organism. For further details of generating bispecific antibodies see, for example, Suresh et al., Methods in Enzymology, 121:210 (1986).

[0352] According to another approach described in WO 96/27011, the interface between a pair of antibody molecules can be engineered to maximize the percentage of heterodimers which are recovered from recombinant cell culture. The preferred interface comprises at least a part of the CH3 region of an antibody constant domain. In this method, one or more small amino acid side chains from the interface of the first antibody molecule are replaced with larger side chains (e.g. tyrosine or tryptophan). Compensatory “cavities” of identical or similar size to the large side chain(s) are created on the interface of the second antibody molecule by replacing large amino acid side chains with smaller ones (e.g. alanine or threonine). This provides a mechanism for increasing the yield of the heterodimer over other unwanted end-products such as homodimers.

[0353] Bispecific antibodies can be prepared as full length antibodies or antibody fragments (e.g. F(ab′)2 bispecific antibodies). Techniques for generating bispecific antibodies from antibody fragments have been described in the literature. For example, bispecific antibodies can be prepared using chemical linkage. Brennan et al. Science 229:81 (1985) describe a procedure wherein intact antibodies are proteolytically cleaved to generate F(ab′)2 fragments. These fragments are reduced in the presence of the dithiol complexing agent sodium arsenite to stabilize vicinal dithiols and prevent intermolecular disulfide formation. The Fab′ fragments generated are then converted to thionitrobenzoate (TNB) derivatives. One of the Fab′-TNB derivatives is then reconverted to the Fab′-thiol by reduction with mercaptoethylamine and is mixed with an equimolar amount of the other Fab′-TNB derivative to form the bispecific antibody. The bispecific antibodies produced can be used as agents for the selective immobilization of enzymes.

[0354] Additionally, Fab′ fragments can be directly recovered from E. coli and chemically coupled to form bispecific antibodies. Shalaby et al., J. Exp. Med. 175:217-225 (1992) describe the production of a fully humanized bispecific antibody F(ab′)2 molecule. Each Fab′ fragment was separately secreted from E. coli and subjected to directed chemical coupling in vitro to form the bispecific antibody. The bispecific antibody thus formed was able to bind to cells overexpressing the ErbB2 receptor and normal human T cells, as well as trigger the lytic activity of human cytotoxic lymphocytes against human breast tumor targets.

[0355] Various techniques for making and isolating bispecific antibody fragments directly from recombinant cell culture have also been described. For example, bispecific antibodies have been produced using leucine zippers. Kostelny et al., J. Immunol. 148(5):1547-1553 (1992). The leucine zipper peptides from the Fos and Jun proteins were linked to the Fab′ portions of two different antibodies by gene fusion. The antibody homodimers were reduced at the hinge region to form monomers and then re-oxidized to form the antibody heterodimers. This method can also be utilized for the production of antibody homodimers. The “diabody” technology described by Hollinger et al., Proc. Natl. Acad. Sci. USA 90:6444-6448 (1993) has provided an alternative mechanism for making bispecific antibody fragments. The fragments comprise a heavy-chain variable domain (VH) connected to a light-chain variable domain (VL) by a linker which is too short to allow pairing between the two domains on the same chain. Accordingly, the VH and VL domains of one fragment are forced to pair with the complementary VL and VH domains of another fragment, thereby forming two antigen-binding sites. Another strategy for making bispecific antibody fragments by the use of single-chain Fv (sFv) dimers has also been reported. See, Gruber et al., J. Immunol. 152:5368 (1994).

[0356] Antibodies with more than two valencies are contemplated. For example, trispecific antibodies can be prepared. Tutt et al., J. Immunol. 147:60 (1991).

[0357] Exemplary bispecific antibodies can bind to two different epitopes, at least one of which originates in the protein antigen of the invention. Alternatively, an anti-antigenic arm of an immunoglobulin molecule can be combined with an arm which binds to a triggering molecule on a leukocyte such as a T-cell receptor molecule (e.g. CD2, CD3, CD28, or B7), or Fc receptors for IgG (FcγR), such as FcγRI (CD64), FcγRII (CD)32) and FcγRIII (CD16) so as to focus cellular defense mechanisms to the cell expressing the particular antigen. Bispecific antibodies can also be used to direct cytotoxic agents to cells which express a particular antigen. These antibodies possess an antigen-binding arm and an arm which binds a cytotoxic agent or a radionuclide chelator, such as EOTUBE, DPTA, DOTA, or TETA. Another bispecific antibody of interest binds the protein antigen described herein and further binds tissue factor (TF).

[0358] 4.13.7 Heteroconjugate Antibodies

[0359] Heteroconjugate antibodies are also within the scope of the present invention. Heteroconjugate antibodies are composed of two covalently joined antibodies. Such antibodies have, for example, been proposed to target immune system cells to unwanted cells (U.S. Pat. No. 4,676,980), and for treatment of HIV infection (WO 91/00360; WO 92/200373; EP 03089). It is contemplated that the antibodies can be prepared in vitro using known methods in synthetic protein chemistry, including those involving crosslinking agents. For example, immunotoxins can be constructed using a disulfide exchange reaction or by forming a thioether bond. Examples of suitable reagents for this purpose include iminothiolate and methyl-4-mercaptobutyrimidate and those disclosed, for example, in U.S. Pat. No. 4,676,980.

[0360] 4.13.8 Effector Function Engineering

[0361] It can be desirable to modify the antibody of the invention with respect to effector function, so as to enhance, e.g., the effectiveness of the antibody in treating cancer. For example, cysteine residue(s) can be introduced into the Fc region, thereby allowing interchain disulfide bond formation in this region. The homodimeric antibody thus generated can have improved internalization capability and/or increased complement-mediated cell killing and antibody-dependent cellular cytotoxicity (ADCC). See Caron et al., J. Exp Med., 176: 1191-1195 (1992) and Shopes, J. Immunol., 148: 2918-2922 (1992). Homodimeric antibodies with enhanced anti-tumor activity can also be prepared using heterobifunctional cross-linkers as described in Wolff et al. Cancer Research, 53: 2560-2565 (1993). Alternatively, an antibody can be engineered that has dual Fc regions and can thereby have enhanced complement lysis and ADCC capabilities. See Stevenson et al., Anti-Cancer Drug Design, 3: 219-230 (1989).

[0362] 4.13.9 Immunoconjugates

[0363] The invention also pertains to immunoconjugates comprising an antibody conjugated to a cytotoxic agent such as a chemotherapeutic agent, toxin (e.g., an enzymatically active toxin of bacterial, fungal, plant, or animal origin, or fragments thereof), or a radioactive isotope (i.e., a radioconjugate).

[0364] Chemotherapeutic agents useful in the generation of such immunoconjugates have been described above. Enzymatically active toxins and fragments thereof that can be used include diphtheria A chain, nonbinding active fragments of diphtheria toxin, exotoxin A chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A chain, alpha-sarcin, Aleurites fordii proteins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII, and PAP-S), momordica charantia inhibitor, curcin, crotin, sapaonaria officinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin, and the tricothecenes. A variety of radionuclides are available for the production of radioconjugated antibodies. Examples include 212Bi, 131I, 131 In, 90Y, and 189Re.

[0365] Conjugates of the antibody and cytotoxic agent are made using a variety of bifunctional protein-coupling agents such as N-succinimidyl-3-(2-pyridyldithiol) propionate (SPDP), iminothiolane (IT), bifunctional derivatives of imidoesters (such as dimethyl adipimidate HCL), active esters (such as disuccinimidyl suberate), aldehydes (such as glutareldehyde), bis-azido compounds (such as bis (p-azidobenzoyl) hexanediamine), bis-diazonium derivatives (such as bis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such as tolyene 2,6-diisocyanate), and bis-active fluorine compounds (such as 1,5-difluoro-2,4-dinitrobenzene). For example, a ricin immunotoxin can be prepared as described in Vitetta et al., Science, 238: 1098 (1987). Carbon-14-labeled 1-isothiocyanatobenzyl-3-methyldiethylene triaminepentaacetic acid (MX-DTPA) is an exemplary chelating agent for conjugation of radionucleotide to the antibody. See WO94/11026.

[0366] In another embodiment, the antibody can be conjugated to a “receptor” (such as streptavidin) for utilization in tumor pretargeting wherein the antibody-receptor conjugate is administered to the patient, followed by removal of unbound conjugate from the circulation using a clearing agent and then administration of a “ligand” (e.g., avidin) that is in turn conjugated to a cytotoxic agent.

[0367] 4.14 Computer Readable Sequences

[0368] In one application of this embodiment, a nucleotide sequence of the present invention can be recorded on computer readable media. As used herein, “computer readable media” refers to any medium which can be read and accessed directly by a computer. Such media include, but are not limited to: magnetic storage media, such as floppy discs, hard disc storage medium, and magnetic tape; optical storage media such as CD-ROM; electrical storage media such as RAM and ROM; and hybrids of these categories such as magnetic/optical storage media. A skilled artisan can readily appreciate how any of the presently known computer readable mediums can be used to create a manufacture comprising computer readable medium having recorded thereon a nucleotide sequence of the present invention. As used herein, “recorded” refers to a process for storing information on computer readable medium. A skilled artisan can readily adopt any of the presently known methods for recording information on computer readable medium to generate manufactures comprising the nucleotide sequence information of the present invention.

[0369] A variety of data storage structures are available to a skilled artisan for creating a computer readable medium having recorded thereon a nucleotide sequence of the present invention. The choice of the data storage structure will generally be based on the means chosen to access the stored information. In addition, a variety of data processor programs and formats can be used to store the nucleotide sequence information of the present invention on computer readable medium. The sequence information can be represented in a word processing text file, formatted in commercially-available software such as WordPerfect and Microsoft Word, or represented in the form of an ASCII file, stored in a database application, such as DB2, Sybase, Oracle, or the like. A skilled artisan can readily adapt any number of data processor structuring formats (e.g. text file or database) in order to obtain computer readable medium having recorded thereon the nucleotide sequence information of the present invention.

[0370] By providing any of the nucleotide sequences SEQ ID NO: 1-245 or a representative fragment thereof, or a nucleotide sequence at least 95% identical to any of the nucleotide sequences of SEQ ID NO: 1-245 in computer readable form, a skilled artisan can routinely access the sequence information for a variety of purposes. Computer software is publicly available which allows a skilled artisan to access sequence information provided in a computer readable medium. The examples which follow demonstrate how software which implements the BLAST (Altschul et al., J. Mol. Biol. 215:403-410 (1990)) and BLAZE (Brutlag et al., Comp. Chem. 17:203-207 (1993)) search algorithms on a Sybase system is used to identify open reading frames (ORFs) within a nucleic acid sequence. Such ORFs may be protein encoding fragments and may be useful in producing commercially important proteins such as enzymes used in fermentation reactions and in the production of commercially useful metabolites.

[0371] As used herein, “a computer-based system” refers to the hardware means, software means, and data storage means used to analyze the nucleotide sequence information of the present invention. The minimum hardware means of the computer-based systems of the present invention comprises a central processing unit (CPU), input means, output means, and data storage means. A skilled artisan can readily appreciate that any one of the currently available computer-based systems are suitable for use in the present invention. As stated above, the computer-based systems of the present invention comprise a data storage means having stored therein a nucleotide sequence of the present invention and the necessary hardware means and software means for supporting and implementing a search means. As used herein, “data storage means” refers to memory which can store nucleotide sequence information of the present invention, or a memory access means which can access manufactures having recorded thereon the nucleotide sequence information of the present invention.

[0372] As used herein, “search means” refers to one or more programs which are implemented on the computer-based system to compare a target sequence or target structural motif with the sequence information stored within the data storage means. Search means are used to identify fragments or regions of a known sequence which match a particular target sequence or target motif. A variety of known algorithms are disclosed publicly and a variety of commercially available software for conducting search means are and can be used in the computer-based systems of the present invention. Examples of such software includes, but is not limited to, Smith-Waterman, MacPattern (EMBL), BLASTN and BLASTA (NPOLYPEPTIDEIA). A skilled artisan can readily recognize that any one of the available algorithms or implementing software packages for conducting homology searches can be adapted for use in the present computer-based systems. As used herein, a “target sequence” can be any nucleic acid or amino acid sequence of six or more nucleotides or two or more amino acids. A skilled artisan can readily recognize that the longer a target sequence is, the less likely a target sequence will be present as a random occurrence in the database. The most preferred sequence length of a target sequence is from about 10 to 300 amino acids, more preferably from about 30 to 100 nucleotide residues. However, it is well recognized that searches for commercially important fragments, such as sequence fragments involved in gene expression and protein processing, may be of shorter length.

[0373] As used herein. “a target structural motif,” or “target motif,” refers to any rationally selected sequence or combination of sequences in which the sequence(s) are chosen based on a three-dimensional configuration which is formed upon the folding of the target motif. There are a variety of target motifs known in the art. Protein target motifs include, but are not limited to, enzyme active sites and signal sequences. Nucleic acid target motifs include, but are not limited to, promoter sequences, hairpin structures and inducible expression elements (protein binding sequences).

[0374] 4.15 Triple Helix Formation

[0375] In addition, the fragments of the present invention, as broadly described, can be used to control gene expression through triple helix formation or antisense DNA or RNA, both of which methods are based on the binding of a polynucleotide sequence to DNA or RNA. Polynucleotides suitable for use in these methods are preferably 20 to 40 bases in length and are designed to be complementary to a region of the gene involved in transcription (triple helix—see Lee et al. Nucl. Acids Res. 6:3073 (1979); Cooney et al., Science 15241:456 (1988); and Dervan et al., Science 251:1360 (1991)) or to the mRNA itself (antisense—Olmno, J. Neurochem. 56:560 (1991); Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRC Press, Boca Raton, Fla. (1988)). Triple helix-formation optimally results in a shut-off of RNA transcription from DNA, while antisense RNA hybridization blocks translation of an mRNA molecule into polypeptide. Both techniques have been demonstrated to be effective in model systems. Information contained in the sequences of the present invention is necessary for the design of an antisense or triple helix oligonucleotide.

[0376] 4.16 Diagnostic Assays and Kits

[0377] The present invention further provides methods to identify the presence or expression of one of the ORFs of the present invention, or homolog thereof, in a test sample, using a nucleic acid probe or antibodies of the present invention, optionally conjugated or otherwise associated with a suitable label.

[0378] In general, methods for detecting a polynucleotide of the invention can comprise contacting a sample with a compound that binds to and forms a complex with the polynucleotide for a period sufficient to form the complex, and detecting the complex, so that if a complex is detected, a polynucleotide of the invention is detected in the sample. Such methods can also comprise contacting a sample under stringent hybridization conditions with nucleic acid primers that anneal to a polynucleotide of the invention under such conditions, and amplifying annealed polynucleotides, so that if a polynucleotide is amplified, a polynucleotide of the invention is detected in the sample.

[0379] In general, methods for detecting a polypeptide of the invention can comprise contacting a sample with a compound that binds to and forms a complex with the polypeptide for a period sufficient to form the complex, and detecting the complex, so that if a complex is detected, a polypeptide of the invention is detected in the sample.

[0380] In detail, such methods comprise incubating a test sample with one or more of the antibodies or one or more of the nucleic acid probes of the present invention and assaying for binding of the nucleic acid probes or antibodies to components within the test sample.

[0381] Conditions for incubating a nucleic acid probe or antibody with a test sample vary. Incubation conditions depend on the format employed in the assay, the detection methods employed, and the type and nature of the nucleic acid probe or antibody used in the assay. One skilled in the art still recognize that any one of the commonly available hybridization, amplification or immunological assay formats can readily be adapted to employ the nucleic acid probes or antibodies of the present invention. Examples of such assays can be found in Chard, T., An Introduction to Radioimmunoassay and Related Techniques. Elsevier Science Publishers, Amsterdam, The Netherlands (1986); Bullock, G. R. et al., Techniques in Immunocytochemistry, Academic Press, Orlando, Fla. Vol. 1 (1982), Vol. 2 (1983), Vol. 3 (1985); Tijssen, P., Practice and Theory of immunoassays: Laboratory Techniques in Biochemistry and Molecular Biology, Elsevier Science Publishers, Amsterdam, The Netherlands (1985). The test samples of the present invention include cells, protein or membrane extracts of cells, or biological fluids such as sputum, blood, serum, plasma, or urine. The test sample used in the above-described method will vary based on the assay format, nature of the detection method and the tissues, cells or extracts used as the sample to be assayed. Methods for preparing protein extracts or membrane extracts of cells are well known in the art and can be readily be adapted in order to obtain a sample which is compatible with the system utilized.

[0382] In another embodiment of the present invention, kits are provided which contain the necessary reagents to carry out the assays of the present invention. Specifically, the invention provides a compartment kit to receive, in close confinement, one or more containers which comprises: (a) a first container comprising one of the probes or antibodies of the present invention; and (b) one or more other containers comprising one or more of the following: wash reagents, reagents capable of detecting presence of a bound probe or antibody.

[0383] In detail, a compartment kit includes any kit in which reagents are contained in separate containers. Such containers include small glass containers, plastic containers or strips of plastic or paper. Such containers allows one to efficiently transfer reagents from one compartment to another compartment such that the samples and reagents are not cross-contaminated, and the agents or solutions of each container can be added in a quantitative fashion from one compartment to another. Such containers will include a container which will accept the test sample, a container which contains the antibodies used in the assay, containers which contain wash reagents (such as phosphate buffered saline, Tris-buffers, etc.), and containers which contain the reagents used to detect the bound antibody or probe. Types of detection reagents include labeled nucleic acid probes, labeled secondary antibodies, or in the alternative, if the primary antibody is labeled, the enzymatic, or antibody binding reagents which are capable of reacting with the labeled antibody. One skilled in the art will readily recognize that the disclosed probes and antibodies of the present invention can be readily incorporated into one of the established kit formats which are well known in the art.

[0384] 4.17 Medical Imaging

[0385] The novel polypeptides and binding partners of the invention are useful in medical imaging of sites expressing the molecules of the invention (e.g. where the polypeptide of the invention is involved in the immune response, for imaging sites of inflammation or infection). See, e.g., Kunkel et al., U.S. Pat. No. 5,413,778. Such methods involve chemical attachment of a labeling or imaging agent, administration of the labeled polypeptide to a subject in a pharmaceutically acceptable carrier, and imaging the labeled polypeptide in vivo at the target site.

[0386] 4.18 Screening Assays

[0387] Using the isolated proteins and polynucleotides of the invention, the present invention further provides methods of obtaining and identifying agents which bind to a polypeptide encoded by an ORF corresponding to any of the nucleotide sequences set forth in SEQ ID NO: 1-245, or bind to a specific domain of the polypeptide encoded by the nucleic acid. In detail, said method comprises the steps of:

[0388] (a) contacting an agent with an isolated protein encoded by an ORF of the present invention, or nucleic acid of the invention; and

[0389] (b) determining whether the agent binds to said protein or said nucleic acid.

[0390] In general, therefore, such methods for identifying compounds that bind to a polynucleotide of the invention can comprise contacting a compound with a polynucleotide of the invention for a time sufficient to form a polynucleotide/compound complex, and detecting the complex, so that if a polynucleotide/compound complex is detected, a compound that binds to a polynucleotide of the invention is identified.

[0391] Likewise, in general, therefore, such methods for identifying compounds that bind to a polypeptide of the invention can comprise contacting a compound with a polypeptide of the invention for a time sufficient to form a polypeptide/compound complex, and detecting the complex, so that if a polypeptide/compound complex is detected, a compound that binds to a polynucleotide of the invention is identified.

[0392] Methods for identifying compounds that bind to a polypeptide of the invention can also comprise contacting a compound with a polypeptide of the invention in a cell for a time sufficient to form a polypeptide/compound complex, wherein the complex drives expression of a receptor gene sequence in the cell, and detecting the complex by detecting reporter gene sequence expression, so that if a polypeptide/compound complex is detected, a compound that binds a polypeptide of the invention is identified.

[0393] Compounds identified via such methods can include compounds which modulate the activity of a polypeptide of the invention (that is, increase or decrease its activity, relative to activity observed in the absence of the compound). Alternatively, compounds identified via such methods can include compounds which modulate the expression of a polynucleotide of the invention (that is, increase or decrease expression relative to expression levels observed in the absence of the compound). Compounds, such as compounds identified via the methods of the invention, can be tested using standard assays well known to those of skill in the art for their ability to modulate activity/expression.

[0394] The agents screened in the above assay can be, but are not limited to, peptides, carbohydrates, vitamin derivatives, or other pharmaceutical agents. The agents can be selected and screened at random or rationally selected or designed using protein modeling techniques.

[0395] For random screening, agents such as peptides, carbohydrates, pharmaceutical agents and the like are selected at random and are assayed for their ability to bind to the protein encoded by the ORF of the present invention. Alternatively, agents may be rationally selected or designed. As used herein, an agent is said to be “rationally selected or designed” when the agent is chosen based on the configuration of the particular protein. For example, one skilled in the art can readily adapt currently available procedures to generate peptides, pharmaceutical agents and the like, capable of binding to a specific peptide sequence, in order to generate rationally designed antipeptide peptides, for example see Hurby et al., Application of Synthetic Peptides: Antisense Peptides,” In Synthetic Peptides, A User's Guide, W. H. Freeman, N.Y. (1992), pp. 289-307, and Kaspczak et al., Biochemistry 28:9230-8 (1989), or pharmaceutical agents, or the like.

[0396] In addition to the foregoing, one class of agents of the present invention, as broadly described, can be used to control gene expression through binding to one of the ORFs or EMFs of the present invention. As described above, such agents can be randomly screened or rationally designed/selected. Targeting the ORF or EMF allows a skilled artisan to design sequence specific or element specific agents, modulating the expression of either a single ORF or multiple ORFs which rely on the same EMF for expression control. One class of DNA binding agents are agents which contain base residues which hybridize or form a triple helix formation by binding to DNA or RNA. Such agents can be based on the classic phosphodiester, ribonucleic acid backbone, or can be a variety of sulfhydryl or polymeric derivatives which have base attachment capacity.

[0397] Agents suitable for use in these methods preferably contain 20 to 40 bases and are designed to be complementary to a region of the gene involved in transcription (triple helix—see Lee et al., Nucl. Acids Res. 6:3073 (1979); Cooney et al. Science 241:456 (1988); and Dervan et al., Science 251:1360 (1991)) or to the mRNA itself (antisense—Okano, J. Neurochem. 56:560 (1991); Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRC Press, Boca Raton, Fla. (1988)). Triple helix-formation optimally results in a shut-off of RNA transcription from DNA, while antisense RNA hybridization blocks translation of an mRNA molecule into polypeptide. Both techniques have been demonstrated to be effective in model systems.

[0398] Information contained in the sequences of the present invention is necessary for the design of an antisense or triple helix oligonucleotide and other DNA binding agents.

[0399] Agents which bind to a protein encoded by one of the ORFs of the present invention can be used as a diagnostic agent. Agents which bind to a protein encoded by one of the ORFs of the present invention can be formulated using known techniques to generate a pharmaceutical composition.

[0400] 4.19 Use of Nucleic Acids as Probes

[0401] Another aspect of the subject invention is to provide for polypeptide-specific nucleic acid hybridization probes capable of hybridizing with naturally occurring nucleotide sequences. The hybridization probes of the subject invention may be derived from any of the nucleotide sequences SEQ ID NO: 1-245. Because the corresponding gene is only expressed in a limited number of tissues, a hybridization probe derived from any of the nucleotide sequences SEQ ID NO: 1-245 can be used as an indicator of the presence of RNA of cell type of such a tissue in a sample.

[0402] Any suitable hybridization technique can be employed, such as, for example, in situ hybridization. PCR as described in U.S. Pat. Nos. 4,683,195 and 4,965,188 provides additional uses for oligonucleotides based upon the nucleotide sequences. Such probes used in PCR may be of recombinant origin, may be chemically synthesized, or a mixture of both. The probe will comprise a discrete nucleotide sequence for the detection of identical sequences or a degenerate pool of possible sequences for identification of closely related genomic sequences.

[0403] Other means for producing specific hybridization probes for nucleic acids include the cloning of nucleic acid sequences into vectors for the production of MRNA probes. Such vectors are known in the art and are commercially available and may be used to synthesize RNA probes in vitro by means of the addition of the appropriate RNA polymerase as T7 or SP6 RNA polymerase and the appropriate radioactively labeled nucleotides. The nucleotide sequences may be used to construct hybridization probes for mapping their respective genomic sequences. The nucleotide sequence provided herein may be mapped to a chromosome or specific regions of a chromosome using well known genetic and/or chromosomal mapping techniques. These techniques include in situ hybridization, linkage analysis against known chromosomal markers, hybridization screening with libraries or flow-sorted chromosomal preparations specific to known chromosomes, and the like. The technique of fluorescent in situ hybridization of chromosome spreads has been described, among other places, in Verma et al (1988) Human Chromosomes: A Manual of Basic Techniques, Pergamon Press, New York N.Y.

[0404] Fluorescent in situ hybridization of chromosomal preparations and other physical chromosome mapping techniques may be correlated with additional genetic map data. Examples of genetic map data can be found in the 1994 Genome Issue of Science (265:1981 f). Correlation between the location of a nucleic acid on a physical chromosomal map and a specific disease (or predisposition to a specific disease) may help delimit the region of DNA associated with that genetic disease. The nucleotide sequences of the subject invention may be used to detect differences in gene sequences between normal, carrier or affected individuals.

[0405] 4.20 Preparation of Support Bound Oligonucleotides

[0406] Oligonucleotides, i.e. small nucleic acid segments, may be readily prepared by, for example, directly synthesizing the oligonucleotide by chemical means, as is commonly practiced using an automated oligonucleotide synthesizer.

[0407] Support bound oligonucleotides may be prepared by any of the methods known to those of skill in the art using any suitable support such as glass, polystyrene or Teflon. One strategy is to precisely spot oligonucleotides synthesized by standard synthesizers. Immobilization can be achieved using passive adsorption (Inouye & Hondo, (1990) J. Clin. Microbiol. 28(6) 1469-72); using UV light (Nagata et al., 1985; Dahlen et al., 1987; Morrissey & Collins, (1989) Mol. Cell Probes 3(2) 189-207) or by covalent binding of base modified DNA (Keller et al, 1988; 1989); all references being specifically incorporated herein.

[0408] Another strategy that may be employed is the use of the strong biotin-streptavidin interaction as a linker. For example, Broude et al. (1994) Proc. Natl. Acad. Sci. USA 91(8) 3072-6, describe the use of biotinylated probes, although these are duplex probes, that are immobilized on streptavidin-coated magnetic beads. Streptavidin-coated beads may be purchased from Dynal. Oslo. Of course, this same linking chemistry is applicable to coating any surface with streptavidin. Biotinylated probes may be purchased from various sources, such as, e.g., Operon Technologies (Alameda, Calif.).

[0409] Nunc Laboratories (Naperville, Ill.) is also selling suitable material that could be used. Nunc Laboratories have developed a method by which DNA can be covalently bound to the microwell surface termed Covalink NH. CovaLink NH is a polystyrene surface grafted with secondary amino groups (>NH) that serve as bridge-heads for further covalent coupling. CovaLink Modules may be purchased from Nunc Laboratories. DNA molecules may be bound to CovaLink exclusively at the 5′-end by a phosphoramidate bond, allowing immobilization of more than 1 μmol of DNA (Rasmussen et al., (1991) Anal. Biochem. 198(1) 138-42).

[0410] The use of CovaLink NH strips for covalent binding of DNA molecules at the 5′-end has been described (Rasmussen et al. (1991). In this technology, a phosphoramidate bond is employed (Chu et al. (1983) Nucleic Acids Res. 11 (8) 6513-29). This is beneficial as immobilization using only a single covalent bond is preferred. The phosphoramidate bond joins the DNA to the CovaLink NH secondary amino groups that are positioned at the end of spacer arms covalently grafted onto the polystyrene surface through a 2 nm long spacer arm. To link an oligonucleotide to CovaLink NH via an phosphoramidate bond, the oligonucleotide terminus must have a 5′-end phosphate group. It is, perhaps, even possible for biotin to be covalently bound to CovaLink and then streptavidin used to bind the probes.

[0411] More specifically, the linkage method includes dissolving DNA in water (7.5 ng/μl) and denaturing for 10 min. at 95° C. and cooling on ice for 10 min. Ice-cold 0.1 M 1-methylimidazole pH 7.0 (1-MeIm7), is then added to a final concentration of 10 mM I-MeIm7. The single-stranded DNA solution is then dispensed into CovaLink NH strips (75 μl/well) standing on ice.

[0412] Carbodiimide 0.2 M 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC), dissolved in 10 mM 1-MeIm7, is made fresh and 25 μl added per well. The strips are incubated for 5 hours at 50° C. After incubation the strips are washed using, e.g., Nunc-Immuno Wash; first the wells are washed 3 times, then they are soaked with washing solution for 5 min., and finally they are washed 3 times (where in the washing solution is 0.4 N NaOH, 0.25% SDS heated to 50° C.).

[0413] It is contemplated that a further suitable method for use with the present invention is that described in PCT Patent Application WO 90/03382 (Southern & Maskos), incorporated herein by reference. This method of preparing an oligonucleotide bound to a support involves attaching a nucleoside 3′-reagent through the phosphate group by a covalent phosphodiester link to aliphatic hydroxyl groups carried by the support. The oligonucleotide is then synthesized on the supported nucleoside and protecting groups removed from the synthetic oligonucleotide chain under standard conditions that do not cleave the oligonucleotide from the support. Suitable reagents include nucleoside phosphoramidite and nucleoside hydrogen phosphorate.

[0414] An on-chip strategy for the preparation of DNA probe for the preparation of DNA probe arrays may be employed. For example, addressable laser-activated photodeprotection may be employed in the chemical synthesis of oligonucleotides directly on a glass surface, as described by Fodor et al. (1991) Science 251(4995) 767-73, incorporated herein by reference. Probes may also be immobilized on nylon supports as described by Van Ness et al (1991) Nucleic Acids Res. 19(12) 3345-50; or linked to Teflon using the method of Duncan & Cavalier (1988) Anal. Biochem. 169(1) 104-8; all references being specifically incorporated herein.

[0415] To link an oligonucleotide to a nylon support, as described by Van Ness et al. (1991), requires activation of the nylon surface via alkylation and selective activation of the 5′-amine of oligonucleotides with cyanuric chloride.

[0416] One particular way to prepare support bound oligonucleotides is to utilize the light-generated synthesis described by Pease et al., (1994) PNAS USA 91(11) 5022-6, incorporated herein by reference). These authors used current photolithographic techniques to generate arrays of immobilized oligonucleotide probes (DNA chips). These methods, in which light is used to direct the synthesis of oligonucleotide probes in high-density, miniaturized arrays, utilize photolabile 5′-protected N-acyl-deoxynucleoside phosphoramidites, surface linker chemistry and versatile combinatorial synthesis strategies. A matrix of 256 spatially defined oligonucleotide probes may be generated in this manner.

[0417] 4.21 Preparation of Nucleic Acid Fragments

[0418] The nucleic acids may be obtained from any appropriate source, such as cDNAs, genomic DNA, chromosomal DNA, microdissected chromosome bands, cosmid or YAC inserts, and RNA, including mRNA without any amplification steps. For example, Sambrook et al. (1989) describes three protocols for the isolation of high molecular weight DNA from mammalian cells (p. 9.14-9.23).

[0419] DNA fragments may be prepared as clones in M13, plasmid or lambda vectors and/or prepared directly from genomic DNA or cDNA by PCR or other amplification methods. Samples may be prepared or dispensed in multiwell plates. About 100-1000 ng of DNA samples may be prepared in 2-500 ml of final volume.

[0420] The nucleic acids would then be fragmented by any of the methods known to those of skill in the art including, for example, using restriction enzymes as described at 9.24-9.28 of Sambrook et al. (1989), shearing by ultrasound and NaOH treatment.

[0421] Low pressure shearing is also appropriate, as described by Schriefer et al. (1990) Nucleic Acids Res. 18(24) 7455-6, incorporated herein by reference). In this method, DNA samples are passed through a small French pressure cell at a variety of low to intermediate pressures. A lever device allows controlled application of low to intermediate pressures to the cell. The results of these studies indicate that low-pressure shearing is a useful alternative to sonic and enzymatic DNA fragmentation methods.

[0422] One particularly suitable way for fragmenting DNA is contemplated to be that using the two base recognition endonuclease. CviJI, described by Fitzgerald et al. (1992) Nucleic Acids Res. 20(14) 3753-62. These authors described an approach for the rapid fragmentation and fractionation of DNA into particular sizes that they contemplated to be suitable for shotgun cloning and sequencing.

[0423] The restriction endonuclease CviJI normally cleaves the recognition sequence PuGCPy between the G and C to leave blunt ends. Atypical reaction conditions, which alter the specificity of this enzyme (CviJI**), yield a quasi-random distribution of DNA fragments form the small molecule pUC19 (2688 base pairs). Fitzgerald et al. (1992) quantitatively evaluated the randomness of this fragmentation strategy, using a CviJI** digest of pUC19 that was size fractionated by a rapid gel filtration method and directly ligated, without end repair, to a lac Z minus M13 cloning vector. Sequence analysis of 76 clones showed that CviJI** restricts pyGCPy and PuGCPu, in addition to PuGCPy sites, and that new sequence data is accumulated at a rate consistent with random fragmentation.

[0424] As reported in the literature, advantages of this approach compared to sonication and agarose gel fractionation include: smaller amounts of DNA are required (0.2-0.5 μg instead of 2-5 μg); and fewer steps are involved (no preligation, end repair, chemical extraction, or agarose gel electrophoresis and elution are needed.

[0425] Irrespective of the manner in which the nucleic acid fragments are obtained or prepared, it is important to denature the DNA to give single stranded pieces available for hybridization. This is achieved by incubating the DNA solution for 2-5 minutes at 80-90° C. The solution is then cooled quickly to 2° C. to prevent renaturation of the DNA fragments before they are contacted with the chip. Phosphate groups must also be removed from genomic DNA by methods known in the art.

[0426] 4.22 Preparation of DNA Arrays

[0427] Arrays may be prepared by spotting DNA samples on a support such as a nylon membrane. Spotting may be performed by using arrays of metal pins (the positions of which correspond to an array of wells in a microtiter plate) to repeated by transfer of about 20 nl of a DNA solution to a nylon membrane. By offset printing, a density of dots higher than the density of the wells is achieved. One to 25 dots may be accommodated in 1 mm2, depending on the type of label used. By avoiding spotting in some preselected number of rows and columns, separate subsets (subarrays) may be formed. Samples in one subarray may be the same genomic segment of DNA (or the same gene) from different individuals, or may be different, overlapped genomic clones. Each of the subarrays may represent replica spotting of the same samples. In one example, a selected gene segment may be amplified from 64 patients. For each patient, the amplified gene segment may be in one 96-well plate (all 96 wells containing the same sample). A plate for each of the 64 patients is prepared. By using a 96-pin device, all samples may be spotted on one 8×12 cm membrane. Subarrays may contain 64 samples, one from each patient. Where the 96 subarrays are identical, the dot span may be 1 mm2 and there may be a 1 mm space between subarrays.

[0428] Another approach is to use membranes or plates (available from NUNC, Naperville. Ill.) which may be partitioned by physical spacers e.g. a plastic grid molded over the membrane, the grid being similar to the sort of membrane applied to the bottom of multiwell plates, or hydrophobic strips. A fixed physical spacer is not preferred for imaging by exposure to flat phosphor-storage screens or x-ray films.

[0429] The present invention is illustrated in the following examples. Upon consideration of the present disclosure, one of skill in the art will appreciate that many other embodiments and variations may be made in the scope of the present invention. Accordingly, it is intended that the broader aspects of the present invention not be limited to the disclosure of the following examples. The present invention is not to be limited in scope by the exemplified embodiments which are intended as illustrations of single aspects of the invention, and compositions and methods which are functionally equivalent are within the scope of the invention. Indeed, numerous modifications and variations in the practice of the invention are expected to occur to those skilled in the art upon consideration of the present preferred embodiments. Consequently, the only limitations which should be placed upon the scope of the invention are those which appear in the appended claims.

[0430] All references cited within the body of the instant specification are hereby incorporated by reference in their entirety.

5. EXAMPLES

5.1 Example 1

[0431] Novel Nucleic Acid Sequences Obtained from Various Libraries

[0432] A plurality of novel nucleic acids were obtained from cDNA libraries prepared from various human tissues and in some cases isolated from a genomic library derived from human chromosome using standard PCR, SBH sequence signature analysis and Sanger sequencing techniques. The inserts of the library were amplified with PCR using primers specific for the vector sequences which flank the inserts. Clones from cDNA libraries were spotted on nylon membrane filters and screened with oligonucleotide probes (e.g., 7-mers) to obtain signature sequences. The clones were clustered into groups of similar or identical sequences. Representative clones were selected for sequencing.

[0433] In some cases, the 5′ sequence of the amplified inserts was then deduced using a typical Sanger sequencing protocol. PCR products were purified and subjected to fluorescent dye terminator cycle sequencing. Single pass gel sequencing was done using a 377 Applied Biosystems (ABI) sequencer to obtain the novel nucleic acid sequences.

5.2 Example 2

[0434] Assemblage of Novel Nucleic Acids

[0435] The nucleic acids of the present invention, were assembled using an EST sequence as a seed. Then a recursive algorithm was used to extend the seed EST into an extended assemblage, by pulling additional sequences from different databases (i.e., Hyseq's database containing EST sequences, dbEST, gb pri, UniGene, and exons from public domain genomic sequences predicated by GenScan) that belong to this assemblage. The algorithm terminated when there was no additional sequences from the above databases that would extend the assemblage. Further, inclusion of component sequences into the assemblage was based on a BLASTN hit to the extending assemblage with BLAST score greater than 300 and percent identity greater than 95%.

[0436] Using PHRAP (Univ. of Washington) or CAP4 (Paracel), full-length gene sequences and their corresponding protein sequences were generated from the assemblage. Any frame shifts and incorrect stop codons were corrected by hand editing. During editing, the sequence was checked using FASTXY algorithm against Genbank (i.e., dbEST, gb pri, UniGene, and Genpept). Other computer programs which may have been used in the editing process were phredPhrap and Consed (University of Washington) and ed-ready, ed-ext and gc-zip-2 (Hyseq, Inc.). In some cases RACE (Rapid Amplification of cDNA Ends) was performed to further extend the sequence in the 5′ direction. The full-length nucleotide sequences are shown in the Sequence Listing as SEQ ID NO: 1-245. The corresponding polypeptide sequences are SEQ ID NO: 246-490.

[0437] Table 1 shows the various tissue sources of SEQ ID NO: 1-245.

[0438] The nearest neighbor results for polypeptides encoded by SEQ ID NO: 1-245 (i.e. SEQ ID NO: 246-490) were obtained by a BLASTP (version 2.0al 19MP-WashU) search against Genpept release 124 using BLAST algorithm. The nearest neighbor result showed the closest homologue with functional annotation for SEQ ID NO: 1-245 from Genpept. The translated amino acid sequences for which the nucleic acid sequence encodes are shown in the Sequence Listing. The homologs with identifiable functions for SEQ ID NO: 1-245 are shown in Table 2 below.

[0439] Using eMatrix software package (Stanford University, Stanford, Calif.) (Wu et al., J. Comp. Biol., Vol. 6 pp. 219-235 (1999) herein incorporated by reference), polypeptides encoded by SEQ ID NO: 1-245 (i.e. SEQ ID NO: 246-490) were examined to determine whether they had identifiable signature regions. Table 3 shows the signature region found in the indicated polypeptide sequences, the description of the signature, the eMatrix p-value(s) and the position(s) of the signature within the polypeptide sequence.

[0440] Using the pFam software program (Sonnhammer et al., Nucleic Acids Res., Vol. 26(1) pp. 320-322 (1998) herein incorporated by reference) polypeptides encoded by SEQ ID NO: 1-245 (i.e. SEQ ID NO: 246-490) were examined for domains with homology to certain peptide domains. Table 4 shows the name of the domain found, the description, the p-value and the pFam score for the identified domain within the sequence.

[0441] The GeneAtlasr™ software package (Molecular Simulations Inc. (MSI). San Diego, Calif.) was used to predict the three-dimensional structure models for the polypeptides encoded by SEQ ID NO 1-216 (i.e. SEQ ID NO: 246-490). Models were generated by (I) PSI-BLAST which is a multiple alignment sequence profile-based searching developed by Altschul et al, (Nucl. Acids. Res. 25, 3389-3408 (1997)), (2) High Throughput Modeling (HTM) (Molecular Simulations Inc. (MSI) San Diego, Calif.,) which is an automated sequence and structure searching procedure (http://www.msi.coni/), and (3) SeqFold™ which is a fold recognition method described by Fischer and Eisenberg (J. Mol. Biol. 209, 779-791 (1998)). This analysis was carried out, in part, by comparing the polypeptides of the invention with the known NMR (nuclear magnetic resonance) and x-ray crystal three-dimensional structures as templates. Table 5 shows, “PDB ID”, the Protein DataBase (PDB) identifier given to template structure; “Chain ID”, identifier of the subcomponent of the PDB template structure; “Compound Information”, information of the PDB template structure and/or its subcomponents; “PDB Function Annotation” gives function of the PDB template as annotated by the PDB files (http:/www.rcsb.org/PDB/); start and end amino acid position of the protein sequence aligned; PSI-BLAST score, the verify score, the SeqFold score, and the Potential(s) of Mean Force (PMF). The verify score is produced by GeneAtlas™ software (MSI), is based on Dr. Eisenberg's Profile-3D threading program developed in Dr. David Eisenberg's laboratory (U.S. Pat. No. 5,436,850 and Luthy, Bowie, and Eisenberg, Nature, 356:83-85 (1992)) and a publication by R. Sanchez and A. Sali, Proc. Natl. Acad. Sci. USA, 95:13597-12502. The verify score produced by GeneAtlas normalizes the verify score for proteins with different lengths so that a unified cutoff can be used to select good models as follows:

Verify score (normalized)=(raw score−1/2 high score)/(1/2 high score)

[0442] The PFM score, produced by GeneAtlas™ software (MSI), is a composite scoring function that depends in part on the compactness of the model, sequence identity in the alignment used to build the model, pairwise and surface mean force potentials (MFP). As given in Table 5, a verify score between 0 to 1.0, with 1 being the best, represents a good model. Similarly, a PMF score between 0 to 1.0, with 1 being the best, represents a good model. A SeqFold™ score of more than 50 is considered significant. A good model may also be determined by one of skill in the art based all the information in Table 5 taken in totality.

[0443] The nucleotide sequence within the sequences that codes for signal peptide sequences and their cleavage sites can be determined from using Neural Network SignalP V1.1 program (from Center for Biological Sequence Analysis. The Technical University of Denmark). The process for identifying prokaryotic and eukaryotic signal peptides and their cleavage sites are also disclosed by Henrik Nielson. Jacob Engelbrecht, Soren Brunak, and Gunnar von Heijne in the publication “Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites” Protein Engineering, Vol. 10, no. 1, pp. 1-6 (1997), incorporated herein by reference. A maximum S score and a mean S score, as described in the Nielson et al, as reference, were obtained for the polypeptide sequences. Table 6 shows the position of the signal peptide in each of the polypeptides and the maximum score and mean score associated with that signal peptide.

[0444] Table 7 correlates each of SEQ ID NO: 1-245 to a specific chromosomal location.

[0445] Table 8 is a correlation table of the novel polynucleotide sequences SEQ ID NO: 1-245, and their corresponding priority full length nucleotide sequences in the priority application U.S. Ser. No. 09/654,935, the contents of which is incorporated herein by reference in its entirety.

1TABLE 1Tissue/RNALibraryTissue OriginSourceNameSEQ ID NO:adult brainGIBCOAB30018 24 38 42 56 63-64 93-94 113 130 183 195-196 206 210227 233 236 240adult brainGIBCOABD0032-4 15 19-21 29 31-32 34-39 41-43 45 54 56 67 80 82 84 8894 103-104 107 113 117 130-131 154 159 178 195 199 206210 220-221 223adult brainClontechABR0012-3 17 33 35 43 56 62 67 84 113 191 220adult brainClontechABR0062-4 34 82 89 101-102 113 127 146 152 158 162 181 191197-198 200-201 214 221-223 234 241adult brainClontechABR0082-4 9-12 15 17 19 21 24 29 36-41 54 64 70 74-75 77 79-8082 84 93-94 97-98 101-102 104 107 109 117 121-124 127131 140 143-144 146 148-149 151-152 155 158 162 164167 169 178 193 196 200-202 204 206 221 223-225 227229 233adult brainBioChainABR0122-3 54adult brainBioChainABR01317 43 209 240adult brainInvitrogenABR01423 43 227 232adult brainInvitrogenABR01543 54 65 67 89 142 159 232adult brainInvitrogenABR0162-3 28 54 56 64 104 159 229adult brainInvitrogenABT0042-3 23 30 33 36-38 40 100 145 152 154 177 191 206 220242culturedStratageneADP0012-3 15 29 36 38 40 43 56 100 104-105 130 142-144 158-159preadipocytes177 182 206 236 240adrenal glandClontechADR00211-12 19-20 28 37-38 42 50 56 70 76 82 84 102 104-105127 130 145 148-150 181 183 189 191 209-210 224-225adult heartGIBCOAHR0012-5 8-9 11-12 19-22 24 29 36 38 40 43 45 47 54 56 62-6370 72 74 76 79 82 84 86 92 94 101-104 107 113 127 130-131137-138 140 143-144 148-149 159 166 169 177-178183 196 206-207 210 214 229-233 236-237adult kidneyGIBCOAKD0012-3 7-9 11-12 15 18 20-21 24 26-27 29 31-33 36-43 52 5456 61-62 64 80 82 91 95 98 101-104 107 113 117 130-131143-144 146 154 159 169 178 181 183 191 195-199 204206 210 214 220 223-225 227 229 233 240 244adult kidneyInvitrogenAKT0026 8-9 11-12 18 33 36-37 40 43 46 56 64 82 84 86-87 91 107113 130 142 144 148-149 152 159 167 169 183 191 193206 223 226 228 232 240-241 244adult lungGIBCOALG0015 15 20 29 43 47 54 56 88 103 130 173 177 183 191 214232 240 244lymph nodeClontechALN0018 29 36 46 104 130 159 183 206 214 240young liverGIBCOALV0012-3 11-12 15 19 37-38 40 43 47 56 62 70 94 103 107 112143-144 162 181 183 191 195 206 214 220 224-225 236-237243adult liverInvitrogenALV0022-3 10-12 15 20 22 26-27 37 50 89 143 148-149 173 181183 191 193 206 217 220 240 244adult liverClontechALV00321 181 232adult ovaryInvitrogenAOV0012-3 8 10-12 14-15 19-23 26-29 31-32 34 36-43 47 50 56 62-6467 70 75 78 82 84 86 89 94 101-102 104 107 109 113118 125 130-131 140 142 144 146 148-150 152 155 158-159162 166-167 169 173 177-178 182-183 189 193 195204 206 210 214 223-225 227 232 240-244adult placentaClontechAPL00143 159 169 206 240placentaInvitrogenAPL00220 26-27 36 38 64 71 100 178 196 220 228 233adult spleenGIBCOASP0012-3 8 26-27 29 35 37 42-43 46-47 54 56 62 64 87 94 104130 143-144 152 159 183 199 206 214 220 227 232 236244adult testisGIBCOATS0015 8 11-12 20 23-24 29 31-32 37-38 41 43 54 56 62 64 86 89104 107 130-131 137-138 159 178 183 195 210 229 232236-237adult bladderInvitrogenBLD0018 54 159 195 206bone marrowClontechBMD0012-5 8-12 19 22 26-27 29 31-32 34 36-38 42-43 46-47 56 63-6470 80 86-87 89 91 93-94 98 103-104 107 109 113 118130-131 144 146 152 159 162 167 178 182 193 199 206-207210 214 220 223 228 232 240 244bone marrowClontechBMD0022-3 5 8 11-12 15 21 26-27 29 36 40 42 45-46 50 54 56 9194 97-98 104-105 107 109 120 124 137-138 140 142 144159 165 167 169 173 183 189 191 193 196 204-206 226232-234 236-237 244bone marrowClontechBMD004232bone marrowClonetechBMD00743 232adult colonInvitrogenCLN00138 43 45-46 50 84 87 143 193 195 222 244mixture ofvariousCTL0162016 tissues-vendorsmRNAs*mixture ofvariousCTL02146 54 159 23216 tissues-vendorsmRNAs*mixture ofvariousCTL028159 23716 tissues-vendorsmRNAs*adult cervixBioChainCVX0012-3 8 11-12 15 21 24 31-32 35-36 39-43 46 56 62-65 70 8287 89 93-94 98 105 107 120 125-126 131 144 148-150 152159 165 178 182-183 189 191 193 195 223 236 240endothelialStrategeneEDT0012-4 8 10-12 15 21-24 28-30 33-34 36-37 40 42-43 45 47 50cells56 62 64 67 70 72 80 82 86 94 103-104 107 109 126 130-131142-144 146 148-149 152 154 158-159 162 169 177-178182-183 191 193 195-199 206 210 214 223-226 229233 236 240-242fetal brainClontechFBR00143 130 199fetal brainClontechFBR00431-32fetal brainClontechFBR0062-4 8 10 29 39 41 43 49 70 77 80 82 84 89 94 104-105 118121-123 142 150-152 154-155 165 178 186 200-201 204206-207 210fetal brainInvitrogenFBT0022-3 8 11-12 29 37 43 67 82 89 134 142-143 152 159 177189 191 193 199 206 210 220 227fetal heartInvitrogenFHR00141fetal kidneyClontechFKD0012-3 10-12 17 29 38 40 43 54 69 75 80 127 159 229 231 236240fetal kidneyClontechFKD00256fetal kidneyInvitrogenFKD00719 36 43 56 159fetal lungClontechFLG0012-3 54 69 109 113fetal lungInvitrogenFLG00310 21 35 43 50 54 69 80 92 125-126 143 148-149 158-159199 221 231-232fetal liver-ColumbiaFLS0011-5 7-12 14-15 18-24 26-28 30 36-38 40-43 50 54 56 62 64spleenUniversity70 72 75 82 84 86 89 91 94-95 98 100 102-105 107 109112-113 121 130-131 137-138 140 142-144 146 151-152158-159 162 165-166 169 177-178 181 183 189 191 193195-198 204-206 210 214 216 220 223-228 230-233 236-237240-241 244fetal liver-ColumbiaFLS0021-4 6 10-12 14-15 17-18 20-22 29-30 33 36 38-40 42 45 56spleenUniversity62-64 70 75 80 82 91-92 94-95 98 103-105 109 112-113121 126 131 142 144 146 148-149 152 162 165-167 169181 183 186 189 191 193 195-199 205-207 214 223 227-228233fetal liver-ColumbiaFLS00394 112 167 181 183 185 223 232spleenUniversityfetal liverInvitrogenFLV0011-3 6-8 15 18 23 36-39 43 62 80 82 143 145 152 177 181191 195 206 232fetal liverClontechFLV0042-3 22 24 36 82 109 122-123 152 162 181 232fetal muscleInvitrogenFMS0015 28 43 47 56 72 78-79 100 137-138 144 152 154 159 169193 207 210 237 241fetal muscleInvitrogenFMS0025 137-138 241fetal skinInvitrogenFSK0012-3 8 10 21 35-36 40 43 54 56 62-63 65 69 71 80 84 91104-105 124 130 132 137-138 142-143 148-151 158-159166 177-178 182 185 197-198 200-201 206 210 217 230232 241fetal skinInvitrogenFSK0022-3 8 11-12 21 24 26-27 29 40 43 50 62 82 88 94 98 104107 142 148-149 169 185 193 195 216 237fetal spleenBioChainFSP001183umbilical cordBioChainFUC0012-3 5 7-8 15 20 26-27 31-32 34 36 38-40 43 45 50 54 56 6276 82 84 94 103-105 107 121-123 130 143-144 146 148-149152 154 158-159 178 193 197-198 210 227 232 237240fetal brainGIBCOHFB0012-3 8 10-12 15 20-22 24 28-29 31-33 36-38 41 43 54 62 6467 70 82 88-89 93 98 101-104 107 109 113 117 130-131140 142 144-145 162 167 178 182-183 189 193 195 197-199207 210 223 227 229 232macrophageInvitrogenHMP0018 169infant brainColumbiaIB20022-3 9-12 15 20-21 23-24 33-34 38 41-43 49 56 63-64 84 89University100 104-105 107 113 118 146 148-150 152 154-155 158162 165-166 173 177-178 182 191 193 195 197-201 206223 227 230-231 237 241infant brainColumbiaIB20032-3 11-12 17 100 113 150 158 166 178 191 220-221 223University227infant brainColumbiaIBM00243 117 173Universityinfant brainColumbiaIBS00123 29 54 94 109 166 220UniversityfibroblastStrategeneLFB0012-3 8 11-12 19 29 36-37 43 45 54 56 104-105 113 130 148-149154 159 169 178 182-183 214 236 240lung tumorInvitrogenLGT0022-3 5-6 8 11-12 20-22 24 38 40-41 43 46 52 54 56 62 64-6570 72 80 82 87 89 93 100 104 107 130-131 140 142-145152 154 159 162 167 177 182-183 195 197-199 206 210214 223 236 244lymphocytesATCCLPC0012-3 11-12 20 22 38 42 50 54 73 80 86 89 94 97 105 127145 159 162 177 206 213-214 232 234leukocyteGIBCOLUC0012-4 8 10-12 15 17 19-22 24 26-27 29 35-38 40-43 47 54 5662 64 70 72 80 82 84 86 89 91 93-94 101-102 104-105 107109 130-131 143-144 146 154 158-159 162 165 167 169177-178 182-183 189 191 193 195 200-202 204 206 210214 217 223 228-229 231-232 236 240-242leukocyteClontechLUC00320 42 80 94 105 140 165 191 205 207 214 231melanomaClontechMEL00442-43 56 64 82 103 107 130 202 206 214 224-225 229 240from cell lineATCC #CRL1424mammaryInvitrogenMMG0012-4 8-9 11-12 15 17 21 26-27 35-36 38-40 43 46 56 61 64-65gland71 80 84 87 89 92 94-95 100-102 107 125 131-132 137-138140 143 145 150 152 154 159 162 166 169 173 177182-183 191 193 195 197-199 206 210 224-225 227 237243-244inducedStrategeneNTD0012-3 29 34 43 45 54 70 89 159 224-225neuron cellsretinoic acid-StrategeneNTR00120 124 130 150 152 178 202 217inducedneuronal cellsneuronal cellsStrategeneNTU00140 43 47 72 131 217 237pituitary glandClontechPIT00415 37-38 43 56 130-131 240placentaClontechPLA0032-3prostateClontechPRT0015 11-12 43 62 65 83 103 134 152 232 237rectumInvitrogenREC0012-3 15 18 26-27 43 54 56 73 80 130 145 152 183 199 244salivary glandClontechSAL00114 17 29 43 47 70 98 104 132 159 178 196 204 232-233236-237salivary glandClontechSALs0337 137-138 244skin fibroblastATCCSFB00143 47skin fibroblastATCCSFB00254skin fibroblastATCCSFB003100small intestineClontechSIN00121 34 46 73-74 86 103 107 130 137-138 144 169 183 193227-228 237 242-244skeletalClontechSKM0015 20 45 79 86 137-138 152 206muscleskeletalClontechSKM002137-138muscleskeletalClonetechSKMS03137-138muscleskeletalNULLSKMS04137-138musclespinal cordClontechSPC00129 40 43 54 69 75 88-89 91 152 159 162 178 191 195 206210 223 229 232adult spleenClontechSPLc016 46 50 70 130 140 152 216 240stomachClontechSTO00118 21 63 67 71 107 159 210 220 229 241 244thalamusClontechTHA0029 21 42 45 89 100 117 162 183 220 226-227 242thymusClonetechTHM0012-3 8 11-12 15 21 23-24 29 38-40 43 46 67 80 82 105 131151 159 162 191 214 244thymusClontechTHMc022-4 10-12 22 26-27 31-32 38 43 47 50 54 80 92 94 101-102127 134 144 146 152 154-155 158-159 162 167 178 182-183191 193 195-196 200-201 205 210 214 216 218 233237 240thyroid glandClontechTHR0012-3 5 8 10-12 17-18 20-21 23-24 29 38 42-43 45 49 54 5661-62 64 67 70 75-76 78 84 91-92 94 103-105 107 109 122-123130 134 143 148-149 155 162 167 169 178 182-183186 191 193 195-198 200-201 214 229 232-233 237 240244tracheaClontechTRC0012-3 15 19 36-37 40 47 54 65 72 89 95 107 204-205 210 232237 244uterusClontechUTR0018 31-32 54 56 178 183 206 232 236 243*The 16 tissue-mRNAs and their vendor source, are as follows: 1) Normal adult brain mRNA (Invitrogen), 2) normal adult kidney mRNA (Invitrogen), 3) normal adult liver mRNA (Invitrogen), 4) normal fetal brain mRNA (Invitrogen), 5) normal fetal kidney mRNA (Invitrogen), 6) normal fetal liver mRNA (Invitrogen), 7) normal fetal skin mRNA (Invitrogen), 8) human adrenal gland mRNA (Clontech), 9) human bone marrow mRNA (Clontech), 10) human leukemia #lymphablastic mRNA (Clontech), 11) human thymus mRNA (Clontech). 12) human lymph node mRNA (Clontech), 13) human spinal cord mRNA (Clontech), 14) human thyroid mRNA (Clontech), 15) human esophagus mRNA (BioChain), 16) human conceptional umbilical cord mRNA (BioChain).

[0446]

2

TABLE 2

SEQ

ID
Accession

%

NO:
Number
Species
Description
Score
Identity

246
AF145657

Drosophila

BcDNA.GH10120
728
38

melanogaster

247
X58141

Homo

mRNA for erythrocyte adducin alpha subunit.
3826
99

sapiens

248
L29296

Homo

(clone: SS20B/E6.0) alpha-adducin gene, exons
3387
99

sapiens

14, 15, 16.

249
AAB63963

Homo

26-MAR-2001 26-MAY-2000 Human prostate
1095
97

sapiens

cancer associated antigen protein sequence SEQ

ID NO: 1325.

250
M29458

Homo

carbonic anhydrase III gene, exon 7.
1441
100

sapiens

251
AJ006529

Gallus gallus

putative phosphatase
867
60

252
Y08302

Homo

mRNA for MAP kinase phosphatase 4.
1996
100

sapiens

253
X53280

Homo

BTF3a mRNA.
1048
100

sapiens

254
AB013790

Ateles

immunoglobulin alpha heavy chain
74
43

belzebuth

255
AK027387

Homo

FLJ14481 fis, clone MAMMA1002351, highly
964
100

sapiens

similar to Mus musculus dynactin subunit p25

(p25) mRNA.

256
AK001686

Homo

FLJ10824 fis, clone NT2RP4001086.
3013
93

sapiens

257
AK001686

Homo

FLJ10824 fis, clone NT2RP4001086.
4089
98

sapiens

258
AK026076

Homo

FLJ22423 fis, clone HRC08678.
689
100

sapiens

259
AY037207

Arabidopsis

AT3g22240/MMP21_1
66
31

thaliana

260
AAW58394

Homo

14-SEP-1998 09-OCT-1997 Human
797
92

sapiens

spermidine/spermine NI-acetyltransferase.

261
AF220051

Homo

hematopoietic stem/progenitor cells protein
844
98

sapiens

MDS031 mRNA, complete cds.

262
AB017563

Homo

gene, exon 10 and complete cds.
2283
100

sapiens

263
J03910

Homo

(clone 14VS) metallothionein-IG (MTIG) gene,
367
98

sapiens

complete cds.

264
X56351

Homo

ALASI (ALASH) mRNA for delta-
3333
100

sapiens

aminolevulinate synthase (housekeeping) (EC

2.3.1.37).

266
U79241

Homo

clone 23759 mRNA. partial cds.
2304
100

sapiens

267
AF068291

Homo

mRNA, partial cds.
699
99

sapiens

268
BC007235

Homo

clone MGC: 15430, mRNA, complete cds.
398
100

sapiens

269
X69151

Homo

mRNA for subunit C of vacuolar proton-
1958
100

sapiens

ATPase V1 domain.

270
AF271784

Homo

mRNA, complete cds.
1017
92

sapiens

271
AB025220

Homo

mRNA for p40phox. complete cds.
1737
100

sapiens

272
AB025220

Homo

mRNA for p40phox. complete cds.
1644
96

sapiens

273
BC001426

Homo

Similar to ubiquinol-cytochrome c reductase
346
100

sapiens

hinge protein, clone MGC: 1361, mRNA,

complete cds.

274
AL050051

Homo

cDNA DKFZp566D193 (from clone
481
98

sapiens

DKFZp566D193); partial cds.

275
BC002517

Homo

Pirin, clone MGC: 2083, mRNA, complete cds.
1543
100

sapiens

276
X69962

Homo

FMR-1 mRNA.
2384
100

sapiens

277
L29074

Homo

X mental retardation syndrome protein (FMRI)
2144
92

sapiens

gene, alternative splice products, complete cds;

and pseudogene, complete sequence.

278
AK001711

Homo

FLJ10849 fis, clone NT2RP4001414, highly
2179
99

sapiens

similar to SEPTIN 2 HOMOLOG.

279
AK027641

Homo

FLJ14735 fis, clone NT2RP3002054.
651
99

sapiens

280
BC009256

Homo

clone MGC: 14860, mRNA, complete cds.
1065
94

sapiens

281
AL110239

Homo

cDNA DKFZp566E144 (from clone
1234
99

sapiens

DKFZp566E144); complete cds.

282
BC008714

Homo

prostatic binding protein, clone MGC: 8531,
1017
100

sapiens

mRNA, complete cds.

283
BC004374

Homo

ARPI (actin-related protein 1, yeast) homolog B
1949
100

sapiens

(centractin beta), clone MGC: 10568, mRNA,

complete cds.

284
AF201334

Homo

mRNA, complete cds.
2395
100

sapiens

285
BC008743

Homo

zyxin, clone MGC: 3071, mRNA, complete cds.
3145
100

sapiens

286
BC005957

Homo

solute carrier family 25 (mitochondrial carrier;
1557
100

sapiens

peroxisomal membrane protein, 34 kD), member

17, clone MGC: 14604, mRNA, complete cds.

287
AF273053

Homo

tumor antigen se89-1 mRNA, complete cds.
3570
82

sapiens

288
AB028893

Homo

U32, U33, U34, U35, RPS11, U35 genes for
595
100

sapiens

ribosomal protein L13a and S11, U32, U33,

U34, U35, and U35 snoRNA, complete cds and

sequence.

289
AC003973

Homo

from chromosome 19, BAC 33152, complete
5273
81

sapiens

sequence.

290
AF253978

Homo

mRNA, partial cds.
487
85

sapiens

291
AF018265
synthetic
immunoglobulin lambda light chain
278
79

construct

292
BC005134

Homo

Similar to ribosomal protein L14, clone
1102
99

sapiens

MGC: 11208, mRNA, complete cds.

293
AK000869

Homo

FLJ10007 fis, clone HEMBA 1000193.
2635
100

sapiens

294
AAB73229

Homo

11-MAY-2001 11-AUG-2000 Human
2127
98

sapiens

phosphatase MTMR7_h.

295
BC003618

Homo

Similar to putative nuclear protein, clone
3042
100

sapiens

MGC: 1819, mRNA, complete cds.

296
AAB54346

Homo

09-MAR-2001 08-MAR-2000 Human
4092
99

sapiens

pancreatic cancer antigen protein sequence SEQ

ID NO: 798.

297
AK000330

Homo

FLJ20323 fis. clone HEP09648.
2229
100

sapiens

298
AF176701

Homo

protein FBL9 mRNA. partial cds.
1072
100

sapiens

299
X54977

Bos taurus

17,000 dalton myosin light chain
789
100

300
AL096746

Homo

cDNA DKFZp586E1322 (from clone
1186
100

sapiens

DKFZp586E1322): partial cds.

301
BC000502

Homo

ribosomal protein L17, clone MGC: 8457,
970
100

sapiens

mRNA, complete cds.

302
AC004079

Homo

clone RP1-167F23 from 7p15, complete
1965
100

sapiens

sequence.

303
X92485

Plasmodium

pval
149
55

vivax

304
AK006347

Mus

putative
429
86

musculus

305
AL137544

Homo

cDNA DKFZp434A 1520 (from clone
974
98

sapiens

DKFZp434A 1520); partial cds.

306
AC006276

Homo

19, cosmid R28379, complete sequence.
900
99

sapiens

307
AK024297

Homo

FLJ14235 fis, clone NT2RP4000167.
2325
100

sapiens

308
AK005941

Mus

putative
460
88

musculus

309
AF265440

Homo

mRNA, complete cds.
1413
100

sapiens

311
AB027251

Homo

for zinc finger protein (ZFD25), complete cds.
4369
100

sapiens

312
AK008240

Mus

putative
455
100

musculus

313
AAB75337

Homo

03-APR-2001 01-JUN-2000 Human secreted
138
60

sapiens

protein sequence encoded by gene 47 SEQ ID

NO: 156.

314
AF321191

Homo

(PRX) mRNA, complete cds, alternatively
7312
99

sapiens

spliced.

315
AF225417

Homo

kDa protein mRNA, complete cds.
3701
99

sapiens

316
AK000265

Homo

FLJ20258 fis, clone COLF7250.
2797
97

sapiens

317
D90070

Homo

ATL-derived PMA-responsive (APR) peptide
278
100

sapiens

mRNA.

318
U79725

Homo

A33 antigen precursor mRNA, complete cds.
1678
100

sapiens

319
M83679

Rattus

RAB15
1077
97

norvegicus

320
AK024715

Homo

FLJ21062 fis, clone CAS01044.
927
98

sapiens

321
AK000075

Homo

FLJ20068 fis, clone COL01755.
1729
99

sapiens

322
AC007954

Homo

14 clone RP11-493G17 and CTD-2516D11 map
4243
100

sapiens

14q24.3, complete sequence.

323
Z33905

Homo

gene for 43 kD acetylcholine receptor-associated
2150
99

sapiens

protein (Rapsyn).

324
AF030027
Equine
71
118
22

herpesvirus 4

325
AJ291606

Xenopus

gamma tubulin ring protein
2024
55

laevis

326
AAB64610

Homo

22-MAR-2001 01-JUN-2000 Human secreted
197
72

sapiens

protein BLAST search protein SEQ ID NO:

120.

327
AAB53677

Homo

09-MAR-2001 08-MAR-2000 Human colon
694
99

sapiens

cancer antigen protein sequence SEQ ID

NO: 1217.

328
AF159055

Homo

zipper-like protein (LZLP) mRNA, complete
116
79

sapiens

cds.

329
AL160111

Homo

1 of a novel human mRNA from chromosome
2126
100

sapiens

22.

330
AF159055

Homo

zipper-like protein (LZLP) mRNA, complete
130
80

sapiens

cds.

331
AK026264

Homo

FLJ22611 fis, clone HS104961.
685
96

sapiens

332
X57809

Homo

rearranged immunoglobulin lambda light chain
1223
100

sapiens

mRNA.

333
AAB87440

Homo

22-MAY-2001 31-AUG-2000 Human gene 32
513
75

sapiens

encoded secreted protein fragment, SEQ ID

NO: 181.

334
AK012475

Mus

putative
2259
84

musculus

335
AF090930

Homo

HQ0478 PRO0478 mRNA, complete cds.
146
72

sapiens

336
AL080196

Homo

cDNA DKFZp434C212 (from clone
2292
94

sapiens

DKFZp434C212).

337
AK019766

Mus

putative
1288
71

musculus

338
X69398

Homo

mRNA for OA3 antigenic surface determinant.
1632
100

sapiens

339
AK019305

Mus

putative
506
96

musculus

340
AL078630

Mus

573K1.15 (mm17M1-6 (novel 7 transmembrane
1023
81

musculus

receptor (rhodopsin family) (olfactory receptor

LIKE) protein))

341
AF118078

Homo

PRO1848
574
100

sapiens

342
AK005566

Mus

putative
1218
94

musculus

343
U71363

Homo

zinc finger protein zfp6 (ZF6) mRNA, partial
1367
70

sapiens

cds.

344
AK015315

Mus

putative
556
76

musculus

345
AF218451

Homo

substrate p130Cas mRNA, complete cds.
4579
99

sapiens

346
AF151046

Homo

HSPC212
1345
87

sapiens

347
AF151046

Homo

HSPC212
817
74

sapiens

348
Z14244

Homo

coxVIIb mRNA for cytochrome c oxidase
426
100

sapiens

subunit VIIb.

349
BC001037

Homo

ribosomal protein L35a, clone MGC: 1639,
581
100

sapiens

mRNA, complete cds.

351
AAB45018

Homo

12-FEB-2001 09-MAR-2000 Human secreted
142
57

sapiens

protein encoded by gene 41 homologue.

352
AAY94885

Homo

12-JUN-2000 22-JUL-1999 Human protein
540
99

sapiens

clone HP10550.

353
AF161557

Homo

HSPC072
472
100

sapiens

354
AAG01438

Homo

06-OCT-2000 21-FEB-2000 Human secreted
353
92

sapiens

protein, SEQ ID NO: 5519.

355
AF161507

Homo

HSPC158
1197
99

sapiens

356
AL122111

Homo

cDNA DKFZp434A1721 (from clone
2868
99

sapiens

DKFZp434A1721).

357
AF349540

Homo

XIII secreted phospholipase A2 mRNA.
1073
100

sapiens

complete cds.

358
AF274714

Homo

protein-related protein (ORPI) mRNA.
2363
100

sapiens

complete cds.

359
AAG03793

Homo

06-OCT-2000 21-FEB-2000 Human secreted
222
67

sapiens

protein, SEQ ID NO: 7874.

360
BC000705

Homo

clone MGC: 861, mRNA, complete cds.
908
100

sapiens

361
AAG03789

Homo

06-OCT-2000 21-FEB-2000 Human secreted
188
60

sapiens

protein, SEQ ID NO: 7870.

362
AAB62810

Homo

02-MAY-2001 06-JUL-2000 Human nervous
501
96

sapiens

system associated protein NSPRT3 amino acid

sequence.

363
AF161370

Homo

mRNA, partial cds.
654
91

sapiens

364
AK011592

Mus

putative
1245
66

musculus

365
AK002154

Homo

FLJ11292 fis, clone PLACE1009665.
230
64

sapiens

366
AF159297

Zea mays

extensin-like protein
349
28

367
AF125096

Homo

HSPC042 protein
137
96

sapiens

368
AF125096

Homo

HSPC042 protein
243
98

sapiens

369
AK001745

Homo

FLJ10883 fis, clone NT2RP4001946, weakly
1880
99

sapiens

similar to PROTEIN-L-ISOASPARTATE O-

METHYLTRANSFERASE (EC 2.1.1.77).

370
AF151783

Homo

(MEG3) mRNA, complete cds.
3651
99

sapiens

371
X16707

Homo

fra-1 mRNA.
1443
100

sapiens

372
AF176555

Homo

anchoring protein 220 mRNA, complete cds.
9783
99

sapiens

373
X78121

Homo

mRNA.
3404
100

sapiens

374
U82670

Homo

Xq28 psHMG17 pseudogene, complete
2513
99

sapiens

sequence; and melanoma antigen family A1

(MAGEA1) and zinc finger protein 275

(ZNF275) genes, complete cds.

375
AK018726

Mus

putative
670
100

musculus

376
BC000187

Homo

cytochrome c oxidase subunit VIc, clone
379
100

sapiens

MGC: 1520, mRNA, complete cds.

377
AAY87548

Homo

18-JUL-2000 03-NOV-1997 Human disease-
729
100

sapiens

associated calmodulin protein (DACP-1).

378
AK003198

Mus

putative
562
100

musculus

379
AK000496

Homo

FLJ20489 fis, clone KAT08285.
333
69

sapiens

380
AF130079

Homo

PRO2852
308
74

sapiens

381
AAY91961

Homo

19-JUL-2000 17-SEP-1999 Human
1293
96

sapiens

cytoskeleton associated protein 16 (CYSKP-16).

382
M15202

Rattus

troponin T class IIIa beta
1155
94

norvegicus

383
AF026276

Homo

skeletal troponin T (TNNT3) gene, complete
1205
94

sapiens

cds.

384
AF090694

Homo

RNA binding protein (NAPOR-2) mRNA,
2519
98

sapiens

complete cds.

385
BC007655

Homo

protein phosphatase 1, regulatory (inhibitor)
1051
100

sapiens

subunit 2, clone MGC: 1327, mRNA, complete

cds.

386
AF161533

Homo

HSPC048
573
100

sapiens

387
BC002801

Homo

p47, clone MGC: 3347, mRNA, complete cds.
1812
96

sapiens

388
AK027878

Homo

FLJ14972 fis, cloneTHYRO1000715.
2669
98

sapiens

389
AF161418

Homo

HSPC300
378
100

sapiens

390
AK010720

Mus

putative
105
28

musculus

391
X66358

Homo

mRNA KKIALRE for serine/threonine protein
1929
99

sapiens

kinase.

392
AF290612

Homo

Q0310 liver nuclear protein mRNA, complete
2246
98

sapiens

cds.

393
U69263

Homo

precursor, mRNA, complete cds.
4516
99

sapiens

394
U69263

Homo

precursor, mRNA, complete cds.
4021
99

sapiens

395
AK000838

Homo

FLJ20831 fis, clone ADKA03080.
761
100

sapiens

396
AK006393

Mus

putative
819
90

musculus

397
AF312033

Mus

ASR2A
4584
97

musculus

398
BC001904

Homo

Similar to phosphoglycerate mutase 2 (muscle),
270
100

sapiens

clone MGC: 2269, mRNA, complete cds.

399
Y14391

Homo

for putative GTP-binding protein.
2042
99

sapiens

400
AF242528

Homo

finger protein 291 (ZNF291) mRNA, complete
294
100

sapiens

cds.

401
AF116695

Homo

PRO2221
173
46

sapiens

402
AAR32020

Homo

11-JUL-1993 14-AUG-1992 Sequence of a
734
66

sapiens

eukaryotic transcription factor (TF).

403
AB049127

Homo

mRNA for MAP/microtubule affinity-regulating
2227
73

sapiens

kinase like 1. complete cds.

404
K03250

Rattus

ribosomal protein S11
824
100

norvegicus

405
AF144233

Homo

binding peptide mRNA, partial cds.
328
96

sapiens

406
AC007055

Homo

14 clone BAC 201F1 map 14q24.3, complete
519
100

sapiens

sequence.

407
AK001752

Homo

FLJ10890 fis, clone NT2RP4002071.
5019
99

sapiens

408
AF090931

Homo

HQ0483$ PRO0483 mRNA, complete cds.
133
58

sapiens

409
A28080

Mycobacterium

34 kDa protein
75
36

avium

subsp.

paratuberculosis

410
AL136704

Homo

cDNA DKFZp566A1524 (from clone
1662
99

sapiens

DKFZp566A1524); complete cds.

411
AL137347

Homo

cDNA DKFZp761M1511 (from clone
473
100

sapiens

DKFZp761M1511); partial cds.

412
AK027527

Homo

FLJ14621 fis, clone NT2RP2000079.
1012
100

sapiens

413
AAG01083

Homo

06-OCT-2000 21-FEB-2000 Human secreted
274
96

sapiens

protein. SEQ ID NO: 5164.

414
BC009405

Homo

adenylate kinase 2, clone MGC: 15301, mRNA,
1094
100

sapiens

complete cds.

415
U34994

Homo

dependent protein kinase catalytic subunit
21178
100

sapiens

(PRKDC) mRNA, complete cds; alternatively

spliced.

416
U47077

Homo

protein kinase catalytic subunit (DNA-PKcs)
21319
99

sapiens

mRNA, complete cds.

417
U22229

Felis catus

ribosomal protein L41
128
100

418
AF361481

Homo

GTP-binding protein 1 (GTPBP3) gene,
1402
94

sapiens

complete cds; nuclear gene for mitochondrial

product.

419
BC000606

Homo

Similar to ribosomal protein L14, clone
1094
100

sapiens

MGC: 1644, mRNA, complete cds.

421
AAY73345

Homo

24-FEB-2000 04-MAY-1999 HTRM clone
2171
73

sapiens

438283 protein sequence.

422
AK000632

Homo

FLJ20625 fis, clone KAT04008.
816
100

sapiens

423
AC004668

Homo

clone CTA-276O3 from 7q22-q31.1, complete
1976
99

sapiens

sequence.

424
AK000496

Homo

FLJ20489 fis, clone KAT08285.
238
73

sapiens

425
AAY02785

Homo

11-JUN-1999 07-JUL-1998 Human secreted
82
43

sapiens

protein encoded by gene 51 clone HUKEX85.

426
AF118092

Homo

PRO2061
1440
96

sapiens

427
AK000382

Homo

FLJ20375 fis, clone HUV00942.
1330
99

sapiens

428
Y15286

Homo

for vacuolar proton-ATPase subunit M9.2.
459
100

sapiens

429
AK014098

Mus

putative
524
68

musculus

430
AF286095

Homo

receptor (IL22R) mRNA, complete cds.
629
86

sapiens

431
AK023266

Homo

FLJ13204 fis, clone NT2RP3004507, weakly
758
90

sapiens

similar to MOB1 PROTEIN.

432
AF047354

Homo

and spleen DNase precursor (LSD) mRNA,
1046
99

sapiens

complete cds.

433
X53682

Homo

LAG-1 gene.
484
100

sapiens

434
AC000064

Homo

BAC clone RG083M05 from 7q21-7q22,
298
100

sapiens

complete sequence.

435
AL390921

Arabidopsis

putative protein
72
44

thaliana

436
AAB87440

Homo

22-MAY-2001 31-AUG-2000 Human gene 32
1572
100

sapiens

encoded secreted protein fragment, SEQ ID

NO: 181.

437
AP003001

Mesorhizobium

O-linked GlcNAc transferase
153
30

loti

438
AK000642

Homo

FLJ20635 fis, clone KAT03466.
1854
99

sapiens

439
Z48810

Homo

mRNA for TX protease precursor.
306
92

sapiens

441
AC003002

Homo

DNA from overlapping chromosome 19-
436
98

sapiens

specific cosmids R29515 and R28253, genomic

sequence, complete sequence.

442
AF109377

Mus

ldlBp
3979
82

musculus

443
AF109377

Mus

ldlBp
2711
81

musculus

444
AAG02042

Homo

06-OCT-2000 21-FEB-2000 Human secreted
797
100

sapiens

protein, SEQ ID NO: 6123.

445
M17877

Plasmodium

interspersed repeat antigen
291
27

falciparum

446
M17877

Plasmodium

interspersed repeat antigen
291
27

falciparum

447
AB025784

Rattus

PPAR gamma coactivator
331
46

norvegicus

448
AK000755

Homo

FLJ20748 fis, clone HEP05772.
831
96

sapiens

449
AK001714

Homo

FLJ10852 fis, clone NT2RP4001498, weakly
2586
100

sapiens

similar to ANKYRIN REPEAT-CONTAINING

PROTEIN AKR1.

450
AB042646

Homo

mRNA, complete cds.
1224
100

sapiens

451
AF125533

Homo

b5 reductase isoform mRNA, complete cds.
1606
100

sapiens

452
AAY02591

Homo

19-JUL-1999 09-OCT-1998 A human
849
100

sapiens

progesterone receptor complex p23-like protein.

453
BC000600

Homo

Similar to from HeLa cyclin-dependent kinase 2
1106
100

sapiens

interacting protein, clone MGC: 849, mRNA,

complete cds.

454
Z46937

Caenorhabdit

similarity with ribosomal protein L21
140
38

is elegans

455
AF161556

Homo

HSPC071
941
100

sapiens

456
AF225971

Homo

(TUBG2) mRNA, complete cds.
2346
99

sapiens

458
AF343664

Homo

receptor translocation associated protein 2c
736
55

sapiens

(IRTA2) mRNA, complete cds, alternatively

spliced.

459
AF191545

Homo

mRNA, complete cds.
4141
99

sapiens

460
AF118082

Homo

PRO1902
202
58

sapiens

461
D00531

Oncorhynchus

apopolysialoglycoprotein
512
30

masou

462
Z11898

Homo

OTF3 mRNA encoding octamer binding protein
1948
100

sapiens

3A.

464
AL162044

Homo

cDNA DKFZp761L0812 (from clone
220
41

sapiens

DKFZp761L0812); partial cds.

465
AL137301

Homo

cDNA DKFZp434N1429 (from clone
543
100

sapiens

DKFZp434N1429); partial cds.

466
AB032593

Homo

for PXR2b, complete cds.
3201
100

sapiens

467
AL050075

Homo

cDNA DKFZp566F0546 (from clone
407
100

sapiens

DKFZp566F0546); partial cds.

468
AK000732

Homo

FLJ20725 fis, clone HEP13903.
1653
99

sapiens

469
AB049638

Homo

mRNA for mitochondrial ribosomal protein L11
941
100

sapiens

(L11mt), complete cds.

470
AB049638

Homo

mRNA for mitochondrial ribosomal protein L11
737
99

sapiens

(L11mt), complete cds.

471
AB014772

Homo

for MOP-3, complete cds.
1722
99

sapiens

472
AAY59808

Homo

18-JAN-2000 03-APR-1998 Human normal
778
100

sapiens

ovarian tissue derived protein 85.

473
AF331500
multiple
recombinant envelope protein
1177
92

sclerosis

associated

retrovirus

element

474
AF257330

Homo

protein mRNA, complete cds.
962
96

sapiens

475
AK000632

Homo

FLJ20625 fis, clone KAT04008.
809
99

sapiens

476
M58511

Homo

iron-responsive element-binding protein/iron
4968
99

sapiens

regulatory protein 2 (IRE-BP2/IRP2) mRNA,

partial cds.

477
AF181989

Homo

beta subunit variant (HBB) mRNA, complete
588
90

sapiens

cds.

478
AC003002

Homo

DNA from overlapping chromosome 19-
752
100

sapiens

specific cosmids R29515 and R28253, genomic

sequence, complete sequence.

479
BC002924

Homo

clone IMAGE: 3956179, mRNA, partial cds.
1221
99

sapiens

480
AF109146

Homo

lectin superfamily 6 (CLECSF6) mRNA,
958
99

sapiens

complete cds.

481
BC005374

Homo

Similar to RIKEN cDNA 1110001E24 gene,
995
100

sapiens

clone MGC: 12490, mRNA, complete cds.

482
X75285

Mus

fibulin-2
5621
81

musculus

483
AC007954

Homo

14 clone RP11-493G17 and CTD-2516D11 map
1342
100

sapiens

14q24.3, complete sequence.

484
AK016295

Mus

putative
116
27

musculus

485
AB028893

Homo

U32, U33, U34, U35, RPS11, U35 genes for
434
100

sapiens

ribosomal protein L13a and S11, U32, U33,

U34, U35, and U35 snoRNA, complete cds and

sequence.

486
BC003681

Homo

clone IMAGE: 3453235, mRNA, partial cds.
2829
96

sapiens

487
AK009235

Mus

putative
1648
92

musculus

488
AF294900

Homo

beta-carotene 15,15′- dioxygenase (BCDO)
2912
100

sapiens

mRNA, complete cds.

489
AAB43979

Homo

08-FEB-2001 08-MAR-2000 Human cancer
1051
86

sapiens

associated protein sequence SEQ ID NO: 1424.

490
AF220025

Homo

motif protein TRIM5 isoform alpha (TRIM5)
1299
95

sapiens

mRNA, complete cds; alternatively spliced.

[0447]

3

TABLE 3

SEQ ID
Accession

NO:
Number
Description
Results*

247
PF00596
Class II Aldolases and Adducin N-
PF00596C 17.24 9.710e−20 217-243

terminal domain proteins.
PF00596B 15.07 4.938e−14

180-202 PF00596D 13.89

4.079e−12 297-315

248
PF00596
Class II Aldolases and Adducin N-
PF00596C 17.24 9.710e−20 217-243

terminal domain proteins.
PF00596B 15.07 4.938e−14

180-202 PF00596D 13.89

4.079e−12 297-315

250
BL00162
Eukaryotic-type carbonic anhydrases
BL00162C 17.78 1.000e−40 88-125

proteins.
BL00162E 14.93 6.478e−34

189-222 BL00162F 22.68

6.727e−30 226-260 BL00162A

22.92 5.179e−26 16-47

BL00162D 15.06 4.960e−22 126-151

BL00162B 21.43 5.345e−17

51-74

252
BL00383
Tyrosine specific protein phosphatases
BL00383E 10.35 1.196e−11 288-299

proteins.

253
PD02749
TRANSCRIPTION PROTEIN
PD02749B 12.75 1.000e−40 84-120

FACTOR BTF3 REGULATION
PD02749C 13.96 3.739e−34

NUCL.
136-170 PD02749A 9.56 6.000e−15

51-64

256
BL00824
Elongation factor 1 beta/beta'/delta
BL00824B 9.21 8.419e−09 281-301

chain proteins.

257
BL00824
Elongation factor 1 beta/beta'/delta
BL00824B 9.21 8.419e−09 281-301

chain proteins.

260
PF00583
Acetyltransferase (GNAT) family.
PF00583A 12.53 3.571e−12 175-186

262
PD01364
MUCIN GLYCOPROTEIN
PD01364B 13.94 1.000e−10 336-352

PRECURSOR MEM.

263
PR00860
VERTEBRATE
PR00860B 7.04 2.929e−20 28-42

METALLOTHIONEIN SIGNATURE
PR00860C 9.61 1.474e−14 42-52

PR00860A 5.46 9.229e−12 6-19

264
BL00599
Aminotransferases class-II pyridoxal-
BL00599B 18.93 8.800e−27 278-307

phosphate attachment sit.
BL00599D 13.25 8.773e−13

411-424 BL00599C 9.13 5.235e−11

334-344

266
PD01769
REDUCTASE PAPS
PD01769C 21.60 8.393e−18 416-452

BIOSYNTHESIS PHOSPHOADENO.

271
PR00497
NEUTROPHIL CYTOSOL FACTOR
PR00497D 11.91 1.176e−28 192-214

P40 SIGNATURE
PR00497E 10.43 1.123e−26

241-261 PR00497A 6.92 1.136e−24

56-74 PR00497B 4.99 1.125e−23

74-93 PR00497C 8.89 1.100e−21

131-147 PR00497F 8.66

1.138e−15 297-309

272
BL50002
Src homology 3 (SH3) domain
BL50002A 14.19 6.538e−11 177-196

proteins profile.

276
PF00013
KH domain proteins family of RNA
PF00013 5.78 2.059e−10 268-280

binding proteins.

277
PF00013
KH domain proteins family of RNA
PF00013 5.78 2.059e−10 268-280

binding proteins.

280
PF00930
Dipeptidyl peptidase IV (DPP IV) N-
PF00930J 8.78 4.231e−09 394-415

terminal region.

282
BL01220
Phosphatidylethanolamine-binding
BL01220B 16.65 1.000e−40 105-146

protein family proteins.
BL01220C 14.75 5.846e−34

146-174 BL01220A 22.62

3.400e−31 67-98 BL01220D

18.75 5.364e−31 189-221

283
BL00406
Actins proteins.
BL00406B 5.47 1.000e−40 88-143

BL00406C 6.75 1.000e−40 147-202

BL00406D 12.58 7.000e−40

270-325 BL00406E 8.44 6.087e−39

327-377 BL00406A 9.95

6.087e−29 11-46

284
BL00227
Tubulin subunits alpha, beta, and
BL00227C 25.48 7.792e−26 119-171

gamma proteins.
BL00227D 18.46 2.286e−20

253-307 BL00227B 19.29

4.720e−13 58-113 BL00227A

24.55 4.649e−12 1-35

285
BL00478
LIM domain proteins.
BL00478B 14.79 3.739e−14 463-478

BL00478B 14.79 3.500e−12

405-420 BL00478B 14.79

6.000e−12 530-545

286
PR00927
ADENINE NUCLEOTIDE
PR00927B 14.66 6.236e−14 146-168

TRANSLOCATOR 1 SIGNATURE

288
BL00783
Ribosomal protein L13 proteins.
BL00783C 22.43 8.071e−20 87-117

BL00783A 14.55 1.600e−19

8-33 BL00783B 12.76 3.500e−12

74-86

289
PD01066
PROTEIN ZINC FINGER ZINC-
PD01066 19.43 2.500e−38 422-461

FINGER METAL-BINDING NU.

291
DM00031
IMMUNOGLOBULIN V REGION.
DM00031A 16.80 8.364e−11 20-68

292
PD02808
PROTEIN RIBOSOMAL L14
PD02808A 12.03 3.739e−38 5-42

PROBABLE 60.
PD02808B 19.19 8.500e−36 85-120

294
BL00383
Tyrosine specific protein phosphatases
BL00383E 10.35 2.756e−12 263-274

proteins.

295
BL01160
Kinesin light chain repeat proteins.
BL01160B 19.54 8.093e−09 510-564

297
PR00706
PYROGLUTAMYL PEPTIDASE I
PR00706B 10.56 6.870e−09 74-87

(C15) FAMILY SIGNATURE

300
PR00453
VON WILLEBRAND FACTOR
PR00453A 12.79 4.750e−15 40-58

TYPE A DOMAIN SIGNATURE

301
BL00464
Ribosomal protein L22 proteins.
BL00464B 28.48 4.960e−35 106-151

BL00464A 29.41 9.700e−23

17-54

302
BL00027
‘Homeobox’ domain proteins.
BL00027 26.43 6.727e−36 158-201

307
BL01113
C1q domain proteins.
BL01113A 17.99 2.558e−09 712-739

310
BL00226
Intermediate filaments proteins.
BL00226D 19.10 9.571e−40 371-418

BL00226B 23.86 4.600e−38

205-253 BL00226C 13.23

9.500e−26 270-301 BL00226A

12.77 4.000e−16 104-119

311
PD01066
PROTEIN ZINC FINGER ZINC-
PD01066 19.43 5.135e−34 6-45

FINGER METAL-BINDING NU.

312
PD01861
PROTEIN NUCLEAR
PD01861A 14.06 4.393e−11 26-50

RIBONUCLEOPROTEIN SMALL

MRNA RNA.

315
BL00192
Cytochrome b/b6 heme-ligand
BL00192A 11.90 3.700e−09 96-136

proteins.

316
PR00049
WILM'S TUMOR PROTEIN
PR00049D 0.00 6.445e−11 661-676

SIGNATURE

318
DM00031
IMMUNOGLOBULIN V REGION.
DM00031B 15.41 4.423e−11 103-137

319
BL01115
GTP-binding nuclear protein ran
BL01115A 10.22 7.455e−13 9-53

proteins.

321
BL00378
Hexokinases proteins.
BL00378A 19.01 8.375e−09 279-307

323
BL00405
43 Kd postsynaptic protein.
BL00405C 10.15 1.000e−40 65-115

BL00405D 6.60 1.000e−40

123-166 BL00405G 7.78 1.000e−40

226-263 BL00405H 16.83

1.000e−40 263-302 BL004051

13.75 1.000e−40 302-339

BL00405J 13.28 1.000e−40 339-373

BL00405K 7.57 1.000e−40

373-413 BL00405B 15.33

6.538e−39 26-58 BL00405F 8.07

1.900e−38 195-226 BL00405E

8.84 1.529e−34 166-192

BL00405A 9.73 1.643e−31 2-26

327
BL00048
Protamine P1 proteins.
BL00048 6.39 8.475e−15 24-51

BL00048 6.39 2.918e−14 26-53

BL00048 6.39 5.279e−14 34-61

BL00048 6.39 5.721e−14 32-59

BL00048 6.39 7.197e−14 11-38

BL00048 6.39 8.082e−14 22-49

BL00048 6.39 2.246e−13 10-37

BL00048 6.39 6.677e−13 33-60

BL00048 6.39 7.092e−13 7-34

BL00048 6.39 7.785e−13 8-35

BL00048 6.39 7.923e−13 23-50

BL00048 6.39 1.926e−12 9-36

BL00048 6.39 1.926e−12 31-58

BL00048 6.39 2.456e−12 20-47

BL00048 6.39 6.294e−12 14-41

BL00048 6.39 7.221e−12 25-52

BL00048 6.39 7.750e−12 12-39

BL00048 6.39 9.868e−12 21-48

BL00048 6.39 1.125e−11 19-46

BL00048 6.39 2.375e−11 13-40

BL00048 6.39 6.875e−11 6-33

BL00048 6.39 8.125e−11 36-63

BL00048 6.39 8.250e−11 18-45

BL00048 6.39 8.250e−11 30-57

BL00048 6.39 1.947e−10 5-32

BL00048 6.39 3.605e−10 4-31

BL00048 6.39 4.908e−10 27-54

BL00048 6.39 5.974e−10 42-69

BL00048 6.39 7.039e−10 15-42

BL00048 6.39 7.750e−10 17-44

BL00048 6.39 7.987e−10 39-66

BL00048 6.39 9.526e−10 1-28

BL00048 6.39 1.225e−09 38-65

BL00048 6.39 3.363e−09 16-43

BL00048 6.39 4.038e−09 3-30

BL00048 6.39 5.950e−09 28-55

BL00048 6.39 6.288e−09 29-56

BL00048 6.39 6.400e−09 40-67

BL00048 6.39 6.738e−09 2-29

BL00048 6.39 7.863e−09 35-62

331
PR00221
CAULIMOVIRUS COAT PROTEIN
PR00221H 12.82 1.217e−09 27-41

SIGNATURE

332
BL00290
Immunoglobulins and major
BL00290A 20.89 1.529e−14 187-210

histocompatibility complex proteins.
BL00290B 13.17 9.000e−12

247-265

334
BL00415
Synapsins proteins.
BL00415N 4.29 8.420e−10 334-378

336
PR00779
INOSITOL 1,4,5-TRISPHOSPHATE-
PR00779F 14.51 5.147e−09 512-535

BINDING PROTEIN RECEPTOR

SIGNATURE

338
DM00179
w KINASE ALPHA ADHESION T-
DM00179 13.97 7.158e−10 107-117

CELL.

339
BL00224
Clathrin light chain proteins.
BL00224B 16.94 8.200e−09 167-220

340
PR00237
RHODOPSIN-LIKE GPCR
PR00237B 13.50 1.000e−11 1-23

SUPERFAMILY SIGNATURE

343
PD00066
PROTEIN ZINC-FINGER METAL-
PD00066 13.92 5.154e−15 321-334

BINDI.
PD00066 13.92 2.800e−14

237-250 PD00066 13.92 8.800e−14

265-278 PD00066 13.92

3.000e−13 293-306 PD00066

13.92 9.217e−11 209-222

345
PR00452
SH3 DOMAIN SIGNATURE
PR00452B 11.65 4.600e−15 20-36

347
BL00563
Stathmin family proteins.
BL00563D 11.38 4.835e−09 279-315

349
BL01105
Ribosomal protein L35Ae proteins.
BL01105A 17.37 1.000e−40 16-61

BL01105B 12.95 1.000e−40 80-120

350
PD02411
PROTEIN TRANSCRIPTION
PD02411 21.89 2.929e−15 2227-2261

REGULATION NUCLEAR.

355
BL00464
Ribosomal protein L22 proteins.
BL00464B 28.48 4.908e−10 128-173

BL00464A 29.41 7.045e−09

69-106

358
BL01013
Oxysterol-binding protein family
BL01013D 26.81 8.000e−26 358-402

proteins.
BL01013A 25.14 7.231e−21

45-81 BL01013C 9.97 1.000e−13

132-142 BL01013B 11.33

1.000e−11 110-121

366
PD02557
UREASE ACCESSORY PROTEIN
PD02557C 10.85 6.262e−09 29-44

UREF NICKEL.

369
BL01279
Protein-L-isoaspartate(D-aspartate) O-
BL01279A 24.27 7.614e−12 67-115

methyltransferase signa.

371
PR00042
FOS TRANSFORMING PROTEIN
PR00042E 9.69 8.200e−25 154-178

SIGNATURE
PR00042D 8.97 9.735e−24

133-155 PR00042C 8.29 4.549e−21

115-132 PR00042B 10.70

2.983e−20 98-115 PR00042A

10.04 6.400e−20 39-57

373
PR00893
RAB ESCORT
PR00893H 7.37 2.588e−34 411-439

(CHOROIDERAEMIA) PROTEIN
PR00893J 1.42 1.500e−28

SIGNATURE
565-586 PR00893D 13.14

1.563e−28 114-138 PR00893C

15.10 2.500e−27 94-115

PR00893K 7.01 1.000e−26 600-620

PR00893I 14.97 2.667e−26

543-563 PR00893A 10.55

1.134e−25 45-64 PR00893F

10.78 3.314e−25 294-313

PR00893E 13.94 1.231e−22 213-230

PR00893G 12.88 5.500e−22

351-368 PR00893B 8.07 6.192e−22

75-93

374
BL00028
Zinc finger. C2H2 type. domain
BL00028 16.07 9.471e−14 508-525

proteins.
BL00028 16.07 9.100e−13

424-441 BL00028 16.07 2.957e−12

536-553 BL00028 16.07

4.115e−11 340-357 BL00028

16.07 8.269e−11 452-469

BL00028 16.07 4.300e−10 312-329

BL00028 16.07 7.600e−10

480-497

375
PF01020
Ribosomal L40e family.
PF01020 15.00 1.000e−40 80-129

377
PR00450
RECOVERIN FAMILY SIGNATURE
PR00450C 12.22 7.840e−10 86-108

PR00450C 12.22 7.380e−09

52-74 PR00450C 12.22 7.835e−09

16-38

381
PF00992
Troponin.
PF00992B 26.31 4.000e−30 178-213

PF00992A 16.67 2.636e−29

100-135 PF00992C 16.35

2.800e−15 244-262

382
PF00992
Troponin.
PF00992B 26.31 4.000e−30 157-192

PF00992A 16.67 2.636e−29

79-114 PF00992C 16.35 2.800e−15

223-241

383
PF00992
Troponin.
PF00992B 26.31 4.000e−30 162-197

PF00992A 16.67 2.636e−29

84-119 PF00992C 16.35 2.800e−15

228-246

384
PD02784
PROTEIN NUCLEAR
PD02784B 26.46 8.307e−10 455-498

RIBONUCLEOPROTEIN.

385
PF01140
Matrix protein (MA), p15.
PF01140D 15.54 9.686e−09 112-147

388
DM00892
3 RETROVIRAL PROTEINASE.
DM00892C 23.55 3.323e−14 340-374

391
PR00109
TYROSINE KINASE CATALYTIC
PR00109B 12.27 6.553e−13 117-136

DOMAIN SIGNATURE

393
PR00453
VON WILLEBRAND FACTOR
PR00453A 12.79 9.571e−16 528-546

TYPE A DOMAIN SIGNATURE
PR00453B 14.65 5.000e−13

567-582

394
PR00453
VON WILLEBRAND FACTOR
PR00453A 12.79 9.571e−16 528-546

TYPE A DOMAIN SIGNATURE
PR00453B 14.65 5.000e−13

567-582

399
PR00326
GTPI/OBG GTP-BINDING
PR00326A 8.75 1.514e−09 184-205

PROTEIN FAMILY SIGNATURE

402
PD00066
PROTEIN ZINC-FINGER METAL-
PD00066 13.92 1.692e−10 235-248

BINDI.

403
BL00239
Receptor tyrosine kinase class II
BL00239B 25.15 1.529e−16 106-154

proteins.

404
BL00056
Ribosomal protein S17 proteins.
BL00056A 28.90 3.769e−32 75-115

BL00056B 20.86 6.727e−23

123-147

406
BL00150
Acylphosphatase proteins.
BL00150 25.33 1.000e−40 9-56

410
PR00245
OLFACTORY RECEPTOR
PR00245D 10.47 5.224e−09 186-198

SIGNATURE

413
BL00019
Actinin-type actin-binding domain
BL00019A 12.56 1.000e−13 38-49

proteins.

414
BL00113
Adenylate kinase proteins.
BL00113B 20.49 5.667e−32 784-828

BL00113D 24.41 2.565e−27

889-920 BL00113C 12.82

2.286e−16 832-847

415
BL00915
Phosphatidylinositol 3-and 4-kinases
BL00915B 22.78 9.022e−19 3750-3788

proteins.
BL00915C 22.43 6.250e−18

3873-3912

416
BL00915
Phosphatidylinositol 3-and 4-kinases
BL00915B 22.78 9.022e−19 3750-3788

proteins.
BL00915C 22.43 6.250e−18

3904-3943

418
PR00326
GIPI/OBG GTP-BINDING
PR00326A 8.75 2.364e−10 186-207

PROTEIN FAMILY SIGNATURE

419
PD02808
PROTEIN RIBOSOMAL L14
PD02808A 12.03 3.739e−38 5-42

PROBABLE 60.
PD02808B 19.19 8.500e−36 85-120

421
PD01066
PROTEIN ZINC FINGER ZINC-
PD01066 19.43 4.767e−31 26-65

FINGER METAL-BINDING NU.

423
BL00143
Insulinase family, zinc-binding region
BL00143B 14.41 4.115e−13 102-117

proteins.

426
BL00514
Fibrinogen beta and gamma chains C-
BL00514C 17.41 1.000e−40 206-243

terminal domain proteins.
BL00514D 15.35 7.000e−16

251-264 BL00514B 16.42

4.000e−15 150-166 BL00514A

11.68 6.885e−12 40-50

427
PR00536
MELANOCYTE STIMULATING
PR00536G 6.26 2.688e−09 333-342

HORMONE RECEPTOR

SIGNATURE

432
PR00130
DNASE I SIGNATURE
PR00130E 14.66 5.871e−16 146-176

PR00130D 8.65 2.862e−15

116-146 PR00130H 14.38

1.106e−11 229-250 PR00130F

11.23 1.086e−10 176-206

PR00130G 7.22 2.340e−10 206-229

PR00130A 11.39 7.000e−10

31-61

433
PR00437
SMALL CXC CYTOKINE FAMILY
PR00437C 14.85 4.696e−09 68-87

SIGNATURE

445
PF00624
Flocculin repeat proteins.
PF00624J 6.21 9.782e−10 429-484

446
PF00624
Flocculin repeat proteins.
PF00624J 6.21 9.782e−10 429-484

447
PF01140
Matrix protein (MA), p15.
PF01140D 15.54 2.256e−09 222-257

449
PF00791
Domain present in ZO-1 and Unc5-like
PF00791B 28.49 8.515e−10 120-175

netrin receptors.

450
BL00027
‘Homeobox’ domain proteins.
BL00027 26.43 1.818e−21 36-79

451
BL00191
Cytochrome b5 family, heme-binding
BL00191K 17.38 4.951e−27 184-228

domain proteins.
BL00191J 11.37 6.447e−17

128-150

454
BL00028
Zinc finger, C2H2 type, domain
BL00028 16.07 8.457e−09 22-39

proteins.

456
BL00227
Tubulin subunits alpha, beta, and
BL00227B 19.29 1.000e−40 51-106

gamma proteins.
106 BL00227C 25.48 1.000e−40

113-165 BL00227D 18.46

1.000e−40 223-277 BL00227A

24.55 2.607e−31 2-36 BL00227F

21.16 4.316e−30 382-436

BL00227E 24.15 2.667e−23 331-366

457
PR00301
70 KD HEAT SHOCK PROTEIN
PR00301C 8.62 8.875e−11 235-244

SIGNATURE

458
DM00179
w KINASE ALPHA ADHESION T-
DM00179 13.97 6.870e−09 47-57

CELL.
DM00179 13.97 8.435e−09 238-248

459
PR00756
MEMBRANE ALANYL
PR00756D 10.58 1.529e−21 367-383

DIPEPTIDASE (MI) FAMILY
PR00756B 14.06 5.737e−16

SIGNATURE
253-269 PR00756A 12.90

1.237e−13 205-221 PR00756E

11.91 4.094e−13 386-399

PR00756C 11.60 6.108e−11 331-342

461
PR00648
GPR3 ORPHAN RECEPTOR
PR00648B 7.41 8.340e−09 1029-1048

SIGNATURE

462
BL00027
‘Homeobox’ domain proteins.
BL00027 26.43 5.500e−27 245-288

466
PD00126
PROTEIN REPEAT DOMAIN TPR
PD00126A 22.53 2.862e−09 515-536

NUCLEA.

469
BL00359
Ribosomal protein L11 proteins.
BL00359A 20.66 5.395e−23 20-56

BL00359B 23.07 4.176e−19 66-107

BL00359C 22.18 2.000e−12

123-157

470
BL00359
Ribosomal protein L11 proteins.
BL00359B 23.07 4.176e−19 40-81

BL00359C 22.18 2.000e−12 97-131

473
PF00429
ENV polyprotein (coat polyprotein).
PF00429 31.08 3.195e−12 299-349

476
BL00450
Aconitase family proteins.
BL00450B 42.34 8.393e−30 281-336

BL00450D 21.14 2.800e−18

560-584 BL00450B 42.34

6.400e−12 341-396 BL00450A

13.76 2.406e−11 246-260

BL00450C 11.95 6.657e−10 507-517

477
BL01033
Globins profile.
BL01033A 16.94 7.923e−18 25-47

BL01033B 13.81 1.000e−15 93-105

480
BL00615
C-type lectin domain proteins.
BL00615A 16.68 5.500e−10 78-96

BL00615B 12.25 7.577e−09 178-192

482
BL01177
Anaphylatoxin domain proteins.
BL01177E 20.64 5.800e−24 1043-1070

BL01177C 17.39 5.333e−19

997-1016 BL01177B 13.61

7.840e−16 703-719 BL01177D

17.50 1.900e−15 1022-1040

487
BL01032
Protein phosphatase 2C proteins.
BL01032H 11.25 8.200e−09 253-266

489
BL00290
Immunoglobulins and major
BL00290A 20.89 1.563e−15 154-177

histocompatibility complex proteins.
BL00290B 13.17 9.000e−12

214-232

490
PR00245
OLFACTORY RECEPTOR
PR00245A 18.03 5.886e−10 461-483

SIGNATURE

*Results include in order: accession number subtype; raw score; p-value; position of signature in amino acid sequence

[0448]

4

TABLE 4

SEQ ID

Pfam

NO:
Pfam Model
Description
E-value
Score

247
Aldolase_II
Class II Aldolase and Adducin N-terminal
7.3e−105
361.8

248
Aldolase_II
Class II Aldolase and Adducin N-terminal
7.3e−105
361.8

249
rrm
RNA recognition motif.
8.8e−06
32.6

250
carb_anhydrase
Eukaryotic-type carbonic anhydrase
7.8e−178
604.2

252
DSPc
Dual specificity phosphatase, catalytic doma
3.6e−69
243.2

253
NAC
NAC domain
4.7e−30
113.3

255
hexapep
Bacterial transferase hexapeptide
6.2e−06
33.1

260
Acetyltransf
Acetyltransferase (GNAT) family
2.8e−19
77.5

262
ig
Immunoglobulin domain
5.2e−20
69.5

263
metalthio
Metallothionein
1.3e−22
88.6

264
aminotran_2
Aminotransferases class-II
2.4e−109
376.7

265
IPP_isomerase
Isopentenyl-diphosphate delta-isomerase
1.6e−128
440.4

266
PAPS_reduct
Phosphoadenosine phosphosulfate reductase
6.2e−14
59.7

271
PX
PX domain
7.4e−31
115.9

272
PX
PX domain
7.4e−31
115.9

276
KH-domain
KH domain
7.2e−13
56.2

277
KH-domain
KH domain
7.2e−13
56.2

278
GTP_CDC
Cell division protein
7.6e−119
408.2

280
abhydrolase_2
Phospholipase/Carboxylesterase
0.013
−41.9

282
PBP
Phosphatidylethanolamine-binding protein
7.8e−88
305.2

283
actin
Actin
1e−174
574.6

284
tubulin
Tubulin/FtsZ family
5e−99
342.4

285
LIM
LIM domain containing proteins
4.6e−36
132.3

286
mito_carr
Mitochondrial carrier proteins
1.4e−41
145.5

288
Ribosomal_L13
Ribosomal protein L13
4.1e−56
199.8

289
zf-C2H2
Zinc finger, C2H2 type
5.4e−268
903.7

291
ig
Immunoglobulin domain
0.053
11.5

292
Ribosomal_L14e
Ribosomal protein L14
3.4e−34
127.0

295
PH
PH domain
3.1e−20
77.3

296
Lysyl_hydro
Lysyl hydrolase
0
2058.2

299
efhand
EF hand
0.075
19.5

300
vwa
von Willebrand factor type A domain
2.8e−35
130.6

301
Ribosomal_L22
Ribosomal protein L22p/L17e
4e−67
236.4

302
homeobox
Homeobox domain
4e−34
126.8

309
IF3
Translation initiation factor IF-3
0.00048
15.1

310
filament
Intermediate filament proteins
9.2e−178
604.0

311
zf-C2H2
Zinc finger, C2H2 type
5.6e−143
488.4

312
Sm
Sm protein
5.6e−26
99.7

314
PDZ
PDZ domain (Also known as DHR or GLGF)
0.037
15.2

316
SH3
SH3 domain
3.6e−12
53.9

318
ig
Immunoglobulin domain
1.5e−12
45.5

319
ras
Ras family
5.1e−94
325.8

321
SAM
SAM domain (Sterile alpha motif)
9.9e−10
45.8

323
TPR
TPR Domain
1.1e−12
55.5

329
rrm
RNA recognition motif.
4.7e−09
43.5

332
ig
Immunoglobulin domain
1e−20
71.8

336
VPS9
Vacuolar sorting protein 9 (VPS9) domain
1.1e−30
115.4

338
ig
Immunoglobulin domain
0.0079
14.2

340
7tm_1
7 transmembrane receptor (rhodopsin family)
2.7e−20
66.6

342
Hydrolase
haloacid dehalogenase-like hydrolase
7.9e−28
105.9

343
zf-C2H2
Zinc finger. C2H2 type
5.1e−35
129.8

345
SH3
SH3 domain
2.2e−14
61.2

349
Ribosomal_L35Ae
Ribosomal protein L35Ae
6e−77
269.0

350
SET
SET domain
1.1e−56
201.7

358
Oxysterol_BP
Oxysterol-binding protein
3.4e−95
329.7

369
PCMT
Protein-L-isoaspartate(D-aspartate) O-methyl
5e−10
1.8

370
PH
PH domain
9.6e−05
22.0

371
bZIP
bZIP transcription factor
3.2e−07
30.8

373
GDI
GDP dissociation inhibitor
7.4e−25
64.8

374
zf-C2H2
Zinc finger, C2H2 type
7.1e−78
272.1

375
ubiquitin
Ubiquitin family
3.7e−61
193.6

377
efhand
EF hand
1.5e−37
138.2

381
Troponin
Troponin
4.7e−42
153.1

382
Troponin
Troponin
4.7e−42
153.1

383
Troponin
Troponin
4.7e−42
153.1

384
rrm
RNA recognition motif.
7.5e−51
182.4

387
UBX
UBX domain
1.5e−25
98.3

388
G-patch
G-patch domain
4.4e−10
46.9

391
pkinase
Eukaryotic protein kinase domain
1.2e−110
381.1

393
EGF
EGF-like domain
3.6e−82
286.4

394
EGF
EGF-like domain
3.6e−82
286.4

398
PGAM
Phosphoglycerate mutase family
6.1e−07
29.2

402
zf-C2H2
Zinc finger, C2H2 type
4e−24
93.6

403
pkinase
Eukaryotic protein kinase domain
1.1e−101
351.3

404
Ribosomal_S17
Ribosomal protein S17
6e−43
148.6

406
Acylphosphatase
Acylphosphatase
8.5e−64
225.4

407
TPR
TPR Domain
1.2e−14
62.1

414
adenylatekinase
Adenylate kinase
1.9e−119
410.3

415
FAT
FAT domain
9.3e−192
650.4

416
FAT
FAT domain
9.3e−192
650.4

418
MMR_HSR1
GTPase of unknown function
0.00015
−32.8

419
Ribosomal_L14e
Ribosomal protein L14
3.4e−34
127.0

421
zf-C2H2
Zinc finger, C2H2 type
5.2e−99
342.3

423
Peptidase_M16
Insulinase (Peptidase family M16)
4.3e−42
153.3

426
fibrinogen_C
Fibrinogen beta and gamma chains, C-term
2.4e−68
238.3

432
DNase_I
Deoxyribonuclease I (DNase I)
1.2e−171
583.6

433
IL8
Small cytokines (intecrine/chemokine), inter
2.3e−33
115.6

437
TPR
TPR Domain
4.4e−08
40.3

440
PDZ
PDZ domain (Also known as DHR or GLGF)
0.038
15.1

445
zf-C2H2
Zinc finger, C2H2 type
2.7e−22
87.5

446
zf-C2H2
Zinc finger, C2H2 type
4.1e−23
90.2

447
rrm
RNA recognition motif.
0.0029
24.3

449
ank
Ank repeat
4.1e−31
116.8

451
Cyt_reductase
FAD/NAD-binding Cytochrome reductase
7.7e−61
215.5

455
Ribosomal_L18p
Ribosomal L18p/L5e family
0.084
−34.1

456
tubulin
Tubulin/FtsZ family
3.4e−283
954.2

457
laminin_G
Laminin G domain
1.1e−51
185.1

458
ig
Immunoglobulin domain
2.7e−23
80.1

459
Peptidase_M1
Peptidase family M1
6.4e−184
533.4

462
pou
Pou domain - N-terminal to homeobox
1.3e−48
175.0

domain

466
TPR
TPR Domain
2.4e−30
114.2

469
Ribosomal_L11
Ribosomal protein L11
7.3e−53
189.0

470
Ribosomal_L11
Ribosomal protein L11
7e−40
145.9

473
ENV_polyprotein
ENV polyprotein (coat polyprotein)
1.5e−37
129.4

476
aconitase
Aconitase family (aconitate hydratase)
2e−189
621.7

477
globin
Globin
5.5e−44
157.8

480
lectin_c
Lectin C-type domain
1.5e−21
85.0

482
EGF
EGF-like domain
1e−22
88.9

487
PP2C
Protein phosphatase 2C
1.1e−13
51.7

489
ig
Immunoglobulin domain
1.8e−20
71.0

490
7tm_1
7 transmembrane receptor (rhodopsin family)
3.1e−13
44.2

[0449]

5

TABLE 5

SEQ ID
PDB
Chain

NO:
ID
ID
Start AA
End AA
PSI BLAST
Verify Score
PMF Score
SeqFold Score
Compound
PDB Annotation

252
1mkp

201
344
3e−40

205.21
PYST1; CHAIN: NULL;
HYDROLASE DUAL SPECIFICITY

PHOSPHATASE, MAP KINASE

HYDROLASE

262
1b2w
L
43
241
8.5e−66

67.25
ANTIBODY (LIGHT CHAIN);
IMMUNE SYSTEM

CHAIN: L; ANTIBODY (HEAVY
IMMUNOGLOBULIN;

CHAIN); CHAIN: H;
IMMUNOGLOBULIN ANTIBODY

ENGINEERING, HUMANIZED AND

CHIMERIC ANTIBODY, FAB, 2 X-RAY

STRUCTURE, THREE-DIMENSIONAL

STRYCTURE, GAMMA-3

INTERFERON, IMMUNE SYSTEM

262
1b6d
A
43
238
3.4e−65

68.72
IMMUNOGLOBULIN; CHAIN: A, B;
IMMUNOGLOBULIN

IMMUNOGLOBULIN, KAPPA LIGHT-

CHAIN DIMER HEADER

262
1bjl
L
43
240
6.8e−67

71.40
FAB FRAGMENT; CHAIN: L, H, J,
COMPLEX (ANTIBODY/ANTIGEN)

K; VASCULAR ENDOTHELIAL
FAB-12; VEGF; COMPLEX

GROWTH FACTOR; CHAIN: V, W;
(ANTIBODY/ANTIGEN), ANGIOGENIC

FACTOR

262
1bog
A
43
241
6.8e−61

67.70
ANTIBODY (CB 4-1); CHAIN: A, B;
COMPLEX (ANTIBODY/PEPTIDE)

PEPTIDE; CHAIN: C;
POLYSPECIFICITY, CROSS

REACTIVITY, FAB-FRAGMENT,

PEPTIDE, 2 HIV-1, COMPLEX

(ANTIBODY/PEPTIDE)

262
1bz7
A
43
232
8.5e−60

69.74
ANTIBODY R24 (LIGHT CHAIN);
IMMUNE SYSTEM ANTIBODY (FAB

CHAIN: A; ANTIBODY R24
FRAGMENT), IMMUNE SYSTEM

(HEAVY CHAIN); CHAIN: B;

262
1cel
L
43
238
5.1e−65

68.83
CAMPATH-1H: LIGHT CHAIN;
ANTIBODY THERAPEUTIC,

CHAIN: L; CAMPATH-1H: HEAVY
ANTIBODY, CD52

CHAIN; CHAIN: H; PEPTIDE

ANTIGEN; CHAIN: P;

262
1dfb
L
43
241
8.5e−66

69.59
IMMUNOGLOBULIN 3D6 FAB

1DFB 3

262
1fvd
A
43
241
6.8e−66

72.66
IMMUNOGLOBULIN FAB

FRAGMENT OF HUMANIZED

ANTIBODY 4D5, VERSION 4 1FVD 3

262
1gcl
L
43
238
1.2e−62

71.86
ENVELOPE PROTEIN GP120;
COMPLEX (HIV ENVELOPE

CHAIN: G; CD4; CHAIN: C;
PROTEIN/CD4/FAB) COMPLEX (HIV

ANTIBODY 17B; CHAIN: L, H;
ENVELOPE PROTEIN/CD4/FAB), HIV-1

EXTERIOR 2 ENVELOPE GPI20. T-

CELL SURFACE GLYCOPROTEIN

CD4. 3 ANTIGEN-BINDING

FRAGMENT OF HUMAN

IMMUNOGLOBULIN 17B, 4

GLYCOSYLATED PROTEIN

262
1itb
B
149
429
12e−22

67.34
INTERLEUKIN-I BETA; CHAIN: A;
COMPLEX

TYPE I INTERLEUKIN-I
(IMMUNOGLOBULIN/RECEPTOR)

RECEPTOR; CHAIN: B;
IMMUNOGLOBULIN FOLD,

TRANSMEMBRANE, GLYCOPROTEIN,

RECEPTOR, 2 SIGNAL, COMPLEX

(IMMUNOGLOBULIN/RECEPTOR)

262
1mco
H
29
427
3.4e−68

93.46
IMMUNOGLOBULIN

IMMUNOGLOBULIN G1 (IGGI)

(MCG) WITH A HINGE DELETION

IMCO 3

262
1osp
L
43
241
1.7e−59

69.80
FAB 184.1; CHAIN: L, H; OUTER
COMPLEX

SURFACE PROTEIN A; CHAIN: O;
(IMMUNOGLOBULIN/LIPOPROTEIN)

OSPA; COMPLEX

(IMMUNOGLOBULIN/LIPOPROTEIN),

OUTER SURFACE 2 PROTEIN A

COMPLEXED WITH FAB184.1,

BORRELIA BURGDORFERI 3 STRAIN

B31

262
1wio
A
49
408
9e−17

75.16
T-CELL SURFACE
GLYCOPROTEIN CD4;

GLYCOPROTEIN CD4; CHAIN: A,
IMMUNOGLOBULIN FOLD,

B;
TRANSMEMBRANE, GLYCOPROTEIN,

T-CELL, 2 MHC LIPOPROTEIN,

POLYMORPHISM

262
2fgw
L
43
241
1.2e−67

67.57
IMMUNOGLOBULIN FAB

FRAGMENT OF A HUMANIZED

VERSION OF THE ANTI-CD18

2FGW 3 ANTIBODY ‘H52’ (HUH52-

OZ FAB) 2FGW 4

262
6fab
L
43
241
5.1e−63

68.83
IMMUNOGLOBULIN ANTIGEN-

BINDING FRAGMENT OF THE

MURINE ANTI-

PHENYLARSONATE 6FAB 3

ANTIBODY 36-71, FAB 36-71 6FAB4

263
1mhu

32
62
1.4e−17

67.02
METALLOTHIONEIN CD-7

METALLOTHIONEIN-2 (ALPHA

DOMAIN) (/NMR$) 1MHUA 2

263
4mt2

1
62
1.7e−08

126.36
METALLOTHIONEIN

METALLOTHIONEIN ISOFORM II

4MT2 3

264
1ax4
A
190
616
5.1e−l0

76.11
TRYPTOPHANASE; CHAIN: A, B,
TRYPTOPHAN BIOSYNTHESIS

C, D;
TRYPTOPHAN INDOLE-LYASE;

TRYPTOPHAN BIOSYNTHESIS,

TRYPTOPHAN INDOLE-LYASE,

PYRIDOXAL 2 5′-PHOSPHATE,

MONOVALENT CATION BINDING

SITE

264
1bjw
A
212
590
5.1e−58

85.17
ASPARTATE
AMINOTRANSFERASE

AMINOTRANSFERASE; CHAIN: A,
AMINOTRANSFERASE, PYRIDOXAL

B;
ENZYME

264
1bs0
A
203
593
3.4e−72

224.70
8-AMINO-7-OXONANOATE
TRANSFERASE AONS, 8-AMINO-7-

SYNTHASE; CHAIN: A;
KETOPELARGONATE SYNTHASE;

PLP-DEPENDENT ACYL-COA

SYNTHASE, BIOTIN BIOSYNTHESIS,

8-2 AMINO-7-OXONANOATE

SYNTHASE, 8-AMINO-7-

KETOPELARGONATE 3 SYNTHASE,

TRANSFERASE

264
1csl
A
242
640
3.4e−45

79.69
CYSTATHIONINE GAMMA-
LYASE CGS; LYASE, LLP-

SYNTHASE; CHAIN: A, B, C, D;
DEPENDENT ENZYMES,

METHIONINE BIOSYNTHESIS

264
1d7u
A
213
597
1.7e−46

78.45
2,2-DIALKYLGLYCINE
LYASE DGD; ENZYME COMPLEXES,

DECARBOXYLASE (PYRUVATE);
CATALYTIC MECHANISM,

CHAIN: A;
DECARBOXYLATION 2 INHIBITOR,

LYASE

264
1qgn
A
215
635
6e−67

88.98
CYSTATHIONINE GAMMA-
LYASE METHIONINE BIOSYNTHESIS,

SYNTHASE; CHAIN: A, B, C, D, E,
PYRIDOXAL 5′-PHOSPHATE,

F, G, H;
GAMMA-2 FAMILY, LYASE

264
1tpl
A
209
612
5.1e−06

86.06
LYASE(CARBON-CARBON)

TYROSINE PHENOL-LYASE

(E.C.4.1.99.2) ITPL 3

264
2gsa
A
170
593
1.4e−72

95.88
GLUTAMATE SEMIALDEHYDE
CHLOROPHYLL BIOSYNTHESIS

AMINOTRANSFERASE; CHAIN: A,
GLUTAMATE SEMIALDEHYDE

B;
AMINOMUTASE; CHLOROPHYLL

BIOSYNTHESIS, PYRIDOXAL-5′-

PHOSPHATE, 2 PYRIDOXAMINE-5′-

PHOSPHATE, ASYMMETRIC DIMER

266
1sur

226
454
3e−31

66.05
PAPS REDUCTASE; CHAIN: NULL;
OXIDOREDUCTASE

PHOSPHOADENOSINE

PHOSPHOSULFATE REDUCTASE;

ASSIMILATORY SULFATE

REDUCTION, 3-PHOSPHO-

ADENYLYL-SULFATE 2 REDUCTASE,

OXIDOREDUCTASE

271
1gri
A
7
231
5.1e−22

57.45
GROWTH FACTOR BOUND
SIGNAL TRANSDUCTION ADAPTOR

PROTEIN 2; 1GRI 5 CHAIN: A, B;
SH2, SH3 1GRI 14

IGRI 6

272
1gri
A
7
231
5.1e−22

57.45
GROWTH FACTOR BOUND
SIGNAL TRANSDUCTION ADAPTOR

PROTEIN 2; 1GRI 5 CHAIN: A, B;
SH2, SH3 1GRI 14

IGRI 6

273
1be3
H
22
85
7.5e−26

95.55
CYTOCHROME BCI COMPLEX;
ELECTRON TRANSPORT UBIQUINOL

CHAIN: A, B, C, D, E, F, G, H, I, J, K;
CYTOCHROMEC

OXIDOREDUCTASE, COMPLEX

ELECTRON TRANSPORT,

CYTOCHROME, MEMBRANE

PROTEIN

276
1dt4
A
258
304
1.5e−09
−0.52
0.07

NEURO-ONCOLOGICAL
IMMUNE SYSTEM KH DOMAIN,

VENTRAL ANTIGEN I; CHAIN: A;
ALPHA-BETA FOLD, RNA-BINDING

MOTIF

276
1dtj
C
258
298
3e−06
−0.27
0.75

RNA-BINDING
IMMUNE SYSTEM KH DOMAIN,

NEUROONCOLOGICAL VENTRAL
ALPHA-BETA FOLD RNA-BINDING

ANTIGEN 2; CHAIN: A, B, C, D;
MOTIF

276
1dtj
D
258
298
3e−06
−0.30
0.93

RNA-BINDING
IMMUNE SYSTEM KH DOMAIN,

NEUROONCOLOGICAL VENTRAL,
ALPHA-BETA FOLD RNA-BINDING

ANTIGEN 2; CHAIN: A, B, C, D;
MOTIF

276
1vig

258
296
1.3e−06
−0.20
0.82

VIGILIN; 1VIG 5 CHAIN: NULL;
RIBONUCLEOPROTEIN RNA-

1VIG 6
BINDING PROTEIN 1VIG 19

276
2fmr

188
252
3.4e−31
0.53
1.00

FMR1 PROTEIN; CHAIN: NULL;
RNA-BINDING PROTEIN KH1; FMR1,

FRAGILE X, MODULAR PROTEINS,

RNA-BINDING PROTEIN, NMR

276
2fmr

188
252
6e−32
0.53
1.00

FMR1 PROTEIN; CHAIN: NULL;
RNA-BINDlNG PROTEIN KH1; FMR1,

FRAGILE X, MODULAR PROTEINS,

RNA-BINDING PROTEIN, NMR

276
2fmr

188
252
6e−32

96.30
FMR1 PROTEIN; CHAIN: NULL;
RNA-BINDING PROTEIN KH1; FMR1,

FRAGILE X, MODULAR PROTEINS,

RNA-BINDING PROTEIN, NMR

276
1dt4
A
258
304
1.5e−09
−0.52
0.07

NEURO-ONCOLOGICAL
IMMUNE SYSTEM KH DOMAIN,

VENTRAL ANTIGEN I; CHAIN: A;
ALPHA-BETA FOLD, RNA-BINDING

MOTIF

276
1dtj
C
258
298
3e−06
−0.27
0.75

RNA-BINDING
IMMUNE SYSTEM KH DOMAIN,

NEUROONCOLOGICAL VENTRAL
ALPHA-BETA FOLD RNA-BINDING

ANTIGEN 2; CHAIN: A, B, C, D;
MOTIF

276
1dtj
D
258
298
3e−06
−0.30
0.93

RNA-BINDING
IMMUNE SYSTEM KH DOMAIN,

NEUROONCOLOGICAL VENTRAL
ALPHA-BETA FOLD RNA-BINDING

ANTIGEN 2; CHAIN: A, B, C, D;
MOTIF

276
1vig

258
296
1.3e−06
−0.20
0.82

VIGILIN; IVIG 5 CHAIN: NULL;
RIBONUCLEOPROTEIN RNA-

IVIG 6
BINDING PROTEIN IVIG 19

276
2fmr

188
252
6e−32
0.53
1.00

FMR1 PROTEIN; CHAIN: NULL;
RNA-BINDING PROTEIN KH1; FMR1,

FRAGILE X, MODULAR PROTEINS,

RNA-BINDING PROTEIN, NMR

276
2fmr

188
252
6e−32

96.99
FMR1 PROTEIN; CHAIN: NULL;
RNA-BINDING PROTEIN KH1; FMR1,

FRAGILE X, MODULAR PROTEINS,

RNA-BINDING PROTEIN, NMR

276
2fmr

188
252
8.5e−32
0.53
1.00

FMR1 PROTEIN; CHAIN: NULL;
RNA-BINDING PROTEIN KH1; FMR1,

FRAGILE X, MODULAR PROTEINS,

RNA-BINDING PROTEIN, NMR

277
1dt4
A
258
304
1.5e−09
−0.52
0.07

NEURO-ONCOLOGICAL
IMMUNE SYSTEM KH DOMAIN,

VENTRAL ANTIGEN 1; CHAIN: A;
ALPHA-BETA FOLD, RNA-BINDING

MOTIF

277
1dtj
C
258
298
3e−06
−0.27
0.75

RNA-BINDING
IMMUNE SYSTEM KH DOMAIN,

NEUROONCOLOGICAL VENTRAL
ALPHA-BETA FOLD RNA-BINDING

ANTIGEN 2; CHAIN: A, B, C, D;
MOTIF

277
1dtj
D
258
298
3e−06
−0.30
0.93

RNA-BINDING
IMMUNE SYSTEM KH DOMAIN,

NEUROONCOLOGICAL VENTRAL
ALPHA-BETA FOLD RNA-BINDING

ANTIGEN 2; CHAIN: A, B, C, D;
MOTIF

277
1vig

258
296
1.3e−06
−0.20
0.82

VIGILIN; IVIG 5 CHAIN: NULL;
RIBONUCLEOPROTEIN RNA-

IVIG 6
BINDING PROTEIN IVIG 19

277
2fmr

188
252
3.4e−31
0.53
1.00

FMR1 PROTEIN; CHAIN: NULL;
RNA-BINDING PROTEIN KH1; FMR1,

FRAGILE X, MODULAR PROTEINS,

RNA-BINDING PROTEIN, NMR

277
2fmr

188
252
6e−32
0.53
1.00

FMR1 PROTEIN; CHAIN: NULL;
RNA-BINDING PROTEIN KH1; FMR1,

FRAGILE X, MODULAR PROTEINS,

RNA-BINDING PROTEIN, NMR

277
2fmr

188
252
6e−32

96.30
FMR1 PROTEIN; CHAIN: NULL;
RNA-BINDING PROTEIN KH1; FMR1,

FRAGILE X, MODULAR PROTEINS,

RNA-BINDING PROTEIN, NMR

277
1dt4
A
258
304
1.5e−09
−0.52
0.07

NEURO-ONCOLOGICAL
IMMUNE SYSTEM KH DOMAIN,

VENTRAL ANTIGEN I; CHAIN: A;
ALPHA-BETA FOLD, RNA-BINDING

MOTIF

277
1dtj
C
258
298
3e−06
−0.27
0.75

RNA-BINDING
IMMUNE SYSTEM KH DOMAIN,

NEUROONCOLOGICAL VENTRAL
ALPHA-BETA FOLD RNA-BINDING

ANTIGEN 2; CHAIN: A, B, C, D;
MOTIF

277
1dtj
D
258
298
3e−06
−0.30
0.93

RNA-BINDING
IMMUNE SYSTEM KH DOMAIN,

NEUROONCOLOGICAL VENTRAL
ALPHA-BETA FOLD RNA-BINDING

ANTIGEN 2; CHAIN: A, B, C, D;
MOTIF

277
1vig

258
296
1.3e−06
−0.20
0.82

VIGILIN; IVIG 5 CHAIN: NULL;
RIBONUCLEOPROTEIN RNA-

IVIG 6
BINDING PROTEIN IVIG 19

277
2fmr

188
252
6e−32
0.53
1.00

FMR1 PROTEIN; CHAIN: NULL;
RNA-BINDING PROTEIN KH1; FMR1,

FRAGILE X, MODULAR PROTEINS,

RNA-BINDING PROTEIN, NMR

277
2fmr

188
252
6e−32

96.99
FMR1 PROTEIN; CHAIN: NULL;
RNA-BINDING PROTEIN KH1; EMRI,

FRAGILE X, MODULAR PROTEINS,

RNA-BINDING PROTEIN, NMR

277
2fmr

188
252
8.5e−32
0.53
1.00

FMR1 PROTEIN; CHAIN: NULL;
RNA-BINDING PROTEIN KH1; FMR1,

FRAGILE X, MODULAR PROTEINS,

RNA-BINDING PROTEIN, NMR

278
1zbd
A
35
239
6.8e−56
−0.01
0.01

RAB-3A; CHAIN: A; RABPHILIN-
COMPLEX (GTP-BINDING/EFFECTOR)

3A; CHAIN: B;
RAS-RELATED PROTEIN RAB3A;

COMPLEX (GTP-

BINDING/EFFECTOR), G PROTEIN,

EFFECTOR, RABCDR, 2 SYNAPTIC

EXOCYTOSIS, RAB PROTEIN, RAB3A,

RARPHILIN

278
3rab
A
37
236
3.4e−56
0.14
−0.07

RAB3A; CHAIN: A;
HYDROLASE G PROTEIN,

VESICULAR TRAFFICKING, GTP

HYDROLYSIS, RAB 2 PROTEIN,

NEUROTRANSMITTER RELEASE,

HYDROLASE

280
1a88
A
225
450
5.1e−20
−0.05
0.03

CHLOROPEROXIDASEL; CHAIN:
HALOPEROXIDASE

A, B, C;
BROMOPEROXIDASE L,

HALOPEROXIDASE L;

HALOPEROXIDASE,

OXIDOREDUCTASE

280
1azw
A
225
449
1e−21
0.15
−0.13

PROLINE IMINOPEPTIDASE;
AMINOPEPTIDASE

CHAIN: A, B;
AMINOPEPTIDASE, PROLINE

IMINOPEPTIDASE, SERINE

PROTEASE, 2 XANTHOMONAS

CAMPESTRIS

280
1brt

239
451
1.7e−20
0.07
0.22

BROMOPEROXIDASE, A2: CHAIN:
HALOPEROXIDASE

NULL;
HALOPEROXIDASE A2,

CHLOROPEROXIDASE A2;

HALOPEROXIDASE,

OXIDOREDUCTASE, PEROXIDASE,

ALPHA/BETA 2 HYDROLASE FOLD,

MUTANT M99T

280
1cqw
A
233
378
5.1e−21
0.22
−0.18

HALOALKANE DEHALOGENASE;
HYDROLASE A/B HYDROLASE FOLD,

I-CHLOROHEXANE CHAIN: A;
DEHALOGENASE I-S BOND

280
1chy
A
235
447
1.7e−21
0.07
−0.17

SOLUBLE EPOXIDE HYDROLASE;
HYDROLASE HYDROLASE,

CHAIN: A, B, C, D;
ALPHA/BETA HYDROLASE FOLD,

EPOXIDE DEGRADATION, 2

EPICHLOROHYDRIN

280
1ekl
B
220
394
1.7e−22
0.07
−0.08

EPOXIDE HYDROLASE; CHAIN: A,
HYDROLASE HOMODIMER,

B;
ALPHA/BETA HYDROLASE FOLD,

DISUBSTITUTED UREA 2 INHIBITOR

280
1evq
A
232
438
1.7e−20
0.34
0.24

SERINE HYDROLASE; CHAIN: A;
HYDROLASE ALPHA/BETA

HYDROLASE FOLD

280
1qfm
A
157
453
8.5e−33
−0.05
0.01

PROLYL OLIGOPEPTIDASE;
HYDROLASE PROLYL

CHAIN: A;
ENDOPEPTIDASE, POST-PROLINE

CLEAVING PROLYL

OLIGOPEPTIDASE, AMNESIA,

ALPHA/BETA-HYDROLASE, BETA-2

PROPELLER

281
1fxx
A
134
302
6.8e−27
−0.08
0.23

EXONUCLEASE I; CHAIN: A;
HYDROLASE

EXODEOXYRIBONUCLEASE I;

ALPHA-BETA DOMAIN, SH3-LIKE

DOMAIN, DNAQ SUPERFAMILY

282
1a44

48
232
3e−83
1.02
1.00

PHOSPHATIDYLETHANOLAMINE-
LIPID-BINDING PROTEIN PEBP.PBP

BINDING PROTEIN; CHAIN:
LIPID-BINDING

NULL;

282
1a44

48
232
3e−83

317.69
PHOSPHATIDYLETHANOLAMINE-
LIPID-BINDING PROTEIN PEBP, PBP

BINDING PROTEIN; CHAIN:
LIPID-BINDING

NULL;

282
1a44

48
232
6.8e−80
1.02
1.00

PHOSPHATIDYLETHANOLAMINE-
LIPID-BINDING PROTEIN PEBP, PBP

BINDING PROTEIN; CHAIN:
LIPID-BINDING

NULL;

282
1beh
A
49
232
6e−82
1.05
1.00

PHOSPHATIDYLETHANOLAMINE
LIPID-BINDING LIPID-BINDING,

BINDING PROTEIN; CHAIN: A, B;
SIGNALLING

282
1beh
A
49
232
6e−82

324.00
PHOSPHATIDYLETHANOLAMINE
LIPID-BINDING LIPID-BINDING,

BINDING PROTEIN; CHAIN: A, B;
SIGNALLING

282
1beh
A
49
232
8.5e−80
1.05
1.00

PHOSPHATIDYLETHANOLAMINE
LIPID-BINDING LIPID-BINDING,

BINDING PROTEIN; CHAIN: A, B;
SIGNALLING

283
1dga
A
8
376
0
0.95
1.00

ACTIN; CHAIN: A; GELSOLIN;
CONTRACTILE PROTEIN ACTIN,

CHAIN: G;
GELSOLIN, CYTOSKELETON

ORGANIZATION, ACTIN-2

ASSOCIATED PROTEIN

283
1esv
A
10
376
0
0.87
1.00

GELSOLIN; CHAIN: S; ALPHA
CONTRACTILE PROTEIN

ACTIN; CHAIN: A
LATRUNCULIN A, GELSOLIN, ACTIN,

DEPOLYMERISATION, 2

SEQUESTRATION

283
1yag
A
8
376
0
0.99
1.00

ACTIN; CHAIN: A; GELSOLIN;
CONTRACTILE PROTEIN ACTIN-

CHAIN: G;
DEPOLYMERIZING FACTOR (ADF);

COMPLEX, ACTIN, GELSOLIN,

CONTRACTILE PROTEIN

283
1yag
A
8
376
0

413.68
ACTIN; CHAIN: A; GELSOLIN;
CONTRACTILE PROTEIN ACTIN-

CHAIN: G;
DEPOLYMERIZING FACTOR (ADF);

COMPLEX, ACTIN, GELSOLIN,

CONTRACTILE PROTEIN

283
2btf
A
7
376
0
0.91
1.00

ACETYLATION AND ACTIN-

BINDING BETA-ACTIN-PROFILIN

COMPLEX 2BTF 3

283
2btf
A
9
376
0

414.62
ACETYLATION AND ACTIN-

BINDING BETA-ACTIN-PROFILIN

COMPLEX 2BTF 3

284
1tub
A
1
461
0

285.64
TUBULIN; CHAIN: A, B;
MICROTUBULES MICROTUBULES,

ALPHA-TUBULIN, BETA-TUBULIN,

GTPASE HELIX

284
1tub
A
1
462
0
0.09
1.00

TUBULIN; CHAIN: A, B;
MICROTUBULES MICROTUBULES,

ALPHA-TUBULIN, BETA-TUBULIN,

GTPASE HELIX

284
1tub
B
1
459
0
0.11
1.00

TUBULIN; CHAIN: A, B;
MICROTUBULES MICROTUBULES,

ALPHA-TUBULIN, BETA-TUBULIN,

GTPASE HELIX

284
1tub
B
1
459
0

307.13
TUBULIN; CHAIN: A, B;
MICROTUBULES MICROTUBULES,

ALPHA-TUBULIN, BETA-TUBULIN,

GTPASE HELIX

285
1a7i

384
437
3e−14
0.43
0.58

QCRP2 (LIM1); CHAIN: NULL;
LIM DOMAIN CONTAINING

PROTEINS LIM DOMAIN

CONTAINING PROTEINS, METAL-

BINDING PROTEIN, ZINC 2 FINGER

285
1a7i

384
441
6.8e−10
0.31
0.80

QCRP2 (LIM1); CHAIN: NULL;
LIM DOMAIN CONTAINING

PROTEINS LIM DOMAIN

CONTAINING PROTEINS, METAL-

BINDING PROTEIN, ZINC 2 FINGER

285
1a7i

443
500
1.5e−16
0.08
0.58

QCRP2 (LIM1); CHAIN: NULL;
LIM DOMAIN CONTAINING

PROTEINS LIM DOMAIN

CONTAINING PROTEINS, METAL-

BINDING PROTEIN, ZINC 2 FINGER

285
1a7i

443
501
1.4e−12
−0.13
0.82

QCRP2 (LIM1); CHAIN: NULL;
LIM DOMAIN CONTAINING

PROTEINS LIM DOMAIN

CONTAINING PROTEINS, METAL-

BINDING PROTEIN, ZINC 2 FINGER

285
1a7i

504
566
4.5e−11
−0.40
0.24

QCRP2 (LIM1); CHAIN: NULL;
LIM DOMAIN CONTAINING

PROTEINS LIM DOMAIN

CONTAINING PROTEINS, METAL-

BINDING PROTEIN, ZINC 2 FINGER

285
1a7i

504
571
1.2e−09
0.38
0.76

QCRP2 (LIM1); CHAIN: NULL;
LIM DOMAIN CONTAINING

PROTEINS LIM DOMAIN

CONTAINING PROTEINS, METAL-

BINDING PROTEIN, ZINC 2 FINGER

285
1b8t
A
375
572
1.4e−23

71.26
CRP1; CHAIN: A;
CONTRACTILE LIM DOMAIN, CRP,

NMR, MUSCLE DIFFERENTIATION,

CONTRACTILE

285
1b8t
A
379
510
1.4e−23
0.01
−0.17

CRP1; CHAIN: A;
CONTRACTILE LIM DOMAIN, CRP,

NMR, MUSCLE DIFFERENTIATION,

CONTRACTILE

285
1ctl

376
437
1.7e−12
−0.22
0.10

AVIAN CYSTEINE RICH PROTEIN;
METAL-BINDING PROTEIN LIM

1CTL 3
DOMAIN CONTAINING PROTEINS

1CTL 15

285
1ctl

444
510
3.4e−15
−0.26
0.05

AVIAN CYSTEINE RICH PROTEIN;
METAL-BINDING PROTEIN LIM

1CTL 3
DOMAIN CONTAINING PROTEINS

1CTL 15

285
1ctl

504
571
5.1e−13
0.03
0.22

AVIAN CYSTEINE RICH PROTEIN;
METAL-BINDING PROTEIN LIM

1CTL 3
DOMAIN CONTAINING PROTEINS

1CTL 15

285
1cxx
A
381
437
1.7e−11
−0.17
0.41

CYSTEINE AND GLYCINE-RICH
SIGNALING PROTEIN LIM DOMAIN

PROTEIN CRP2; CHAIN: A;
CONTAINING PROTEINS, METAL-

BINDING PROTEIN

285
1cxx
A
443
496
5.1e−13
0.38
0.53

CYSTEINE AND GLYCINE-RICH
SIGNALING PROTEIN LIM DOMAIN

PROTEIN CRP2; CHAIN: A;
CONTAINING PROTEINS, METAL-

BINDING PROTEIN

285
1cxx
A
501
568
3.4e−12
0.41
0.87

CYSTEINE AND GLYCINE-RICH
SIGNALING PROTEIN LIM DOMAIN

PROTEIN CRP2; CHAIN: A;
CONTAINING PROTEINS, METAL-

BINDING PROTEIN

285
1iml

382
440
1.4e−10
−0.25
0.41

CYSTEINE RICH INTESTINAL
METAL-BINDING PROTEIN CRIP;

PROTEIN; CHAIN: NULL;
METAL-BINDING PROTEIN, LIM

DOMAIN PROTEIN

285
1iml

384
451
4.5e−17
0.21
0.22

CYSTEINE RICH INTESTINAL
METAL-BINDING PROTEIN CRIP;

PROTEIN; CHAIN: NULL;
METAL-BINDING PROTEIN, LIM

DOMAIN PROTEIN

285
1iml

443
510
1.4e−15
−0.13
0.09

CYSTEINE RICH INTESTINAL
METAL-BINDING PROTEIN CRIP;

PROTEIN; CHAIN: NULL;
METAL-BINDING PROTEIN, LIM

DOMAIN PROTEIN

285
1iml

443
513
3e−20
0.13
0.12

CYSTEINE RICH INTESTINAL
METAL-BINDING PROTEIN CRIP;

PROTEIN; CHAIN: NULL;
METAL-BINDING PROTEIN, LIM

DOMAIN PROTEIN

285
1iml

502
569
1.5e−12
0.32
0.93

CYSTEINE RICH INTESTINAL
METAL-BINDING PROTEIN CRIP;

PROTEIN; CHAIN: NULL;
METAL-BINDING PROTEIN, LIM

DOMAIN PROTEIN

285
1iml

502
571
3.4e−11
0.28
0.99

CYSTEINE RICH INTESTINAL
METAL-BINDING PROTEIN CRIP;

PROTEIN; CHAIN: NULL;
METAL-BINDING PROTEIN, LIM

DOMAIN PROTEIN

285
1zfo

381
410
1.4e−06
−0.13
0.29

LASP-1; CHAIN: NULL;
METAL-BINDING PROTEIN LIM

DOMAIN, ZINC-FINGER, METAL-

BINDING PROTEIN

285
1zfo

502
535
0.0012
−0.34
0.15

LASP-1; CHAIN: NULL;
METAL-BINDING PROTEIN LIM

DOMAIN, ZINC-FINGER, METAL-

BINDING PROTEIN

288
1ffk
G
5
114
9e−49
−0.14
1.00

23S RRNA; CHAIN: 0; 5S RRNA;
RIBOSOME 50S RIBOSOMAL

CHAIN: 9; RIBOSOMAL PROTEIN
PROTEIN L2P, HMAL2, HL4; 50S

L2; CHAIN: A; RIBOSOMAL
RIBOSOMAL PROTEIN L3P, HMAL3,

PROTEIN L3; CHAIN: B;
HL1; 50S RIBOSOMAL PROTEIN L4E,

RIBOSOMAL PROTEIN L4; CHAIN:
HMAL4, HL6; 50S RIBOSOMAL

C; RIBOSOMAL PROTEIN L5;
PROTEIN L5P, HMAL5, HL13; 30S

CHAIN: D; RIBOSOMAL PROTEIN
RIBOSOMAL PROTEIN HS6; 50S

L7AE; CHAIN: E; RIBOSOMAL
RIBOSOMAL PROTEIN L13P, HMAL13;

PROTEIN L10E; CHAIN: F;
50S RIBOSOMAL PROTEIN L14P,

RIBOSOMAL PROTEIN L13;
HMAL14, HL27; 50S RIBOSOMAL

CHAIN: G; RIBOSOMAL PROTEIN
PROTEIN L15P, HMAL15, HL9; 50S

L14; CHAIN: H; RIBOSOMAL
RIBOSOMAL PROTEIN L18P, HMAL18,

PROTEIN L15E; CHAIN: I;
HL12; 50S RIBOSOMAL PROTEIN

RIBOSOMAL PROTEIN L15;
L18E, HL29, L19; 50S RIBOSOMAL

CHAIN: J; RIBOSOMAL PROTEIN
PROTEIN L19E, HMAL19, HL24; 50S

L18; CHAIN: K; RIBOSOMAL
RIBOSOMAL PROTEIN L21E, HL31;

PROTEIN L18E; CHAIN: L;
50S RIBOSOMAL PROTEIN L22P,

RIBOSOMAL PROTEIN L19;
HMAL22, HL23; 50S RIBOSOMAL

CHAIN: M; RIBOSOMAL PROTEIN
PROTEIN L23P, HMAL23, HL25, L21;

L21E; CHAIN: N; RIBOSOMAL
50S RIBOSOMAL PROTEIN L24P,

PROTEIN L22; CHAIN: O;
HMAL24, HL16, HL15; 50S

RIBOSOMAL PROTEIN L23;
RIBOSOMAL PROTEIN L24E,

CHAIN: P; RIBOSOMAL PROTEIN
HL21/HL22; 50S RIBOSOMAL

L24; CHAIN: Q; RIBOSOMAL
PROTEIN L29P, HMAL29, HL33; 50S

PROTEIN L24E; CHAIN: R;
RIBOSOMAL PROTEIN L30P, HMAL30,

RIBOSOMAL PROTEIN L29;
HL20, HL16; 50S RIBOSOMAL

CHAIN: S; RIBOSOMAL PROTEIN
PROTEIN L31E, L34, HL30; 50S

L30; CHAIN: T; RIBOSOMAL
RIBOSOMAL PROTEIN L32E, HL5; 50S

PROTEIN L31E; CHAIN: U;
RIBOSOMAL PROTEIN L37E, L35E;

RIBOSOMAL PROTEIN L32E;
50S RIBOSOMAL PROTEINS L39E,

CHAIN: V; RIBOSOMAL PROTEIN
HL39E, HL46E; 50S RIBOSOMAL

L37AE; CHAIN: W; RIBOSOMAL
PROTEIN L44E, LA, HLA; 50S

PROTEIN L37E; CHAIN: X;
RIBOSOMAL PROTEIN L6P, HMAL6,

RIBOSOMAL PROTEIN L39E;
HL10 RIBOSOME ASSEMBLY, RNA-

CHAIN: Y; RIBOSOMAL PROTEIN
RNA, PROTEIN-RNA, PROTEIN-

L44E; CHAIN: Z; RIBOSOMAL
PROTEIN

PROTEIN L6; CHAIN: 1;

288
1ffk
G
7
135
5.1e−32
0.18
1.00

23S RRNA; CHAIN: 0; 5S RRNA;
RIBOSOME 50S RIBOSOMAL

CHAIN: 9; RIBOSOMAL PROTEIN
PROTEIN L2P, HMAL2, HL4; 50S

L2; CHAIN: A; RIBOSOMAL
RIBOSOMAL PROTEIN L3P, HMAL3,

PROTEIN L3; CHAIN: B;
HL1; 50S RIBOSOMAL PROTEIN L4E,

RIBOSOMAL PROTEIN L4; CHAIN:
HMAL4, HL6; 50S RIBOSOMAL

C; RIBOSOMAL PROTEIN L5;
PROTEIN L5P, HMAL5, HL13; 30S

CHAIN: D; RIBOSOMAL PROTEIN
RIBOSOMAL PROTEIN HS6; 50S

L7AE; CHAIN: E; RIBOSOMAL
RIBOSOMAL PROTEIN L13P, HMAL13;

PROTEIN L10E; CHAIN: F;
50S RIBOSOMAL PROTEIN L14P,

RIBOSOMAL PROTEIN L13;
HMAL14, HL27; 50S RIBOSOMAL

CHAIN: G; RIBOSOMAL PROTEIN
PROTEIN L15P, HMAL15, HL9; 50S

L14; CHAIN: H; RIBOSOMAL
RIBOSOMAL PROTEIN L18P, HMAL18,

PROTEIN L15E; CHAIN: I;
HL12; 50S RIBOSOMAL PROTEIN

RIBOSOMAL PROTEIN L15;
L18E, HL29, L19; 50S RIBOSOMAL

CHAIN: J; RIBOSOMAL PROTEIN
PROTEIN L19E, HMAL19, HL24; 50S

L18; CHAIN: K; RIBOSOMAL
RIBOSOMAL PROTEIN L21E, HL31;

PROTEIN L18E; CHAIN: L;
50S RIBOSOMAL PROTEIN L22P,

RIBOSOMAL PROTEIN L19;
HMAL22, HL23; 50S RIBOSOMAL

CHAIN: M; RIBOSOMAL PROTEIN
PROTEIN L23P, HMAL23, HL25, L21;

L21E; CHAIN: N; RIBOSOMAL
50S RIBOSOMAL PROTEIN L24P,

PROTEIN L22; CHAIN: O;
HMAL24, HL16, HL15; 50S

RIBOSOMAL PROTEIN L23;
RIBOSOMAL PROTEIN L24E,

CHAIN: P; RIBOSOMAL PROTEIN
HL21/HL22; 50S RIBOSOMAL

L24; CHAIN: Q; RIBOSOMAL
PROTEIN L29P, HMAL29, HL33; 50S

PROTEIN L24E; CHAIN: R;
RIBOSOMAL PROTEIN L30P, HMAL30,

RIBOSOMAL PROTEIN L29;
HL20, HL16; 50S RIBOSOMAL

CHAIN: S; RIBOSOMAL PROTEIN
PROTEIN L31E, L34, HL30; 50S

L30; CHAIN: T; RIBOSOMAL
RIBOSOMAL PROTEIN L32E, HL5; 50S

PROTEIN L31E; CHAIN: U;
RIBOSOMAL PROTEIN L37E, L35E;

RIBOSOMAL PROTEIN L32E;
50S RIBOSOMAL PROTEINS L39E,

CHAIN: V; RIBOSOMAL PROTEIN
HL39E, HL46E; 50S RIBOSOMAL

L37AE; CHAIN: W; RIBOSOMAL
PROTEIN L44E, LA, HLA; 50S

PROTEIN L37E; CHAIN: X;
RIBOSOMAL PROTEIN L6P, HMAL6,

RIBOSOMAL PROTEIN L39E;
HL10 RIBOSOME ASSEMBLY, RNA-

CHAIN: Y; RIBOSOMAL PROTEIN
RNA, PROTEIN-RNA, PROTEIN-

L44E; CHAIN: Z; RIBOSOMAL
PROTEIN

PROTEIN L6; CHAIN: I;

289
1alh
A
1023
1104
1.4e−40
0.06
0.98

QGSR ZINC FINGER PEPTIDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

289
1alh
A
1051
1132
9e−44
0.09
0.84

QGSR ZINC FINGER PEPTIDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

289
1alh
A
1611
1715
1.2e−39
0.04
0.46

QGSR ZINC FINGER PEPTIDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

289
1alh
A
1826
1906
1.7e−30
−0.47
0.45

QGSR ZINC FINGER PEPTIDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

289
1alh
A
1854
1934
6.8e−31
−0.10
0.05

QGSR ZINC FINGER PEPTIDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

289
1alh
A
559
639
5.1e−27
0.05
0.17

QGSR ZINC FINGER PEPTIDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

289
1alh
A
592
668
1.5e−29
0.15
0.11

QGSR ZINC FINGER PEPTIDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

289
1alh
A
911
992
6e−45
0.22
0.93

QGSR ZINC FINGER PEPTIDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

289
1alh
A
939
1020
3e−42
0.04
0.72

QGSR ZINC FINGER PEPTIDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

289
1alh
A
967
1047
4.5e−42
−0.00
0.78

QGSR ZINC FINGER PEPTIDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

289
1alh
A
995
1075
9e−42
0.21
1.00

QGSR ZINC FINGER PEPTIDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

289
1mey
C
1022
1103
1.4e−39
0.28
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1050
1131
1.7e−41
0.34
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1078
1159
1.7e−43
0.35
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1106
1187
3.4e−45
0.16
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1134
1215
6.8e−47
−0.08
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1162
1243
5.1e−48
0.45
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1190
1271
1.7e−48
0.44
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1218
1299
1.4e−49
0.22
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1246
1327
1.4e−49
0.05
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1274
1355
3.4e−50
0.29
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1302
1383
3.4e−49
0.04
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1330
1411
1e−47
0.24
0.99

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1358
1439
8.5e−47
0.50
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1386
1467
1.7e−47
0.31
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1414
1495
1.2e−48
0.50
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1414
1496
1.4e−49

103.44
DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1442
1523
1.4e−49
0.38
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1470
1551
1e−49
0.31
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1498
1579
1.7e−49
0.13
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1526
1607
3.4e−49
0.34
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1554
1635
1.7e−49
0.26
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1582
1663
1.7e−48
0.09
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1610
1686
1.7e−44
0.28
0.99

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1666
1742
8.5e−44
0.52
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1689
1770
5.1e−49
0.41
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1717
1798
1.4e−49
0.03
0.98

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1745
1822
3.4e−45
−0.22
0.12

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1825
1906
1e−49
−0.28
0.48

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1853
1934
1e−49
−0.20
0.78

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
1881
1938
1.7e−33
0.35
0.58

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
558
639
3.4e−44
−0.04
0.55

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
586
667
3.4e−46
−0.05
0.82

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
614
695
1.4e−47
0.23
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
642
723
8.5e−49
0.03
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
698
779
1e−49
0.11
0.98

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
726
807
6.8e−50
0.19
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
754
835
6.8e−50
0.05
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
782
863
1e−49
0.34
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
810
891
3.4e−49
0.32
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
838
935
3.4e−44
0.04
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
866
963
8.5e−41
0.03
0.98

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
910
991
3.4e−42
0.16
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
C
994
1075
1.4e−39
0.59
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1mey
G
908
935
1.5e−10
0.46
0.94

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

289
1tf6
A
1051
1196
1.2e−33
0.18
0.86

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

289
1tf6
A
1106
1272
1.7e−36

113.59
TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

289
1tf6
A
1163
1308
1.7e−36
−0.10
0.86

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

289
1tf6
A
1275
1420
6.8e−37
0.07
0.99

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

289
1tf6
A
1387
1532
1.4e−36
0.39
0.90

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

289
1tf6
A
1443
1588
3.4e−37
0.20
0.76

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

289
1tf6
A
1555
1695
1.2e−33
−0.13
0.64

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

289
1tf6
A
1667
1808
1e−33
−0.29
0.25

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

289
1tf6
A
532
676
1.7e−30
0.04
0.17

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

289
1tf6
A
643
788
3.4e−36
0.06
0.95

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

289
1tf6
A
699
849
6.8e−38
−0.10
0.94

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

289
1tf6
A
811
951
3.4e−30
0.05
0.87

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

289
1tf6
A
867
1033
6.8e−31
−0.12
0.42

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

289
1ubd
C
1020
1131
1.5e−54
0.04
0.94

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
1077
1187
1e−55
0.05
0.94

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
1104
1244
3e−53
−0.46
0.93

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
1160
1271
1.5e−52
0.00
0.72

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
1198
1299
3.4e−34
0.18
0.58

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
1216
1327
6e−52
0.06
0.89

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
1226
1327
1.4e−34
0.30
0.98

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENI, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
1245
1356
1.2e−52
0.33
0.99

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
1272
1383
7.5e−50
0.01
0.78

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
1328
1439
3e−50
0.26
0.86

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
1384
1496
4.5e−52
0.11
0.93

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
1469
1579
4.5e−55
0.03
1.00

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
1506
1607
3.4e−34
0.09
1.00

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
1524
1635
4.5e−49
−0.29
0.99

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
1562
1663
1e−32
0.04
0.94

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
1608
1714
6e−52
0.12
0.31

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
1618
1714
3.4e−30
−0.01
0.49

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
1636
1742
7.5e−51
−0.22
0.83

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
1674
1770
6.8e−32
−0.19
0.90

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
1725
1822
1.7e−30
−0.13
0.12

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
540
639
6.8e−29
−0.21
0.06

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
561
667
1.5e−31
0.20
0.41

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
584
695
3e−42
−0.19
0.86

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
589
695
3.4e−32
−0.17
0.86

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
619
724
1.5e−47
0.04
0.51

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
640
752
1.2e−52
−0.15
0.77

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
650
751
1.2e−33
−0.06
0.92

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
668
779
7.5e−51
0.01
0.57

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
725
835
7.5e−53
−0.06
0.93

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
734
835
1e−33
0.22
0.93

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
790
891
8.5e−33
0.26
0.87

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
808
935
9e−53
0.00
0.95

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
818
935
1.2e−31
−0.14
0.92

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
864
991
9e−53
0.04
0.83

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
874
991
1.5e−27
−0.28
0.66

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
1ubd
C
964
1076
3e−53
0.10
0.99

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

289
2gli
A
1022
1188
3e−72
−0.09
0.96

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

289
2gli
A
1106
1273
7.5e−71
0.05
0.89

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

289
2gli
A
1190
1329
1.3e−67
0.30
1.00

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

289
2gli
A
1254
1382
5.1e−34
0.12
0.98

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

289
2gli
A
1302
1469
4.5e−67
0.04
0.86

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAlN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

289
2gli
A
1386
1525
4.5e−67
0.19
1.00

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

289
2gli
A
1414
1580
6e−71
−0.20
0.92

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FlNGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

289
2gli
A
1498
1716
1.5e−66
−0.17
0.16

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

289
2gli
A
1534
1662
1.7e−32
0.03
0.63

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

289
2gli
A
1554
1744
4.5e−67
−0.17
0.59

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

289
2gli
A
1590
1713
1.7e−30
−0.13
0.78

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

289
2gli
A
1638
1768
4.5e−65
0.18
0.86

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

289
2gli
A
1646
1797
8.5e−33
0.00
0.62

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

289
2gli
A
558
694
3.4e−33
−0.28
0.62

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

289
2gli
A
587
725
1.5e−53
−0.31
0.19

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

289
2gli
A
614
781
1.5e−63
−0.20
0.49

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

289
2gli
A
622
753
1e−33
0.11
0.46

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

289
2gli
A
642
809
1.5e−68
0.01
0.96

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

289
2gli
A
670
837
3e−66
−0.19
0.84

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

289
2gli
A
726
893
6e−68
0.00
0.98

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

289
2gli
A
734
862
1.5e−33
0.06
0.82

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

289
2gli
A
790
934
1.7e−30
−0.04
0.40

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BlNDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

289
2gli
A
838
992
1.5e−69
−0.00
0.69

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

289
2gli
A
874
993
1.7e−26
−0.10
0.81

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

289
2gli
A
910
1077
4.5e−70
−0.01
0.96

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

289
2gli
A
938
1105
1.5e−69
0.03
0.87

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER (GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

291
1cic
B
20
66
1.5e−23
−0.58
0.06

IG HEAVY CHAIN V REGIONS;
IMMUNOGLOBULIN

CHAIN: A; IG HEAVY CHAIN V
IMMUNOGLOBULIN, FAB COMPLEX,

REGIONS; CHAIN: B; IG HEAVY
IDIOTOPE, ANTI-IDIOTOPE

CHAIN V REGIONS; CHAIN: C; IG

HEAVY CHAIN V REGIONS;

CHAIN: D;

291
1fsk
C
20
66
8.5e−22
−0.56
0.00

MAJOR POLLEN ALLERGEN BET
IMMUNE SYSTEM BET V I-A, BETVI

V I-A; CHAIN: A, D, G, J;
ALLERGEN; BV16 FAB-FRAGMENT,

IMMUNOGLOBULIN KAPPA
KAPPA MOPC21 CODING SEQUENCE;

LIGHT CHAIN; CHAIN: B, E, H, K;
HEAVY CHAIN OF THE

ANTIBODY HEAVY CHAIN FAB;
MONOCLONAL ANTIBODY MST2;

CHAIN: C, F, I, L;
BET V I, BV16 FAB FRAGMENT,

ANTIBODY ALLERGEN COMPLEX

291
1jhl
11
20
66
6.8e−22
−0.72
0.09

COMPLEX(ANTIBODY-ANTIGEN)

FV FRAGMENT (IGG1, KAPPA)

(LIGHT AND HEAVY VARIABLE

DOMAINS 1JHL 3 NON-

COVALENTLY ASSOCIATED) OF

MONOCLONAL ANTI-HEN EGG

1JHL 4 LYSOZYME ANTIBODY

DI1.15 COMPLEX WITH

PHEASANT EGG 1JHL 5

LYSOZYME 1JHL 6

292
1vsg
A
123
181
0.00075
0.36
0.09

GLYCOPROTEIN VARIANT

SURFACE GLYCOPROTEIN (N-

TERMINAL DOMAIN) 1VSG 3

295
1btk
A
30
118
6e−09
0.21
0.07

BRUTON'S TYROSINE KINASE;
TRANSFERASE BRUTON'S

CHAIN: A, B;
AGAMMAGLOBULINEMIA

TYROSINE KINASE, BTK;

TRANSFERASE, PH DOMAIN, BTK

MOTIF, ZINC BINDING, X-LINKED 2

AGAMMAGLOBULINEMIA,

TYROSINE-PROTEIN KINASE

295
1btn

30
110
1.3e−08
0.20
0.25

BETA-SPECTRIN; 1BTN 4 CHAIN:
SIGNAL TRANSDUCTION PROTEIN

NULL; 1BTN 5

295
1tb8
A
22
114
1.5e−18
0.62
0.92

DUAL ADAPTOR OF
SIGNALING PROTEIN DAPPI, PHISH,

PHOSPHOTYROSINE AND 3-
BAM32; PLECKSTRIN, 3-

CHAIN: A;
PHOSPHOINOSITIDES, INOSITOL

TETRAKISPHOSPHATE 2 SIGNAL

TRANSDUCTION PROTEIN, ADAPTOR

PROTEIN

295
1fgy
A
9
115
1.5e−14
0.48
0.77

GRP1; CHAIN: A;
SIGNALING PROTEIN ARFI GUANINE

NUCLEOTIDE EXCHANGE FACTOR

AND PH DOMAIN

295
1pls

1
115
1.5e−14
0.69
0.95

PHOSPHORYLATION

PLECKSTRIN (N-TERMINAL

PLECKSTRIN HOMOLOGY

DOMAIN) MUTANT 1PLS 3 WITH

LEU GLU (HIS)6 ADDED TO THE C

TERMINUS 1PLS 4 (INS(G105-

LEHHHHHH)) (NMR, 25

STRUCTURES) 1PLS 5

295
1pms

33
114
1.5e−11
0.13
0.01

SOS 1; CHAIN: NULL;
SIGNAL TRANSDUCTION SON OF

SEVENLESS; PLECKSTRIN, SON OF

SEVENLESS, SIGNAL

TRANSDUCTION

295
1qqg
A
33
204
3e−18
0.20
−0.14

INSULIN RECEPTOR SUBSTRATE
SIGNAL TRANSDUCTION IRS-1;

1; CHAIN: A, B;
BETA-SANDWHICH, SIGNAL

TRANSDUCTION

296
1qgq
A
296
467
4.5e−05
−0.21
0.13

SPORE COAT POLYSACCHARIDE
TRANSFERASE

BIOSYNTHESIS PROTEIN CHAIN:
GLYCOSYLTRANSFERASE

A;

297
1erj
A
106
437
1.7e−59
0.03
0.34

TRANSCRIPTIONAL REPRESSOR
TRANSCRIPTION INHIBITOR BETA-

TUP1; CHAIN: A, B, C;
PROPELLER

297
1erj
A
183
481
5.1e−58
0.24
−0.09

TRANSCRIPTIONAL REPRESSOR
TRANSCRIPTION INHIBITOR BETA-

TUP1; CHAIN: A, B, C;
PROPELLER

297
1erj
A
5
251
1.7e−47
−0.04
0.34

TRANSCRIPTIONAL REPRESSOR
TRANSCRIPTION INHIBITOR BETA-

TUP1; CHAIN: A, B, C;
PROPELLER

297
1erj
A
54
352
6.8e−50
0.21
0.95

TRANSCRIPTIONAL REPRESSOR
TRANSCRIPTION INHIBITOR BETA-

TUP1; CHAIN: A, B, C;
PROPELLER

297
1got
B
170
479
3.4e−56
0.24
−0.14

GT-ALPHA/GI-ALPHA CHIMERA;
COMPLEX (GTP-

CHAIN: A; GT-BETA; CHAIN: B;
BINDING/TRANSDUCER) BETA1,

GT-GAMMA; CHAIN: G;
TRANSDUCIN BETA SUBUNIT;

GAMMA1, TRANSDUCIN GAMMA

SUBUNIT; COMPLEX (GTP-

BINDING/TRANSDUCER), G PROTEIN,

HETEROTRIMER 2 SIGNAL

TRANSDUCTION

297
1got
B
2
252
3.4e−39
−0.24
0.16

GT-ALPHA/GI-ALPHA CHIMERA;
COMPLEX (GTP-

CHAIN: A; GT-BETA; CHAIN: B;
BINDING/TRANSDUCER) BETA1,

GT-GAMMA; CHAIN: G;
TRANSDUCIN BETA SUBUNIT;

GAMMA1, TRANSDUCIN GAMMA

SUBUNIT; COMPLEX (GTP-

BINDING/TRANSDUCER), G PROTEIN,

HETEROTRIMER 2 SIGNAL

TRANSDUCTION

297
1got
B
31
297
3.4e−44
0.33
0.98

GT-ALPHA/GI-ALPHA CHIMERA;
COMPLEX (GTP-

CHAIN: A; GT-BETA; CHAIN: B;
BINDING/TRANSDUCER) BETA1,

GT-GAMMA; CHAIN: G;
TRANSDUCIN BETA SUBUNIT;

GAMMA1, TRANSDUCIN GAMMA

SUBUNIT; COMPLEX (GTP-

BINDING/TRANSDUCER), G PROTEIN,

HETEROTRIMER 2 SIGNAL

TRANSDUCTION

297
1got
B
35
369
3.4e−66

59.96
GT-ALPHA/GI-ALPHA CHIMERA;
COMPLEX (GTP-

CHAIN: A; GT-BETA; CHAIN: B;
BINDING/TRANSDUCER) BETA1,

GT-GAMMA; CHAIN: G;
TRANSDUCIN BETA SUBUNIT;

GAMMA1, TRANSDUCIN GAMMA

SUBUNIT; COMPLEX (GTP-

BINDING/TRANSDUCER), G PROTEIN,

HETEROTRIMER 2 SIGNAL

TRANSDUCTION

297
1got
B
52
349
8.5e−51
0.12
0.96

GT-ALPHA/GI-ALPHA CHIMERA;
COMPLEX (GTP-

CHAIN: A; GT-BETA; CHAIN: B;
BINDING/TRANSDUCER) BETA1,

GT-GAMMA; CHAIN: G;
TRANSDUCIN BETA SUBUNIT;

GAMMA1,TRANSDUCIN GAMMA

SUBUNIT; COMPLEX (GTP-

BINDING/TRANSDUCER), G PROTEIN,

HETEROTRIMER 2 SIGNAL

TRANSDUCTION

297
1got
B
98
389
3.4e−66
0.28
0.77

GT-ALPHA/GI-ALPHA CHIMERA;
COMPLEX (GTP-

CHAIN: A; GT-BETA; CHAIN: B;
BINDING/TRANSDUCER) BETA1,

GT-GAMMA; CHAIN: G;
TRANSDUCIN BETA SUBUNIT;

GAMMA1, TRANSDUCIN GAMMA

SUBUNIT; COMPLEX (GTP-

BINDING/TRANSDUCER), G PROTEIN,

HETEROTRIMER 2 SIGNAL

TRANSDUCTION

298
1a4y
A
32
208
7.5e−12
0.44
0.58

RIBONUCLEASE INHIBITOR;
COMPLEX (INHIBITOR/NUCLEASE)

CHAIN: A, D; ANGIOGENIN;
COMPLEX (INHIBITOR/NUCLEASE),

CHAIN: B, E;
COMPLEX (RI-ANG), HYDROLASE 2

MOLECULAR RECOGNITION,

EPITOPE MAPPING, LEUCINE-RICH 3

REPEATS

298
1a4y
A
49
223
1.4e−10
0.05
0.98

RIBONUCLEASE INHIBITOR;
COMPLEX (INHIBITOR/NUCLEASE)

CHAIN: A, D; ANGIOGENIN;
COMPLEX (INHIBITOR/NUCLEASE),

CHAIN: B, E;
COMPLEX (RI-ANG), HYDROLASE 2

MOLECULAR RECOGNITION,

EPITOPE MAPPING, LEUCINE-RICH 3

REPEATS

298
1a9n
A
112
218
0.00051
0.18
0.40

U2 RNA HAIRPIN IV; CHAIN: Q, R;
COMPLEX (NUCLEAR PROTEIN/RNA)

U2 A′; CHAIN: A, C; U2 B″; CHAIN:
COMPLEX (NUCLEAR

B, D;,
PROTEIN/RNA), RNA,

SNRNP, RIBONUCLEOPROTEIN

298
1d0b
A
49
219
5.1e−13
0.22
0.64

INTERNALIN B; CHAIN: A;
CELL ADHESION LEUCINE RICH

REPEAT, CALCIUM BINDING, CELL

ADHESION

298
1dce
A
53
174
1.7e−07
0.02
0.05

RAB
TRANSFERASE CRYSTAL

GERANYLGERANYLTRANSFERA
STRUCTURE, RAB

SE ALPHA SUBUNIT; CHAIN: A, C;
GERANYLGERANYLTRANSFERASE,

RAB
2.0 A 2 RESOLUTION, N-

GERANYLGERANYLTRANSFERA
FORMYLMETHIONINE, ALPHA

SE BETA SUBUNIT; CHAIN: B, D;
SUBUNIT, BETA SUBUNIT

298
1ds9
A
113
216
1.2e−09
−0.06
0.04

OUTER ARM DYNEIN; CHAIN: A;
CONTRACTILE PROTEIN LEUCINE-

RICH REPEAT, BETA-BETA-ALPHA

CYLINDER, DYNEIN, 2

CHLAMYDOMONAS, FLAGELLA

298
1fol
A
124
210
1.7e−09
0.13
0.37

NUCLEAR RNA EXPORT FACTOR
RNA BINDING PROTEIN TAP (NFX1);

1; CHAIN: A, B;
RIBONUCLEOPROTEIN (RNP, RBD OR

RRM) AND LEUCINE-RICH-REPEAT 2

(LRR)

298
1fol
B
124
210
1.7e−09
0.06
0.13

NUCLEAR RNA EXPORT FACTOR
RNA BINDING PROTEIN TAP (NFX1);

1; CHAIN: A, B;
RIBONUCLEOPROTEIN (RNP, RBD OR

RRM) AND LEUCINE-RICH-REPEAT 2

(LRR)

298
1fqv
A
129
214
5.1e−11
0.28
0.46

SKP2; CHAIN: A, C, E, G, I, K, M, O;
LIGASE CYCLIN A/CDK2-

SKP1; CHAIN: B, D, F, H, J, I, N, P;
ASSOCIATED PROTEIN P45; CYCLIN

A/CDK2-ASSOCIATED PROTEIN P19;

SKP1, SKP2, F-BOX, LRR, LEUCINE-

RICH REPEAT, SCF, UBIQUITIN, 2 E3,

UBIQUITIN PROTEIN LIGASE

298
1fqv
A
33
140
1.5e−08
0.04
−0.02

SKP2; CHAIN: A, C, E, G, I, K, M, O;
LIGASE CYCLIN A/CDK2-

SKP1; CHAIN: B, D, F, H, J, L, N, P;
ASSOCIATED PROTEIN P45; CYCLIN

A/CDK2-ASSOCIATED PROTEIN P19;

SKP1, SKP2, F-BOX, LRR, LEUCINE-

RICH REPEAT, SCF, UBIQUITIN, 2 E3,

UBIQUITIN PROTEIN LIGASE

298
1fqv
A
39
191
3e−21
0.95
1.00

SKP2; CHAIN: A, C, E, G, I, K, M, O;
LIGASE CYCLIN A/CDK2-

SKP1; CHAIN: B, D, F, H, J, L, N, P;
ASSOCIATED PROTEIN P45; CYCLIN

A/CDK2-ASSOCIATED PROTEIN P19;

SKP1, SKP2, F-BOX, LRR, LEUCINE-

RICH REPEAT, SCF, UBIQUITIN, 2 E3,

UBIQUITIN PROTEIN LIGASE

298
1fqv
A
49
207
6.8e−19
0.54
0.96

SKP2; CHAIN: A, C, E, G, I, K, M, O;
LIGASE CYCLIN A/CDK2-

SKP1; CHAIN: B, D, F, H, J, L, N, P;
ASSOCIATED PROTEIN P45; CYCLIN

A/CDK2-ASSOCIATED PROTEIN P19;

SKP1, SKP2, F-BOX, LRR, LEUCINE-

RICH REPEAT, SCF, UBIQUITIN, 2 E3,

UBIQUITIN PROTEIN LIGASE

298
1fqv
A
70
199
4.5e−19
0.85
0.92

SKP2; CHAIN: A, C, E, G, I, K, M, O;
LIGASE CYCLIN A/CDK2-

SKP1; CHAIN: B, D, F, H, J, L, N, P;
ASSOCIATED PROTEIN P45; CYCLIN

A/CDK2-ASSOCIATED PROTEIN P19;

SKP1, SKP2, F-BOX, LRR, LEUCINE-

RICH REPEAT, SCF, UBIQUITIN, 2 E3,

UBIQUITIN PROTEIN LIGASE

298
1fs2
A
129
214
5.1e−11
−0.35
0.27

SKP2; CHAIN: A, C; SKP1; CHAIN:
LIGASE CYCLIN A/CDK2-

B, D;
ASSOCIATED P45; CYCLIN A/CDK2-

ASSOCIATED P19; SKP1, SKP2, F-BOX,

LRRS, LEUCINE-RICH REPEATS, SCF,

2 UBIQUITIN, E3, UBIQUITIN

PROTEIN LIGASE

298
1fs2
A
49
207
6.8e−19
0.64
0.77

SKP2; CHAIN: A, C; SKP1; CHAIN:
LIGASE CYCLIN A/CDK2-

B, D;
ASSOCIATED P45; CYCLIN A/CDK2-

ASSOCIATED P19; SKP1, SKP2, F-BOX,

LRRS, LEUCINE-RICH REPEATS, SCF,

2 UBIQUITIN, E3, UBIQUITIN

PROTEIN LIGASE

298
1yrg
A
111
220
1e−08
−0.38
0.23

GTPASE-ACTIVATING PROTEIN
TRANSCRIPTION RNA1P; RANGAP;

RNA1_SCHPO; CHAIN: A, B;
GTPASE-ACTIVATING PROTEIN FOR

SPI1, GTPASE-ACTIVATING PROTEIN,

GAP, RNA1P, RANGAP, LRR,

LEUCINE-2 RICH REPEAT PROTEIN,

TWINNING, HEMIHEDRAL

TWINNING, 3 MEROHEDRAL

TWINNING, MEROHEDRY

298
2bnh

113
223
1.4e−08
0.31
0.76

RIBONUCLEASE INHIBITOR;
ACETYLATION RNASE INHIBITOR,

CHAIN: NULL;
RIBONUCLEASE/ANGIOGENIN

INHIBITOR ACETYLATION,

LEUCINE-RICH REPEATS

298
2bnh

53
217
1e−10
0.32
1.00

RIBONUCLEASE INHIBITOR;
ACETYLATION RNASE INHIBITOR,

CHAIN: NULL;
RIBONUCLEASE/ANGIOGENIN

INHIBITOR ACETYLATION,

LEUCINE-RICH REPEATS

299
1brl
B
4
151
3.4e−44
0.91
1.00

MYOSIN; CHAIN: A, B, C, D, E, F,
MUSCLE PROTEIN MDE; MUSCLE

G, H;
PROTEIN

299
1brl
B
4
151
3.4e−44

219.13
MYOSIN; CHAIN: A, B, C, D, E, F,
MUSCLE PROTEIN MDE; MUSCLE

G, H;
PROTEIN

299
1cdm
A
4
149
1.7e−56
0.60
1.00

CALCIUM-BINDING PROTEIN

CALMODULIN COMPLEXED

WITH CALMODULIN-BINDING

DOMAIN OF 1CDM 3

CALMODULIN-DEPENDENT

PROTEIN KINASE II 1CDM 4

299
1cdm
A
4
149
1.7e−56

103.28
CALCIUM-BINDING PROTEIN

CALMODULIN COMPLEXED

WITH CALMODULIN-BINDING

DOMAIN OF 1CDM 3

CALMODULIN-DEPENDENT

PROTEIN KINASE II 1CDM 4

299
1cll

4
149
6.8e−62
0.49
1.00

CALCIUM-BINDING PROTEIN

CALMODULIN (VERTEBRATE)

1CLL 3

299
1cll

4
150
6.8e−62

113.59
CALCIUM-BINDING PROTEIN

CALMODULIN (VERTEBRATE)

1CLL 3

299
1exr
A
4
150
1.4e−59
0.40
1.00

CALMODULIN; CHAIN: A;
METAL TRANSPORT CALMODULIN,

HIGH RESOLUTION, DISORDER

299
1tcf

3
151
1.7e−48

89.97
TROPONIN C; CHAIN: NULL;
CALCIUM-REGULATED MUSCLE

CONTRACTION MUSCLE

CONTRACTION, CALCIUM-BINDING,

TROPONIN, E-F HAND, 2 OPEN

CONFORMATION REGULATORY

DOMAIN, CALCIUM-REGULATED 3

MUSCLE CONTRACTION

299
1tcf

4
148
1.7e−48
0.38
1.00

TROPONIN C; CHAIN: NULL;
CALCIUM-REGULATED MUSCLE

CONTRACTION MUSCLE

CONTRACTION, CALCIUM-BINDING,

TROPONIN, E-F HAND, 2 OPEN

CONFORMATION REGULATORY

DOMAIN, CALCIUM-REGULATED 3

MUSCLE CONTRACTION

299
1top

4
148
5.1e−49
0.57
1.00

CONTRACTILE SYSTEM PROTEIN

TROPONIN C 1TOP 3

299
1top

4
151
5.1e−49

83.80
CONTRACTILE SYSTEM PROTEIN

TROPONIN C 1TOP 3

299
1vrk
A
2
149
1.2e−60
0.72
1.00

CALMODULIN; CHAIN: A; RS20;
CALMODULIN, CALCIUM BINDING,

CHAIN: B;
HELIX-LOOP-HELIX, SIGNALLING, 2

COMPLEX(CALCIUM-BINDING

PROTEIN/PEPTIDE)

299
1vrk
A
2
151
1.2e−60

115.21
CALMODULIN; CHAIN: A; RS20;
CALMODULIN, CALCIUM BINDING,

CHAIN: B;
HELIX-LOOP-HELIX, SIGNALLING, 2

COMPLEX(CALCIUM-BINDING

PROTEIN/PEPTIDE)

300
1aox
A
36
215
1.7e−28
0.37
0.83

INTEGRIN ALPHA 2 BETA;
INTEGRIN INTEGRIN, CELL

CHAIN: A, B;
ADHESION, GLYCOPROTEIN

300
1atz
A
38
226
1.5e−23

72.47
VON WILLEBRAND FACTOR;
COLLAGEN-BINDING COLLAGEN-

CHAIN: A, B;
BINDING, HEMOSTASIS,

DINUCLEOTIDE BINDING FOLD

300
1atz
A
39
218
1.5e−23
0.88
1.00

VON WILLEBRAND FACTOR;
COLLAGEN-BINDING COLLAGEN-

CHAIN: A, B;
BINDING, HEMOSTASIS,

DINUCLEOTIDE BINDING FOLD

300
1auq

23
227
1.4e−35

62.36
A1 DOMAIN OF VON
WILLEBRAND WILLEBRAND, BLOOD

WILLEBRAND FACTOR; CHAIN:
COAGULATION, PLATELET,

NULL;
GLYCOPROTEIN

300
1auq

29
227
1.4e−35
0.57
1.00

A1 DOMAIN OF VON
WILLEBRAND WILLEBRAND, BLOOD

WILLEBRAND FACTOR; CHAIN:
COAGULATION, PLATELET,

NULL;
GLYCOPROTEIN

300
1ck4
A
39
217
5.1e−29
0.58
1.00

INTEGRIN ALPHA-1; CHAIN: A, B;
STRUCTURAL PROTEIN 1-DOMAIN,

METAL BINDING, COLLAGEN,

ADHESION

300
1fns
A
36
227
5.1e−34
0.70
0.98

IMMUNOGLOBULIN NMC-4 IGG1;
IMMUNE SYSTEM VON

CHAIN: L; IMMUNOGLOBULIN
WILLEBRAND FACTOR,

NMC-4 IGG1; CHAIN: H; VON
GLYCOPROTEIN IBA (A; ALPHA)

WILLEBRAND FACTOR; CHAIN:
BINDING, 2 COMPLEX

A;
(WILLEBRAND/IMMUNOGLOBULIN),

BLOOD COAGULATION TYPE 3 2B

VON WILLEBRAND DISEASE

300
1ido

39
224
5.1e−31

59.31
INTEGRIN; CHAIN: NULL;
CELL ADHESION PROTEIN A-

DOMAIN INTEGRIN, CELL ADHESION

PROTEIN, GLYCOPROTEIN,

EXTRACELLULAR 2 MATRIX,

CYTOSKELETON

300
1ido

41
217
5.1e−31
0.61
1.00

INTEGRIN; CHAIN: NULL;
CELL ADHESION PROTEIN A-

DOMAIN INTEGRIN, CELL ADHESION

PROTEIN, GLYCOPROTEIN,

EXTRACELLULAR 2 MATRIX,

CYTOSKELETON

300
1lfa
A
38
226
8.5e−23
0.53
0.99

CDI1A; ILFA 5 CHAIN: A, B; 1LFA 6
CELL ADHESION LFA-1, ALPHA-

L\,BETA-2 INTEGRIN, A-DOMAIN;

ILFA 8

300
1lfa
A
38
227
8.5e−23

53.04
CDI1A; ILFA 5 CHAIN: A, B; ILFA 6
CELL ADHESION LFA-L ALPHA-

L\, BETA-2 INTEGRIN, A-DOMAIN;

ILFA 8

300
1qc5
A
37
217
1.4e−28
0.41
0.94

ALPHAI BETA1 INTEGRIN;
CELL ADHESION INTEGRIN, CELL

CHAIN: A; ALPHAI BETA1
ADHESION

INTEGRIN; CHAIN: B;

301
1bxe
A
13
153
1.7e−33
−0.14
0.71

RIBOSOMAL PROTEIN L22;
RNA BINDING PROTEIN RIBOSOMAL

CHAIN: A;
PROTEIN, PROTEIN SYNTHESIS, RNA

BINDING, 2 ANTIBIOTICS

RESISTANCE, RNA BINDING

PROTEIN

301
1flk
0
2
152
1.7e−44
0.02
1.00

23S RRNA; CHAIN: 0; 5S RRNA;
RIBOSOME 50S RIBOSOMAL

CHAIN: 9; RIBOSOMAL PROTEIN
PROTEIN L2P, HMAL2, HL4; 50S

L2; CHAIN: A; RIBOSOMAL
RIBOSOMAL PROTEIN L3P, HMAL3,

PROTEIN L3; CHAIN: B;
HL1; 50S RIBOSOMAL PROTEIN L4E,

RIBOSOMAL PROTEIN L4; CHAIN:
HMAL4, HL6; 50S RIBOSOMAL

C; RIBOSOMAL PROTEIN L5;
PROTEIN L5P, HMAL5, HL13; 30S

CHAIN: D; RIBOSOMAL PROTEIN
RIBOSOMAL PROTEIN HS6; 50S

L7AE; CHAIN: E; RIBOSOMAL
RIBOSOMAL PROTEIN L13P, HMAL13;

PROTEIN L10E; CHAIN: F;
50S RIBOSOMAL PROTEIN L14P,

RIBOSOMAL PROTEIN L13;
HMAL14, HL27; 50S RIBOSOMAL

CHAIN: G; RIBOSOMAL PROTEIN
PROTEIN L15P, HMAL15, HL9; 50S

L14; CHAIN: H; RIBOSOMAL
RIBOSOMAL PROTEIN L18P, HMAL18,

PROTEIN L15E; CHAIN: I;
HL12; 50S RIBOSOMAL PROTEIN

RIBOSOMAL PROTEIN L15;
L18E, HL29, L19; 50S RIBOSOMAL

CHAIN: J; RIBOSOMAL PROTEIN
PROTEIN L19E, HMAL19, HL24; 50S

L18; CHAIN: K; RIBOSOMAL
RIBOSOMAL PROTEIN L21E, HL31;

PROTEIN L18E; CHAIN: L;
50S RIBOSOMAL PROTEIN L22P,

RIBOSOMAL PROTEIN L19;
HMAL22, HL23; 50S RIBOSOMAL

CHAIN: M; RIBOSOMAL PROTEIN
PROTEIN L23P, HMAL23, HL25, L21;

L21E; CHAIN: N; RIBOSOMAL
50S RIBOSOMAL PROTEIN L24P,

PROTEIN L22; CHAIN: O;
HMAL24, HL16, HL15; 50S

RIBOSOMAL PROTEIN L23;
RIBOSOMAL PROTEIN L24E,

CHAIN: P; RIBOSOMAL PROTEIN
HL21/HL22; 50S RIBOSOMAL

L24; CHAIN: Q; RIBOSOMAL
PROTEIN L29P, HMAL29, HL33; 50S

PROTEIN L24E; CHAIN: R;
RIBOSOMAL PROTEIN L30P, HMAL30,

RIBOSOMAL PROTEIN L29;
HL20, HL16; 50S RIBOSOMAL

CHAIN: S; RIBOSOMAL PROTEIN
PROTEIN L31E, L34, HL30; 50S

L30; CHAIN: T; RIBOSOMAL
RIBOSOMAL PROTEIN L32E, HL5; 50S

PROTEIN L31E; CHAIN: U;
RIBOSOMAL PROTEIN L37E, L35E;

RIBOSOMAL PROTEIN L32E;
50S RIBOSOMAL PROTEINS L39E,

CHAIN: V; RIBOSOMAL PROTEIN
HL39E, HL46E; 50S RIBOSOMAL

L37AE; CHAIN: W; RIBOSOMAL
PROTEIN L44E, LA, HLA; 50S

PROTEIN L37E; CHAIN: X;
RIBOSOMAL PROTEIN L6P, HMAL6,

RIBOSOMAL PROTEIN L39E;
HL10 RIBOSOME ASSEMBLY, RNA-

CHAIN: Y; RIBOSOMAL PROTEIN
RNA, PROTEIN-RNA, PROTEIN-

L44E; CHAIN: Z; RIBOSOMAL
PROTEIN

PROTEIN L6; CHAIN: I;

302
1ahd
P
143
208
1e−33
−0.16
0.98

DNA-BINDING PROTEIN

ANTENNAPEDIA PROTEIN

(HOMEODOMAIN) MUTANT

WITH CYS 39 1AHD 3 REPLACED

BY SER (C39S) COMPLEX WITH

DNA (NMR, 1AHD 4.16

STRUCTURES) 1AHD 5

302
1ahd
P
143
209
1e−33

72.79
DNA-BINDING PROTEIN

ANTENNAPEDIA PROTEIN

(HOMEODOMAIN) MUTANT

WITH CYS 39 1AHD 3 REPLACED

BY SER (C39S) COMPLEX WITH

DNA (NMR, 1AHD 4.16

STRUCTURES) 1AHD 5

302
1b72
A
137
203
1.5e−30

69.28
HOMEOBOX PROTEIN HOX-B1;
PROTEIN/DNA HOMEODOMAIN,

CHAIN: A; PBX1; CHAIN: B; DNA
DNA, COMPLEX, DNA-BINDING

CHAIN: D; DNA CHAIN: E;
PROTEIN, PROTEIN/DNA

302
1b72
A
143
203
1.5e−30
−0.07
0.99

HOMEOBOX PROTEIN HOX-B1;
PROTEIN/DNA HOMEODOMAIN,

CHAIN: A; PBX1; CHAIN: B; DNA
DNA, COMPLEX, DNA-BINDING

CHAIN: D; DNA CHAIN: E;
PROTEIN, PROTEIN/DNA

302
1b72
A
147
204
1.7e−27
−0.29
1.00

HOMEOBOX PROTEIN HOX-B1;
PROTEIN/DNA HOMEODOMAIN,

CHAIN: A; PBX1; CHAIN: B; DNA
DNA, COMPLEX, DNA-BINDING

CHAIN: D; DNA CHAIN: E;
PROTEIN, PROTEIN/DNA

302
1b8i
A
143
202
4.5e−30

61.07
ULTRABITHORAX HOMEOTIC
TRANSCRIPTION/DNA

PROTEIN IV; CHAIN: A;
ULTRABITHORAX; PBX PROTEIN;

HOMEOBOX PROTEIN
DNA BINDING, HOMEODOMAIN,

EXTRADENTICLE; CHAIN: B; DNA
HOMEOTIC PROTEINS,

(5′-CHAIN: C; DNA (5′-CHAIN: D;
DEVELOPMENT, 2 SPECIFICITY

302
1b8i
A
144
201
4.5e−30
0.09
0.83

ULTRABITHORAX HOMEOTIC
TRANSCRIPTION/DNA

PROTEIN IV; CHAIN: A;
ULTRABITHORAX; PBX PROTEIN;

HOMEOBOX PROTEIN
DNA BINDING, HOMEODOMAIN,

EXTRADENTICLE; CHAIN: B; DNA
HOMEOTIC PROTEINS,

(5′-CHAIN: C; DNA (5′-CHAIN: D;
DEVELOPMENT, 2 SPECIFICITY

302
1ftz

142
210
1.2e−28

71.20
DNA-BINDING FUSHI TARAZU

PROTEIN (HOMEODOMAIN)

(NMR, 20 STRUCTURES) 1FTZ 3

302
1ftz

144
208
1.2e−28
−0.30
0.59

DNA-BINDING FUSHI TARAZU

PROTEIN (HOMEODOMAIN)

(NMR, 20 STRUCTURES) 1FTZ 3

302
1san

148
209
3.4e−31

69.53
DNA-BINDING PROTEIN

ANTENNAPEDIA PROTEIN

(HOMEODOMAIN) MUTANT

WITH CYS 39 1SAN 3 REPLACED

BY SER AND RESIDUES 1-6

DELETED (C39S,DEL 1-6) 1SAN 4

(NMR, 20 STRUCTURES) 1SAN 5

302
1san

149
208
3.4e−31
0.00
1.00

DNA-BINDING PROTEIN

ANTENNAPEDIA PROTEIN

(HOMEODOMAIN) MUTANT

WITH CYS 39 1SAN 3 REPLACED

BY SER AND RESIDUES 1-6

DELETED (C39S,DEL 1-6) 1SAN 4

(NMR, 20 STRUCTURES) 1SAN 5

302
9ant
A
147
202
5.1e−31
0.38
1.00

ANTENNAPEDIA PROTEIN;
COMPLEX (DNA-BINDING

CHAIN: A, B; DNA; CHAIN: C, D, E,
PROTEIN/DNA) HD; HOMEODOMAIN,

F;
COMPLEX (DNA-BINDING

PROTEIN/DNA)

302
9ant
A
147
202
5.1e−31

68.47
ANTENNAPEDIA PROTEIN;
COMPLEX (DNA-BINDING

CHAIN: A, B; DNA; CHAIN: C, D, E,
PROTEIN/DNA) HD; HOMEODOMAIN,

F;
COMPLEX (DNA-BINDING

PROTEIN/DNA)

307
1ddv
A
4
96
0.0003
0.48
0.46

GLGF-DOMAIN PROTEIN HOMER;
SIGNALING PROTEIN PROTEIN-

CHAIN: A; METABOTROPIC
LIGAND COMPLEX, POLYPROLINE

GLUTAMATE RECEPTOR
RECOGNITION, BETA TURN

MGLUR5; CHAIN: B;

307
1ddw
A
4
96
0.00015
0.62
0.69

GLGF-DOMAIN PROTEIN HOMER;
SIGNALING PROTEIN PLECKSTRIN

CHAIN: A;
HOMOLOGY DOMAIN FOLD

307
1rrp
B
7
101
1.5e−25
0.57
0.96

RAN; CHAIN: A, C; NUCLEAR
COMPLEX (SMALL

PORE COMPLEX PROTEIN
GTPASE/NUCLEAR PROTEIN)

NUP358; CHAIN: B, D;
COMPLEX (SMALL

GTPASE/NUCLEAR PROTEIN), SMALL

GTPASE, 2 NUCLEAR TRANSPORT

309
2ife
A
159
237
1.2e−16
0.62
0.89

TRANSLATION INITIATION
GENE REGULATION INITIATION

FACTOR IF3; CHAIN: A;
FACTOR

310
1f5n
A
107
167
0.0049
−0.27
0.03

INTERFERON-INDUCED
SIGNALING PROTEIN GBP, GTP

GUANYLATE-BINDING PROTEIN
HYDROLYSIS, GDP, GMP,

1; CHAIN: A;
INTERFERON INDUCED, DYNAMIN 2

RELATED, LARGE GTPASE FAMILY,

GMPPNP, GPPNHP,

310
1osm
A
9
99
1.5e−15
1.73
−0.20

OMPK36; CHAIN: A, B, C;
OUTER MEMBRANE PROTEIN

OSMOPORIN; OUTER MEMBRANE

PROTEIN, NON-SPECIFIC PORIN,

OSMOPORIN, 2 BETA-BARREL,

TRANSMEMBRANE

310
1qq4
A
14
119
1.2e−11
1.84
0.04

ALPHA-LYTIC PROTEASE;
HYDROLASE DOUBLE BETA

CHAIN: A;
BARREL, BACTERIAL SERINE

PROTEASE

310
1qq4
A
8
96
3e−09
1.29
−0.08

ALPHA-LYTIC PROTEASE;
HYDROLASE DOUBLE BETA

CHAIN: A;
BARREL, BACTERIAL SERINE

PROTEASE

310
1tal

14
119
1e−11
1.63
−0.06

ALPHA-LYTIC PROTEASE;
SERINE PROTEASE SERINE

CHAIN: NULL;
PROTEASE, LOW TEMPERATURE,

HYDROLASE, 2 SERINE PROTEINASE

310
1tal

8
99
1.2e−10
1.03
−0.20

ALPHA-LYTIC PROTEASE;
SERINE PROTEASE SERINE

CHAIN: NULL;
PROTEASE, LOW TEMPERATURE,

HYDROLASE, 2 SERINE PROTEINASE

311
1alh
A
116
195
8.5e−18
−0.02
0.27

QGSR ZINC FINGER PEPTIDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

311
1alh
A
339
448
1.2e−39
−0.24
0.11

QGSR ZINC FINGER PEPTIDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

311
1alh
A
619
728
6e−37
−0.46
0.12

QGSR ZINC FINGER PEPTIDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

311
1mey
C
105
195
3.4e−32
−0.06
0.22

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

311
1mey
C
142
223
1.7e−39
−0.08
0.95

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

311
1mey
C
170
251
1.7e−42
0.19
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

311
1mey
C
198
279
1.2e−44
0.17
0.99

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

311
1mey
C
226
307
3.4e−46
0.27
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

311
1mey
C
254
335
1.7e−46
−0.02
0.99

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

311
1mey
C
282
363
8.5e−47
−0.26
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

311
1mey
C
310
391
1.5e−46
−0.08
0.99

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

311
1mey
C
338
419
1.7e−46
0.07
0.98

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

311
1mey
C
366
447
3.4e−47
0.08
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

311
1mey
C
394
475
6.8e−49
0.32
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

311
1mey
C
422
503
1e−49
0.06
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

311
1mey
C
450
531
3.4e−49
0.18
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

311
1mey
C
478
559
1.2e−48
0.37
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

311
1mey
C
478
560
3.4e−49

108.14
DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

311
1mey
C
506
587
8.5e−49
0.14
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

311
1mey
C
534
615
1.5e−48
0.14
0.99

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

311
1mey
C
562
643
6.8e−49
−0.00
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

311
1mey
C
590
671
6.8e−49
0.04
0.82

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

311
1mey
C
618
699
1.7e−49
−0.22
0.94

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

311
1mey
C
646
727
1.2e−50
−0.03
0.98

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

311
1mey
C
674
755
1.2e−50
0.23
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

311
1mey
C
702
783
6.8e−51
0.31
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

311
1mey
C
730
811
3.4e−50
0.08
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

311
1mey
C
758
839
1.7e−50
−0.03
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

311
1mey
C
786
852
1.5e−40
−0.09
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

311
1tf6
A
199
345
1.7e−34
0.00
0.98

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

311
1tf6
A
394
560
1.7e−37

116.05
TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

311
1tf6
A
395
540
1.7e−37
0.21
0.88

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

311
1tf6
A
507
652
3.4e−36
−0.03
0.48

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

311
1tf6
A
563
708
1.4e−36
−0.36
0.45

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

311
1tf6
A
619
764
1.4e−36
−0.22
0.46

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

311
1tf6
A
703
852
6.8e−38
0.19
0.98

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

311
1ubd
C
116
223
5.1e−25
−0.02
0.86

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

311
1ubd
C
147
251
1.5e−41
−0.11
0.94

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

311
1ubd
C
168
279
6e−51
−0.09
0.66

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

311
1ubd
C
201
307
8.5e−32
0.06
1.00

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

311
1ubd
C
203
307
6e−53
−0.15
0.93

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

311
1ubd
C
224
336
3e−52
−0.10
0.72

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

311
1ubd
C
308
447
1.5e−48
−0.40
0.54

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

311
1ubd
C
371
476
3e−50
−0.17
0.86

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

311
1ubd
C
374
475
1e−34
−0.10
0.80

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

311
1ubd
C
394
503
1.5e−54
−0.13
0.69

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

311
1ubd
C
420
559
7.5e−57
−0.17
0.46

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

311
1ubd
C
430
531
1.7e−34
0.22
0.98

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

311
1ubd
C
458
559
1.7e−33
−0.07
0.93

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

311
1ubd
C
504
615
1.3e−51
0.16
0.80

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

311
1ubd
C
598
699
1.7e−34
−0.42
0.21

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

311
1ubd
C
616
755
3e−49
−0.41
0.21

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

311
1ubd
C
626
727
1.7e−34
−0.33
0.45

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

311
1ubd
C
672
784
3e−57

93.95
YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

311
1ubd
C
682
783
1.7e−34
−0.02
0.89

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

311
1ubd
C
700
811
3e−57
−0.12
0.90

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

311
1ubd
C
728
839
1.5e−54
0.00
0.99

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

311
1ubd
C
738
839
1.4e−34
−0.08
0.98

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

311
1ubd
C
756
852
1.2e−44
−0.20
0.51

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

311
2gli
A
119
250
1.4e−28
−0.17
0.98

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

311
2gli
A
143
281
6e−55
0.02
0.53

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

311
2gli
A
198
334
8.5e−32
−0.17
0.98

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

311
2gli
A
201
337
1.5e−65
0.34
0.86

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

311
2gli
A
226
365
4.5e−66
0.06
0.95

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

311
2gli
A
310
477
4.5e−64
0.04
0.60

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

311
2gli
A
346
474
5.1e−32
0.08
0.84

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

311
2gli
A
394
533
7.5e−72
0.06
1.00

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

311
2gli
A
422
561
7.5e−72

102.20
ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

311
2gli
A
430
558
3.4e−33
0.32
0.78

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

311
2gli
A
478
617
1.2e−68
−0.09
0.65

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

311
2gli
A
570
698
1.2e−33
−0.19
0.07

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

311
2gli
A
654
782
1.2e−33
0.17
0.55

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

311
2gli
A
674
841
4.5e−70
−0.08
0.63

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

311
2gli
A
682
810
5.1e−33
0.03
0.62

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

311
2gli
A
710
841
6.8e−34
−0.14
0.84

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

311
2gli
A
730
852
6e−60
0.12
0.80

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

311
2gli
A
738
851
3.4e−29
0.17
0.80

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

312
1b34
A
7
81
4.5e−23
0.29
0.30

SMALL NUCLEAR
RNA BINDING PROTEIN SNRNP,

RIBONUCLEOPROTEIN SM D1;
SPLICING, SPLICEOSOME, SM, CORE

CHAIN: A; SMALL NUCLEAR
SNRNP DOMAIN, 2 SYSTEMIC LUPUS

RIBONUCLEOPROTEIN SM D2;
ERYTHEMATOSUS, SLE

CHAIN: B;

312
1b34
A
9
71
3.4e−17
0.08
0.04

SMALL NUCLEAR
RNA BINDING PROTEIN SNRNP,

RIBONUCLEOPROTEIN SM D1;
SPLICING, SPLICEOSOME, SM, CORE

CHAIN: A; SMALL NUCLEAR
SNRNP DOMAIN, 2 SYSTEMIC LUPUS

RIBONUCLEOPROTEIN SM D2;
ERYTHEMATOSUS, SLE

CHAIN: B;

312
1b34
B
7
72
1.2e−12
0.46
0.18

SMALL NUCLEAR
RNA BINDING PROTEIN SNRNP,

RIBONUCLEOPROTEIN SM D1;
SPLICING, SPLICEOSOME, SM, CORE

CHAIN: A; SMALL NUCLEAR
SNRNP DOMAIN, 2 SYSTEMIC LUPUS

RIBONUCLEOPROTEIN SM D2;
ERYTHEMATOSUS, SLE

CHAIN: B;

312
1d3b
A
5
72
1.7e−14
0.28
0.07

SMALL NUCLEAR
RNA BINDING PROTEIN D3 CORE

RIBONUCLEOPROTEIN SM D3;
SNRNP PROTEIN; B CORE SNRNP

CHAIN: A, C, E, G, I, K; SMALL
PROTEIN SNRNP, SPLICING, SM,

NUCLEAR RIBONUCLEOPROTEIN
CORE SNRNP DOMAIN, SYSTEMIC

ASSOCIATED CHAIN: B, D, F, H, J,
LUPUS 2 ERYTHEMATOSUS, SLE,

L;
RNA BINDING PROTEIN

312
1d3b
A
7
76
1.1e−20
0.63
0.05

SMALL NUCLEAR
RNA BINDING PROTEIN D3 CORE

RIBONUCLEOPROTEIN SM D3;
SNRNP PROTEIN; B CORE SNRNP

CHAIN: A, C, E, G, I, K; SMALL
PROTEIN SNRNP, SPLICING, SM,

NUCLEAR RIBONUCLEOPROTEIN
CORE SNRNP DOMAIN, SYSTEMIC

ASSOCIATED CHAIN: B, D, F, H, J,
LUPUS 2 ERYTHEMATOSUS, SLE,

L;
RNA BINDING PROTEIN

312
1d3b
B
10
78
7.5e−18
0.34
−0.06

SMALL NUCLEAR
RNA BINDING PROTEIN D3 CORE

RIBONUCLEOPROTEIN SM D3;
SNRNP PROTEIN; B CORE SNRNP

CHAIN: A, C, E, G, I, K; SMALL
PROTEIN SNRNP, SPLICING, SM,

NUCLEAR RIBONUCLEOPROTEIN
CORE SNRNP DOMAIN, SYSTEMIC

ASSOCIATED CHAIN: B, D, F, H, J,
LUPUS 2 ERYTHEMATOSUS, SLE,

L;
RNA BINDING PROTEIN

312
1d3b
B
9
70
1.7e−15
−0.01
0.04

SMALL NUCLEAR
RNA BINDING PROTEIN D3 CORE

RIBONUCLEOPROTEIN SM D3;
SNRNP PROTEIN; B CORE SNRNP

CHAIN: A, C, E, G, I, K; SMALL
PROTEIN SNRNP, SPLICING, SM,

NUCLEAR RIBONUCLEOPROTEIN
CORE SNRNP DOMAIN, SYSTEMIC

ASSOCIATED CHAIN: B, D, F, H, J,
LUPUS 2 ERYTHEMATOSUS, SLE,

L;
RNA BINDING PROTEIN

312
1d3b
D
4
70
6.8e−16
0.76
−0.05

SMALL NUCLEAR
RNA BINDING PROTEIN D3 CORE

RIBONUCLEOPROTEIN SM D3;
SNRNP PROTEIN; B CORE SNRNP

CHAIN: A, C, E, G, I, K; SMALL
PROTEIN SNRNP, SPLICING, SM,

NUCLEAR RIBONUCLEOPROTEIN
CORE SNRNP DOMAIN, SYSTEMIC

ASSOCIATED CHAIN: B, D, F, H, J,
LUPUS 2 ERYTHEMATOSUS, SLE,

L;
RNA BINDING PROTEIN

312
1d3b
D
9
78
1.5e−17
0.11
−0.01

SMALL NUCLEAR
RNA BINDING PROTEIN D3 CORE

RIBONUCLEOPROTEIN SM D3;
SNRNP PROTEIN; B CORE SNRNP

CHAIN: A, C, E, G, I, K; SMALL
PROTEIN SNRNP, SPLICING, SM,

NUCLEAR RIBONUCLEOPROTEIN
CORE SNRNP DOMAIN, SYSTEMIC

ASSOCIATED CHAIN: B, D, F, H, J,
LUPUS 2 ERYTHEMATOSUS, SLE,

L;
RNA BINDING PROTEIN

314
1b8q
A
101
173
1.3e−06
0.08
0.15

NEURONAL NITRIC OXIDE
OXIDOREDUCTASE PDZ DOMAIN,

SYNTHASE; CHAIN: A;
NNOS, NITRIC OXIDE SYNTHASE

HEPTAPEPTIDE; CHAIN: B;

314
1be9
A
113
175
8.5e−05
0.19
0.99

PSD-95; CHAIN: A; CRIPT; CHAIN:
PEPTIDE RECOGNITION PEPTIDE

B;
RECOGNITION, PROTEIN

LOCALIZATION

314
1pdr

113
175
0.0012
0.13
0.90

HUMAN DISCS LARGE PROTEIN;
SIGNAL TRANSDUCTION HDLG,

CHAIN: NULL;
DHR3 DOMAIN; SIGNAL

TRANSDUCTION, SH3 DOMAIN,

REPEAT

314
1qlc
A
119
172
0.00034
0.27
0.99

POSTSYNAPTIC DENSITY
PEPTIDE RECOGNITION PSD-95; PDZ

PROTEIN 95; CHAIN: A;
DOMAIN, NEURONAL NITRIC OXIDE

SYNTHASE, NMDA RECEPTOR 2

BINDING

314
3pdz
A
109
190
3e−09
0.73
0.76

TYROSINE PHOSPHATASE (PTP-
HYDROLASE PDZ DOMAIN, HUMAN

BAS, TYPE 1); CHAIN: A;
PHOSPHATASE, HPTPIE, PTP-BAS,

SPECIFICITY 2 OF BINDING

316
1a4y
A
805
893
4.5e−05
0.52
0.60

RIBONUCLEASE INHIBITOR;
COMPLEX (INHIBITOR/NUCLEASE)

CHAIN: A, D; ANGIOGENIN;
COMPLEX (INHIBITOR/NUCLEASE),

CHAIN: B, E;
COMPLEX (RI-ANG), HYDROLASE 2

MOLECULAR RECOGNITION,

EPITOPE MAPPING LEUCINE-RICH 3

REPEATS

316
1a4y
A
815
877
7.5e−08
0.54
1.00

RIBONUCLEASE INHIBITOR;
COMPLEX (INHIBITOR/NUCLEASE)

CHAIN: A, D; ANGIOGENIN;
COMPLEX (INHIBITOR/NUCLEASE),

CHAIN: B, E;
COMPLEX (RI-ANG), HYDROLASE 2

MOLECULAR RECOGNITION,

EPITOPE MAPPING, LEUCINE-RICH 3

REPEATS

316
1aoj
A
590
647
6e−16
−0.80
0.30

EPS8; CHAIN: A, B;
SIGNAL TRANSDUCTION SRC

HOMOLOGY DOMAIN; SIGNAL

TRANSDUCTION, SH3 DOMAIN, EPS8,

PROLINE RICH PEPTIDE

316
1tud

577
627
1.1e−07
−0.30
0.64

ALPHA-SPECTRIN; CHAIN: NULL;
CYTOSKELETON CAPPING PROTEIN,

CALCIUM-BINDING, DUPLICATION,

REPEAT, 2 SH3 DOMAIN,

316
2nmb
A
155
263
9e−14
−0.13
0.10

NUMB PROTEIN; CHAIN: A; GPPY
CELL CYCLE/GENE REGULATION

PEPTIDE; CHAIN: B;
COMPLEX, SIGNAL TRANSDUCTION,

PHOSPHOTYROSINE BINDING 2

DOMAIN (PTB), ASYMETR IC CELL

DIVISION, CELL CYCLE/GENE 3

REGULATION

318
1a5f
H
38
246
1.4e−20

69.16
MONOCLONAL ANTI-E-SELECTIN
IMMUNOGLOBULIN

7A9 ANTIBODY; CHAIN: L, H;
IMMUNOGLOBULIN, FAB,

ANTIBODY, ANTI-E-SELECTIN

318
1adq
L
41
241
6.8e−29
0.18
0.35

IGG4 REA; CHAIN: A; RF-AN
COMPLEX

IGM/LAMBDA; CHAIN: H, L;
(IMMUNOGLOBULIN/AUTOANTIGEN)

COMPLEX

(IMMUNOGLOBULIN/AUTOANTIGEN),

RHEUMATOID FACTOR 2 AUTO-

ANTIBODY COMPLEX

318
1ac6
H
38
255
1.7e−22

64.20
ANTIBODY CTM01; CHAIN: L, H;
IMMUNOGLOBULIN

IMMUNOGLOBULIN, FAB

FRAGMENT, HUMANISATION

318
1afv
H
38
236
1.7e−23
0.11
1.00

HUMAN IMMUNODEFICIENCY
COMPLEX (VIRAL

VIRUS TYPE 1 CAPSID CHAIN: A,
CAPSID/IMMUNOGLOBULIN) HIV-I

B; ANTIBODY FAB25.3
CA, HIV CA, HIV P24, P24; FAB, FAB

FRAGMENT; CHAIN: H, K, L, M;
LIGHT CHAIN, FAB HEAVY CHAIN

COMPLEX (VIRAL

CAPSID/IMMUNOGLOBULIN), HIV,

CAPSID PROTEIN, 2 P24

318
1aqk
H
39
247
3.4e−20

65.54
FAB B7-15A2; CHAIN: L, H;
IMMUNOGLOBULIN HUMAN FAB,

ANTI-TETANUS TOXOID, HIGH

AFFINITY, CRYSTAL 2 PACKING

MOTIF, PROGRAMMING

PROPENSITY TO CRYSTALLIZE, 3

IMMUNOGLOBULIN

318
1aqk
L
40
260
1.7e−26

64.54
FAB B7-15A2; CHAIN: L, H;
IMMUNOGLOBULIN HUMAN FAB,

ANTI-TETANUS TOXOID, HIGH

AFFINITY, CRYSTAL 2 PACKING

MOTIF, PROGRAMMING

PROPENSITY TO CRYSTALLIZE, 3

IMMUNOGLOBULIN

318
1aqk
L
41
241
1.7e−26
0.21
0.74

FAR B7-15A2; CHAIN: L, H;
IMMUNOGLOBULIN HUMAN FAB,

ANTI-TETANUS TOXOID, HIGH

AFFINITY, CRYSTAL 2 PACKING

MOTIF, PROGRAMMING

PROPENSITY TO CRYSTALLIZE, 3

IMMUNOGLOBULIN

318
1ay1
H
50
236
8.5e−23
−0.10
0.28

TP7 FAB; CHAIN: L, H;
IMMUNOGLOBULIN

IMMUNOGLOBULIN, ANTBODY,

FAB, ENZYME INHIBITOR, PCR, 2

HOT START

318
1b2w
H
39
247
1.2e−19

63.67
ANTIBODY (LIGHT CHAIN);
IMMUNE SYSTEM

CHAIN: L; ANTIBODY (HEAVY
IMMUNOGLOBULIN;

CHAIN); CHAIN: H;
IMMUNOGLOBULIN ANTIBODY

ENGINEERING, HUMANIZED AND

CHIMERIC ANTIBODY, FAB, 2 X-RAY

STRUCTURE, THREE-DIMENSIONAL,

STRYCTURE, GAMMA-3

INTERFERON, IMMUNE SYSTEM

318
1b2w
L
38
259
1.5e−23

64.13
ANTIBODY (LIGHT CHAIN):
IMMUNE SYSTEM

CHAIN: L; ANTIBODY (HEAVY
IMMUNOGLOBULIN;

CHAIN): CHAIN: H;
IMMUNOGLOBULIN ANTIBODY

ENGINEERING, HUMANIZED AND

CHIMERIC ANTIBODY, FAB, 2 X-RAY

STRUCTURE, THREE-DIMENSIONAL

STRYCTURE, GAMMA-3

INTERFERON, IMMUNE SYSTEM

318
1b2w
L
39
232
1.5e−23
−0.00
0.07

ANTIBODY (LIGHT CHAIN);
IMMUNE SYSTEM

CHAIN: L; ANTIBODY (HEAVY
IMMUNOGLOBULIN;

CHAIN); CHAIN: H;
IMMUNOGLOBULIN ANTIBODY

ENGINEERING, HUMANIZED AND

CHIMERIC ANTIBODY, FAB, 2 X-RAY

STRUCTURE, THREE-DIMENSIONAL

STRYCTURE, GAMMA-3

INTERFERON, IMMUNE SYSTEM

318
1b4j
H
39
247
1.2e−19

67.97
ANTIBODY; CHAIN: L, H;
ANTIBODY ENGINEERING

ANTIBODY ENGINEERING,

HUMANIZED AND CHIMERIC

ANTIBODIES, 2 FAB, X-RAY

STRUCTURES, GAMMA-INTERFERON

318
1baf
H
37
259
8.5e−21

65.16
IMMUNOGLOBULIN FAB

FRAGMENT OF MURINE

MONOCLONAL ANTIBODY AN02

COMPLEX 1BAF 3 WITH ITS

HAPTEN (2,2,6,6-TETRAMETHYL-

1-PIPERIDINYLOXY-1BAF 4

DINITROPHENYL) 1BAF 5

318
1bih
A
90
246
8.5e−20
0.30
0.41

HEMOLIN; CHAIN: A, B;
INSECT IMMUNITY INSECT

IMMUNITY, LPS-BINDING,

HOMOPHILIC ADHESION

318
1bjl
L
39
232
1e−22
0.22
0.11

FAB FRAGMENT; CHAIN: L, H, J,
COMPLEX (ANTIBODY/ANTIGEN)

K; VASCULAR ENDOTHELIAL
FAB-12; VEGF; COMPLEX

GROWTH FACTOR; CHAIN: V, W;
(ANTIBODY/ANTIGEN), ANGIOGENIC

FACTOR

318
1bjm
A
40
241
1.7e−26
0.07
0.11

LOC-LAMBDA I TYPE LIGHT-
IMMUNOGLOBULIN BENCE-JONES

CHAIN DIMER; 1BJM 6 CHAIN: A,
PROTEIN; 1BJM 8 BENCE JONES,

B; 1BJM 7
ANTIBODY, MULTIPLE

QUATERNARY STRUCTURES 1BJM 13

318
1bm3
H
37
259
6.8e−21

68.28
IMMUNOGLOBULIN OPG2 FAB,
IMMUNE SYSTEM

CONSTANT DOMAIN; CHAIN: L;
IMMUNOGLOBULIN

IMMUNOGLOBULIN OPG2 FAB,

VARIABLE DOMAIN; CHAIN: H;

318
1ct8
H
37
254
5.1e−22

64.09
CATALYTIC ANTIBODY 19A4
CATALYTIC ANTIBODY CATALYTIC

(LIGHT CHAIN); CHAIN: L;
ANTIBODY, TERPENOID SYNTHASE,

CATALYTIC ANTIBODY 19A4
CARBOCATION, 2 CYCLIZATION

(HEAVY CHAIN); CHAIN: H;
CASCADE

318
1cic
B
38
257
5.1e−22

67.07
IG HEAVY CHAIN V REGIONS;
IMMUNOGLOBULIN

CHAIN: A; IG HEAVY CHAIN V
IMMUNOGLOBULIN, FAB COMPLEX,

REGIONS; CHAIN: B; IG HEAVY
IDIOTOPE, ANTI-IDIOTOPE

CHAIN V REGIONS; CHAIN: C; IG

HEAVY CHAIN V REGIONS;

CHAIN D;

318
1cs6
A
45
247
1.7e−32
0.03
0.77

AXONIN-I; CHAIN: A;
CELL ADHESION NEURAL CELL

ADHESION

318
1ct8
B
38
259
3.4e−22

64.34
7C8 FAB FRAGMENT; SHORT
IMMUNE SYSTEM ABZYME

CHAIN; CHAIN: A, C; 7C8 FAB
TRANSITION STATE ANALOG,

FRAGMENT; LONG CHAIN;
IMMUNE SYSTEM

CHAIN: B, D

318
1cvs
C
174
249
1.7e−12
0.27
0.34

FIBROBLAST GROWTH FACTOR
GROWTH FACTOR/GROWTH FACTOR

2; CHAIN: A, B; FIBROBLAST
RECEPTOR FGF, FGFR,

GROWTH FACTOR RECEPTOR 1;
IMMUNOGLOBULIN-LIKE, SIGNAL

CHAIN: C, D;
TRANSDUCTION, 2 DIMERIZATION,

GROWTH FACTOR/GROWTH FACTOR

RECEPTOR

318
1cvs
D
174
249
1.7e−12
0.22
0.34

FIBROBLAST GROWTH FACTOR
GROWTH FACTOR/GROWTH FACTOR

2; CHAIN: A, B; FIBROBLAST
RECEPTOR FGF, FGFR,

GROWTH FACTOR RECEPTOR 1;
IMMUNOGLOBULIN-LIKE, SIGNAL

CHAIN: C, D;
TRANSDUCTION, 2 DIMERIZATION,

GROWTH FACTOR/GROWTH FACTOR

RECEPTOR

318
1dee
A
39
232
3.4e−23
0.15
0.06

IGM RF 2A2; CHAIN: A, C, E; IGM
IMMUNE SYSTEM FAB-IBP COMPLEX

RF 2A2; CHAIN: B, D, F;
CRYSTAL STRUCTURE 2.7A

IMMUNOGLOBULIN G BINDING
RESOLUTION BINDING 2 OUTSIDE

PROTEIN A; CHAIN: G, H;
THE ANTIGEN COMBINING SITE

SUPERANTIGEN FAB VH3 3

SPECIFICITY

318
1ev2
E
173
249
1.7e−13
0.13
0.25

FIBROBLAST GROWTH FACTOR
GROWTH FACTOR/GROWTH FACTOR

2; CHAIN: A, B, C, D; FIBROBLAST
RECEPTOR FGF2; FGFR2;

GROWTH FACTOR RECEPTOR 2;
IMMUNOGLOBULIN (IG)LIKE

CHAIN: E, F, G, H;
DOMAINS BELONGING TO THE I-SET

2 SUBGROUP WITHIN IG-LIKE

DOMAINS, B-TREFOIL FOLD

318
1evl
C
174
249
1.7e−12
0.37
0.13

FIBROBLAST GROWTH FACTOR
GROWTH FACTOR/GROWTH FACTOR

1; CHAIN: A, B; FIBROBLAST
RECEPTOR FGFI; EGERI;

GROWTH FACTOR RECEPTOR 1;
IMMUNOGLOBULIN (IG) LIKE

CHAIN: C, D;
DOMAINS BELONGING TO THE I-SET

2 SUBGROUP WITHIN IG-LIKE

DOMAINS, B-TREFOIL FOLD

318
1fai
H
38
254
3.4e−19

63.84
IMMUNOGLOBULIN FAB

FRAGMENT FROM A

MONOCLONAL ANTI-ARSONATE

ANTIBODY, R19.9 1FAI 3

(IGG2B,KAPPA) 1FAI 4

318
1thg
A
154
247
1.5e−08
0.27
0.16

TELOKIN; CHAIN: A
CONTRACTILE PROTEIN

IMMUNOGLOBULIN FOLD, BETA

BARREL

318
1fvd
B
37
247
5.1e−21

66.24
IMMUNOGLOBULIN FAB

FRAGMENT OF HUMANIZED

ANTIBODY 4D5, VERSION 4 IFVD 3

318
1hnf

43
232
1.3e−23
0.02
0.10

TLYMPHOCYTE ADHESION

GLYCOPROTEIN CD2 (HUMAN)

IHNF 3

318
1iai
H
38
254
5.1e−20

65.01
IDIOTYPIC FAB 730.1.4 (IGG1) OF
COMPLEX (IMMUNOGLOBULIN

VIRUS IIAI 5 CHAIN: L, H; 1IAI 7
IGG1/IGG2A)

ANTI-IDIOTYPIC FAB 409.5.3

(IGG2A); IIAI 9 CHAIN: M, I 1IAI

10

318
1lil
A
40
241
1.7e−25
0.18
0.13

LAMBDA III BENCE JONES
IMMUNOGLOBULIN

PROTEIN CLE; CHAIN: A, B
IMMUNOGLOBULIN, BENCE JONES

PROTEIN

318
1nca
H
38
254
1.5e−21

67.34
HYDROLASE(O-GLYCOSYL) N9

NEURAMINIDASE-NC41

(E.C.3.2.1.18) COMPLEX WITH FAB

1NCA 3

318
1nsn
H
37
254
1.4e−22

65.27
IGG FAB (IGG1, KAPPA): 1NSN 4
COMPLEX

CHAIN: L, H; 1NSN 5
(IMMUNOGLOBULIN/HYDROLASE)

STAPHYLOCOCCAL NUCLEASE:
N10 FAB IMMUNOGLOBULIN: 1NSN 7

1NSN 9 CHAIN: S; 1NSN 10
STAPHYLOCOCCAL NUCLEASE

RIBONUCLEATE, 1NSN 11

IMMUNOGLOBULIN.

STAPHYLOCOCCAL NUCLEASE 1NSN

25

318
1wio
A
47
262
7.5e−28
0.19
0.29

T-CELL SURFACE
GLYCOPROTEIN CD4;

GLYCOPROTEIN CD4; CHAIN: A,
IMMUNOGLOBULIN FOLD.

B;
TRANSMEMBRANE, GLYCOPROTEIN,

T-CELL, 2 MHC LIPOPROTEIN,

POLYMORPHISM

318
25c8
H
38
255
5.1e−23

64.25
IGG 5C8; CHAIN: L, H;
CATALYTIC ANTIBODY CATALYTIC

ANTIBODY, FAB, RING CLOSURE

REACTION

318
25c8
H
50
236
5.1e−23
0.12
0.19

IGG 5C8; CHAIN: L, H;
CATALYTIC ANTIBODY CATALYTIC

ANTIBODY, FAB, RING CLOSURE

REACTION

318
2cgr
H
37
254
1.2e−17

65.11
IMMUNOGLOBULIN IGG2B

(KAPPA) FAB FRAGMENT

COMPLEXED WITH ANTIGEN

2CGR 3 N-(P-CYANOPHENYL)-N′-

(DIPHENYLEMETHYL)

GUANIDINEACETIC ACID 2CGR 4

318
2tb4
L
40
241
1.5e−25
0.29
0.37

IMMUNOGLOBULIN

IMMUNOGLOBULIN FAB 2FB4 4

318
2fgw
L
39
232
1.2e−23
0.27
0.01

IMMUNOGLOBULIN FAB

FRAGMENT OF A HUMANIZED

VERSION OF THE ANTI-CD18

2FGW 3 ANTIBODY ‘H52’ (HUH52-

OZ FAB) 2FGW 4

318
2mcg
I
40
241
1.2e−27
0.14
0.30

IMMUNOGLOBULIN

IMMUNOGLOBULIN LAMBDA

LIGHT CHAIN DIMER (/MCG$)

2MCG 3 (TRIGONAL FORM) 2MCG 4

318
2pcp
B
38
255
3.4e−21

68.25
IMMUNOGLOBULIN; CHAIN: A, B,
IMMUNOGLOBULIN

C, D;
IMMUNOGLOBULIN

318
32c2
B
50
236
3.4e−23
0.21
0.13

IGG1 ANTIBODY 32C2; CHAIN: A;
IMMUNE SYSTEM FAB, ANTIBODY,

IGG1 ANTIBODY 32C2; CHAIN: B;
AROMATASE, P450

318
3fct
B
37
247
8.5e−19

66.99
METAL CHELATASE CATALYTIC
IMMUNE SYSTEM METAL

ANTIBODY; CHAIN: A, C; METAL
CHELATASE, CATALYTIC

CHELATASE CATALYTIC
ANTIBODY, FAB FRAGMENT,

ANTIBODY; CHAIN: B, D;
IMMUNE 2 SYSTEM

318
3ncm
A
168
245
4.5e−09
0.09
−0.14

NEURAL CELL ADHESION
CELL ADHESION PROTEIN NCAM

MOLECULE, LARGE ISOFORM;
MODULE 2; CELL ADHESION.

CHAIN: A;
GLYCOPROTEIN, HEPARIN-BINDING,

GPI-ANCHOR, 2 NEURAL ADHESION

MOLECULE, IMMUNOGLOBULIN

FOLD, HOMOPHILIC 3 BINDING,

CELL ADHESION PROTEIN

318
7fab
L
40
241
1.7e−26
0.00
0.17

IMMUNOGLOBULIN

IMMUNOGLOBULIN FAB' NEW

(LAMBDA LIGHT CHAIN) 7FAB 3

318
8fab
A
43
241
1.4e−26
0.39
0.18

IMMUNOGLOBULIN FAB

FRAGMENT FROM HUMAN

IMMUNOGLOBULIN IGG1

(LAMBDA, HIL) 8FAB 3

319
1cly
A
8
171
1.4e−63

109.08
RAS-RELATED PROTEIN RAP-1A;
SIGNALING PROTEIN GTP-BINDING

CHAIN: A; PROTO-ONKOGENE
PROTEINS, PROTEIN-PROTEIN

SERINE/THREONINE PROTEIN
COMPLEX, EFFECTORS

KINASE CHAIN: B;

319
1cly
A
9
171
1.4e−63
0.82
1.00

RAS-RELATED PROTEIN RAP-1A;
SIGNALING PROTEIN GTP-BINDING

CHAIN: A; PROTO-ONKOGENE
PROTEINS, PROTEIN-PROTEIN

SERINE/THREONINE PROTEIN
COMPLEX, EFFECTORS

KINASE CHAIN: B;

319
1ctq
A
8
172
6.8e−65

108.57
TRANSFORMING PROTEIN P21/H-
SIGNALING PROTEIN G PROTEIN,

RAS-1; CHAIN: A;
GTP HYDROLYSIS, KINETIC

CRYSTALLOGRAPHY, 2 SIGNALING

PROTEIN

319
1ctq
A
9
171
6.8e−65
0.88
1.00

TRANSFORMING PROTEIN P21/H-
SIGNALING PROTEIN G PROTEIN,

RAS-1; CHAIN: A;
GTP HYDROLYSIS, KINETIC

CRYSTALLOGRAPHY, 2 SIGNALING

PROTEIN

319
1cxz
A
3
172
3.4e−55

108.33
HIS-TAGGED TRANSFORMING
SIGNALING PROTEIN PROTEIN-

PROTEIN RHOA(0-181); CHAIN: A;
PROTEIN COMPLEX, ANTIPARALLEL

PKN; CHAIN: B;
COILED-COIL

319
1d5c
A
9
165
6e−67
0.83
1.00

RAB6 GTPASE; CHAIN: A;
ENDOCYTOSIS/EXOCYTOSIS G-

PROTEIN, GTPASE, RAB6,

VESICULAR TRAFFICKING

319
1d5c
A
9
169
5.1e−63
0.87
1.00

RAB6 GTPASE; CHAIN: A;
ENDOCYTOSIS/EXOCYTOSIS G-

PROTEIN, GTPASE, RAB6,

VESICULAR TRAFFICKING

319
1ds6
A
9
170
1.5e−55
0.73
1.00

RAS-RELATED C3 BOTULINUM
SIGNALING PROTEIN P21-RAC2; RHO

TOXIN SUBSTRATE 2; CHAIN: A;
GDI 2, RHO-GDI BETA, LY-GDI; BETA

RHO GDP-DISSOCIATION
SANDWHICH, PROTEIN-PROTEIN

INHIBITOR 2; CHAIN: B;
COMPLEX, G-DOMAIN, 2

IMMUNOGLOBULIN FOLD, WALKER

FOLD, GTP-BINDING PROTEIN

319
1ek0
A
9
169
5.1e−61
0.93
1.00

GTP-BINDING PROTEIN YPT51;
ENDOCYTOSIS/EXOCYTOSIS G

CHAIN: A;
PROTEIN, VESICULAR TRAFFIC, GTP

HYDROLYSIS, YPT/RAB 2 PROTEIN,

ENDOCYTOSIS, HYDROLASE

319
1kao

8
172
1.2e−59

109.78
RAP2A; CHAIN: NULL;
GTP-BINDING PROTEIN GTP-

BINDING PROTEIN, SMALL G

PROTEIN, RAP2, GDP, RAS

319
1kao

9
169
1.2e−59
0.96
1.00

RAP2A; CHAIN: NULL;
GTP-BINDING PROTEIN GTP-

BINDING PROTEIN, SMALL G

PROTEIN, RAP2, GDP, RAS

319
1tx4
B
6
170
1.1e−56

97.67
P50-RHOGAP; CHAIN: A;
COMPLEX(GTPASE

TRANSFORMING PROTEIN RHOA;
ACTIVATN/PROTO-ONCOGENE)

CHAIN: B;
GTPASE-ACTIVATING PROTEIN

RHOGAP; COMPLEX (GTPASE

ACTIVATION/PROTO-ONCOGENE).

GTPASE, 2 TRANSITION STATE. GAP

319
1tx4
B
7
170
1.1e−56
0.65
1.00

P50-RHOGAP; CHAIN: A;
COMPLEX(GTPASE

TRANSFORMING PROTEIN RHOA;
ACTIVATN/PROTO-ONCOGENE)

CHAIN: B;
GTPASE-ACTIVATING PROTEIN

RHOGAP; COMPLEX (GTPASE

ACTIVATION/PROTO-ONCOGENE),

GTPASE, 2 TRANSITION STATE, GAP

319
1zbd
A
3
178
5.1e−70

154.65
RAB-3A; CHAIN: A; RABPHILIN-
COMPLEX (GTP-BINDING/EFFECTOR)

3A; CHAIN: B;
RAS-RELATED PROTEIN RAB3A;

COMPLEX (GTP-

BINDING/EFFECTOR), G PROTEIN,

EFFECTOR, RABCDR, 2 SYNAPTIC

EXOCYTOSIS, RAB PROTEIN, RAB3A,

RABPHILIN

319
1zbd
A
5
175
5.1e−70
0.92
1.00

RAB-3A; CHAIN: A; RABPHILIN-
COMPLEX (GTP-BINDING/EFFECTOR)

3A; CHAIN: B;
RAS-RELATED PROTEIN RAB3A;

COMPLEX (GTP-

BINDING/EFFECTOR), G PROTEIN,

EFFECTOR, RABCDR, 2 SYNAPTIC

EXOCYTOSIS, RAB PROTEIN, RAB3A,

RABPHILIN

319
3rab
A
4
172
1.5e−70
0.71
1.00

RAB3A; CHAIN: A;
HYDROLASE G PROTEIN,

VESICULAR TRAFFICKING, GTP

HYDROLYSIS, RAB 2 PROTEIN,

NEUROTRANSMITTER RELEASE,

HYDROLASE

319
3rab
A
4
172
1.5e−70

170.48
RAB3A; CHAIN: A;
HYDROLASE G PROTEIN,

VESICULAR TRAFFICKING, GTP

HYDROLYSIS, RAB 2 PROTEIN,

NEUROTRANSMITTER RELEASE,

HYDROLASE

321
1b0x
A
227
287
1.5e−05
1.26
0.99

EPHA4 RECEPTOR TYROSINE
TRANSFERASE RECEPTOR

KINASE; CHAIN: A;
TYROSINE KINASE, PROTEIN

INTERACTION MODULE, 2

DIMERIZATION DOMAIN,

TRANSFERASE

321
1b4f
A
226
297
1.2e−13
0.85
0.74

EPHB2; CHAIN: A, B, C, D, E, F, G,
SIGNAL TRANSDUCTION SAM

H;
DOMAIN, EPH RECEPTOR, SIGNAL

TRANSDUCTION, OLIGOMER

321
1sgg

226
287
3e−06
0.84
0.92

EPHRIN TYPE-B RECEPTOR 2;
TYROSINE-PROTEIN KINASE NMR,

CHAIN: NULL;
RECEPTOR OLIGOMERIZATION, EPH

RECEPTORS, TYROSINE 2

PHOSPHORYLATION, SIGNAL

TRANSDUCTION, TYROSINE-

PROTEIN 3 KINASE

323
1a17

114
266
3.4e−12
0.15
0.43

SERINE/THREONINE PROTEIN
HYDROLASE TETRATRICOPEPTIDE,

PHOSPHATASE 5; CHAIN: NULL;
TRP; HYDROLASE, PHOSPHATASE,

PROTEIN-PROTEIN INTERACTIONS,

TPR, 2 SUPER-HELIX, X-RAY

STRUCTURE

323
1a17

130
279
4.5e−14
0.30
−0.01

SERINE/THREONINE PROTEIN
HYDROLASE TETRATRICOPEPTIDE,

PHOSPHATASE 5; CHAIN: NULL;
TRP; HYDROLASE, PHOSPHATASE,

PROTEIN-PROTEIN INTERACTIONS,

TPR, 2 SUPER-HELIX, X-RAY

STRUCTURE

323
1a17

157
318
6e−08
0.17
−0.02

SERINE/THREONINE PROTEIN
HYDROLASE TETRATRICOPEPTIDE,

PHOSPHATASE 5; CHAIN: NULL;
TRP; HYDROLASE, PHOSPHATASE,

PROTEIN-PROTEIN INTERACTIONS,

TPR, 2 SUPER-HELIX, X-RAY

STRUCTURE

323
1a17

246
380
6.8e−13
0.22
0.22

SERINE/THREONINE PROTEIN
HYDROLASE TETRATRICOPEPTIDE,

PHOSPHATASE 5; CHAIN: NULL;
TRP; HYDROLASE, PHOSPHATASE,

PROTEIN-PROTEIN INTERACTIONS,

TPR, 2 SUPER-HELIX, X-RAY

STRUCTURE

323
1a17

293
400
1.7e−13
0.34
−0.12

SERINE/THREONINE PROTEIN
HYDROLASE TETRATRICOPEPTIDE,

PHOSPHATASE 5; CHAIN: NULL;
TRP; HYDROLASE, PHOSPHATASE,

PROTEIN-PROTEIN INTERACTIONS,

TPR, 2 SUPER-HELIX, X-RAY

STRUCTURE

323
1a17

4
143
5.1e−16
0.43
0.07

SERINE/THREONINE PROTEIN
HYDROLASE TETRATRICOPEPTIDE,

PHOSPHATASE 5; CHAIN: NULL;
TRP; HYDROLASE, PHOSPHATASE,

PROTEIN-PROTEIN INTERACTIONS,

TPR, 2 SUPER-HELIX, X-RAY

STRUCTURE

323
1b89
A
11
275
0.00017
0.05
0.04

CLATHRIN HEAVY CHAIN:
CLATHRIN CLATHRIN, TRISKELION,

CHAIN: A;
COATED VESICLES, ENDOCYTOSIS,

SELF-2 ASSEMBLY, ALPHA-ALPHA

SUPERHELIX

323
1e96
B
162
318
6.8e−11
0.31
0.11

RAS-RELATED C3 BOTULINUM
SIGNALLING COMPLEX RAC1:

TOXIN SUBSTRATE 1; CHAIN: A;
P67PHOX; SIGNALLING COMPLEX,

NEUTROPHIL CYTOSOL FACTOR
GTPASE, NADPH OXIDASE, PROTEIN-

2 (NCF-2) CHAIN: B;
PROTEIN 2 COMPLEX, TPR MOTIF

323
1e96
B
2
109
6.8e−10
0.31
−0.06

RAS-RELATED C3 BOTULINUM
SIGNALLING COMPLEX RAC1;

TOXIN SUBSTRATE 1; CHAIN: A;
P67PHOX; SIGNALLING COMPLEX,

NEUTROPHIL CYTOSOL FACTOR
GTPASE, NADPH OXIDASE, PROTEIN-

2 (NCF-2) CHAIN: B;
PROTEIN 2 COMPLEX, TPR MOTIF

323
1e96
B
245
392
1.2e−08
0.16
−0.14

RAS-RELATED C3 BOTULINUM
SIGNALLING COMPLEX RAC1;

TOXIN SUBSTRATE 1; CHAIN: A;
P67PHOX; SIGNALLING COMPLEX,

NEUTROPHIL CYTOSOL FACTOR
GTPASE, NADPH OXIDASE, PROTEIN-

2 (NCF-2) CHAIN: B;
PROTEIN 2 COMPLEX, TPR MOTIF

323
1e96
B
82
232
1.2e−10
0.27
−0.02

RAS-RELATED C3 BOTULINUM
SIGNALLING COMPLEX RAC1;

TOXIN SUBSTRATE 1; CHAIN: A;
P67PHOX; SIGNALLING COMPLEX,

NEUTROPHIL CYTOSOL FACTOR
GTPASE, NADPH OXIDASE, PROTEIN-

2 (NCF-2) CHAIN: B;
PROTEIN 2 COMPLEX, TPR MOTIF

323
1elr
A
11
114
1.7e−15
0.50
0.90

TPR2A-DOMAIN OF HOP; CHAIN:
CHAPERONE HOP, TPR-DOMAIN,

A; HSP90-PEPTIDE MEEVD;
PEPTIDE-COMPLEX, HELICAL

CHAIN: B;
REPEAT, HSP90, 2 PROTEIN BINDING

323
1elr
A
121
233
1.2e−12
0.42
0.22

TPR2A-DOMAIN OF HOP; CHAIN:
CHAPERONE HOP, TPR-DOMAIN,

A; HSP90-PEPTIDE MEEVD;
PEPTIDE-COMPLEX, HELICAL

CHAIN: B;
REPEAT, HSP90, 2 PROTEIN BINDING

323
1elr
A
169
274
3.4e−13
0.04
0.06

TPR2A-DOMAIN OF HOP; CHAIN:
CHAPERONE HOP, TPR-DOMAIN.

A; HSP90-PEPTIDE MEEVD;
PEPTIDE-COMPLEX, HELICAL

CHAIN: B;
REPEAT, HSP90, 2 PROTEIN BINDING

323
1elr
A
1
74
1e−09
0.40
−0.01

TPR2A-DOMAIN OF HOP; CHAIN:
CHAPERONE HOP, TPR-DOMAIN.

A; HSP90-PEPTIDE MEEVD;
PEPTIDE-COMPLEX, HELICAL

CHAIN: B;
REPEAT, HSP90, 2 PROTEIN BINDING

323
1elr
A
212
313
1.2e−15
0.58
−0.05

TPR2A-DOMAIN OF HOP; CHAIN:
CHAPERONE HOP, TPR-DOMAIN,

A; HSP90-PEPTIDE MEEVD;
PEPTIDE-COMPLEX, HELICAL

CHAIN: B;
REPEAT, HSP90, 2 PROTEIN BINDING

323
1elr
A
252
356
1.2e−13
0.05
0.05

TPR2A-DOMAIN OF HOP; CHAIN:
CHAPERONE HOP, TPR-DOMAIN,

A; HSP90-PEPTIDE MEEVD;
PEPTIDE-COMPLEX, HELICAL

CHAIN: B;
REPEAT, HSP90, 2 PROTEIN BINDING

323
1elr
A
332
411
1e−11
0.04
−0.18

TPR2A-DOMAIN OF HOP; CHAIN:
CHAPERONE HOP, TPR-DOMAIN,

A; HSP90-PEPTIDE MEEVD;
PEPTIDE-COMPLEX, HELICAL

CHAIN: B;
REPEAT, HSP90, 2 PROTEIN BINDING

323
1elr
A
56
157
1.5e−07
−0.03
0.21

TPR2A-DOMAIN OF HOP; CHAIN:
CHAPERONE HOP, TPR-DOMAIN,

A; HSP90-PEPTIDE MEEVD;
PEPTIDE-COMPLEX, HELICAL

CHAIN: B;
REPEAT, HSP90, 2 PROTEIN BINDING

323
1elr
A
88
194
1.7e−13
0.19
0.28

TPR2A-DOMAIN OF HOP; CHAIN:
CHAPERONE HOP, TPR-DOMAIN,

A: HSP90-PEPTIDE MEEVD;
PEPTIDE-COMPLEX, HELICAL

CHAIN: B;
REPEAT, HSP90, 2 PROTEIN BINDING

323
1elw
A
126
244
3.4e−11
0.18
0.81

TPR1-DOMAIN OF HOP; CHAIN: A,
CHAPERONE HOP, TPR-DOMAIN.

B: HSC70-PEPTIDE; CHAIN: C, D;
PEPTIDE-COMPLEX, HELICAL

REPEAT, HSC70, 2 HSP70, PROTEIN

BINDING

323
1elw
A
249
366
1e−11
0.20
0.19

TPR1-DOMAIN OF HOP; CHAIN: A,
CHAPERONE HOP, TPR-DOMAIN.

B: HSC70-PEPTIDE; CHAIN: C, D;
PEPTIDE-COMPLEX, HELICAL

REPEAT, HSC70, 2 HSP70, PROTEIN

BINDING

323
1elw
A
293
393
3.4e−11
0.29
−0.08

TPR1-DOMAIN OF HOP; CHAIN: A,
CHAPERONE HOP, TPR-DOMAIN,

B; HSC70-PEPTIDE; CHAIN: C, D;
PEPTIDE-COMPLEX, HELICAL

REPEAT, HSC70, 2 HSP70, PROTEIN

BINDING

323
1elw
A
4
121
3.4e−14
0.56
0.62

TPR1-DOMAIN OF HOP; CHAIN: A,
CHAPERONE HOP, TPR-DOMAIN,

B; HSC70-PEPTIDE; CHAIN: C, D;
PEPTIDE-COMPLEX, HELICAL

REPEAT, HSC70, 2 HSP70, PROTEIN

BINDING

323
1elw
A
81
208
1.2e−08
0.18
−0.11

TPR1-DOMAIN OF HOP; CHAIN: A,
CHAPERONE HOP, TPR-DOMAIN,

B; HSC70-PEPTIDE; CHAIN: C, D;
PEPTIDE-COMPLEX, HELICAL

REPEAT, HSC70, 2 HSP70, PROTEIN

BINDING

323
1fch
A
104
410
1e−31
0.02
−0.02

PEROXISOMAL TARGETING
SIGNALING PROTEIN PEROXISMORE

SIGNAL 1 RECEPTOR; CHAIN: A,
RECEPTOR 1, PTS1-BP, PEROXIN-5,

B; PTS1-CONTAINING PEPTIDE;
PTS1 PROTEIN-PEPTIDE COMPLEX,

CHAIN: C, D;
TETRATRICOPEPTIDE REPEAT, TPR,

2 HELICAL REPEAT

323
1fch
A
11
317
1.2e−29
0.37
0.87

PEROXISOMAL TARGETING
SIGNALING PROTEIN PEROXISMORE

SIGNAL 1 RECEPTOR; CHAIN: A,
RECEPTOR 1, PTS1-BP, PEROXIN-5,

B; PTSI-CONTAINING PEPTIDE;
PTS1 PROTEIN-PEPTIDE COMPLEX,

CHAIN: C, D;
TETRATRICOPEPTIDE REPEAT, TPR,

2 HELICAL REPEAT

323
1fch
A
2
263
3.4e−23
0.36
0.99

PEROXISOMAL TARGETING
SIGNALING PROTEIN PEROXISMORE

SIGNAL 1 RECEPTOR; CHAIN: A,
RECEPTOR 1, PTS1-BP, PEROXIN-5,

B; PTS1-CONTAINING PEPTIDE;
PTS1 PROTEIN-PEPTIDE COMPLEX,

CHAIN: C, D;
TETRATRICOPEPTIDE REPEAT, TPR,

2 HELICAL REPEAT

323
1qqe
A
120
375
3.4e−10
0.14
0.58

VESICULAR TRANSPORT
PROTEIN TRANSPORT HELIX-TURN-

PROTEIN SEC17; CHAIN: A;
HELIX TPR-LIKE REPEAT, PROTEIN

TRANSPORT

323
1qqe
A
221
388
3.4e−10
0.01
−0.09

VESICULAR TRANSPORT
PROTEIN TRANSPORT HELIX-TURN-

PROTEIN SEC17; CHAIN: A;
HELIX TPR-LIKE REPEAT, PROTEIN

TRANSPORT

323
1qqe
A
3
188
1e−11
0.48
0.19

VESICULAR TRANSPORT
PROTEIN TRANSPORT HELIX-TURN-

PROTEIN SEC17; CHAIN: A;
HELIX TPR-LIKE REPEAT, PROTEIN

TRANSPORT

323
1qqe
A
68
359
3.4e−10

54.55
VESICULAR TRANSPORT
PROTEIN TRANSPORT HELIX-TURN-

PROTEIN SEC17; CHAIN: A;
HELIX TPR-LIKE REPEAT, PROTEIN

TRANSPORT

324
1b4f
A
28
74
0.00045
0.19
0.90

EPHB2; CHAIN: A, B, C, D, E, F, G,
SIGNAL TRANSDUCTION SAM

H;
DOMAIN, EPH RECEPTOR, SIGNAL

TRANSDUCTION, OLIGOMER

329
1b7f
A
421
559
5.1e−20
−0.15
0.98

SXL-LETHAL PROTEIN; CHAIN: A,
RNA-BINDING PROTEIN/RNA TRA

B; RNA (5′-
PRE-MRNA; SPLICING REGULATION,

R(P*GP*UP*UP*GP*UP*UP*UP*UP
RNP DOMAIN, RNA COMPLEX

*UP*UP*UP*U)- CHAIN: P, Q;

329
1cvj
A
423
547
1.7e−21
0.00
0.52

POLYDENYLATE BINDING
GENE REGULATION/RNA POLY(A)

PROTEIN 1; CHAIN: A, B, C, D, E,
BINDING PROTEIN 1, PABP 1; RRM,

F, G, H; RNA (5′-
PROTEIN-RNA COMPLEX, GENE

R(*AP*AP*AP*AP*AP*AP*AP*AP*
REGULATION/RNA

AP*AP*A)-3′); CHAIN: M, N, O, P,

Q, R, S, T;

329
1cvj
B
423
535
3.4e−20
0.09
0.63

POLYDENYLATE BINDING
GENE REGULATION/RNA POLY(A)

PROTEIN 1; CHAIN: A, B, C, D, E,
BINDING PROTEIN 1, PABP 1; RRM,

F, G, H; RNA (5′-
PROTEIN-RNA COMPLEX, GENE

R(*AP*AP*AP*AP*AP*AP*AP*AP*
REGULATION/RNA

AP*AP*A)-3′); CHAIN: M, N, O, P,

Q, R, S, T;

329
1cvj
F
423
502
3.4e−17
054
0.87

POLYDENYLATE BINDING
GENE REGULATION/RNA POLY(A)

PROTEIN 1; CHAIN: A, B, C, D, E,
BINDING PROTEIN 1, PABP 1; RRM,

F, G, H; RNA (5′-
PROTEIN-RNA COMPLEX, GENE

R(*AP*AP*AP*AP*AP*AP*AP*AP*
REGULATION/RNA

AP*AP*A)-3′); CHAIN: M, N, O, P,

Q, R, S, T;

329
1cvj
H
423
535
1.4e−17
−0.03
0.49

POLYDENYLATE BINDING
GENE REGULATION/RNA POLY(A)

PROTEIN 1; CHAIN: A, B, C, D, E,
BINDING PROTEIN 1, PABP 1; RRM,

F, G, H; RNA (5′-
PROTEIN-RNA COMPLEX, GENE

R(*AP*AP*AP*AP*AP*AP*AP*AP*
REGULATION/RNA

AP*AP*A)-3′); CHAIN: M, N, O, P,

Q, R, S, T;

329
1d8z
A
418
496
6.8e−19
012
0.82

HU ANTIGEN C; CHAIN: A;
RNA BINDING PROTEIN RNA-

BINDING DOMAIN

329
1hal

416
544
1.7e−17
−0.01
0.03

HNRNP A1; CHAIN: NULL;
NUCLEAR PROTEIN

HETEROGENEOUS NUCLEAR

RIBONUCLEOPROTEIN A1, NUCLEAR

PROTEIN, HNRNP, RBD, RRM, RNP,

RNA BINDING, 2

RIBONUCLEOPROTEIN

329
2sxl

421
496
1.2e−16
0.37
0.96

SEX-LETHAL PROTEIN; CHAIN:
RNA-BINDING DOMAIN RNA-

NULL;
BINDING DOMAIN, ALTERNATIVE

SPLICING

329
2upl
A
415
550
1e−17
−0.04
0.05

HETEROGENEOUS NUCLEAR
COMPLEX

RIBONUCLEOPROTEIN A1;
(RIBONUCLEOPROTEIN/DNA) HNRNP

CHAIN: A; 12-NUCLEOTIDE
A1, UPI; COMPLEX

SINGLE-STRANDED TELOMETRIC
(RIBONUCLEOPROTEIN/DNA).

DNA; CHAIN: B;
HETEROGENEOUS NUCLEAR 2

RIBONUCLEOPROTEIN A1

329
3sxl
A
421
559
1.7e−19
0.05
0.89

SEX-LETHAL; CHAIN: A, B, C,
RNA BINDING DOMAIN RNA

BINDING DOMAIN, RBD, RNA

RECOGNITION MOTIF, RRM, 2

SPLICING INHIBITOR,

TRANSLATIONAL INHIBITOR, SEX 3

DETERMINATION, X CHROMOSOME

DOSAGE COMPENSATION

332
1adq
L
57
268
6e−98
0.86
1.00

IGG4 REA; CHAIN: A; RF-AN
COMPLEX

IGM/LAMBDA; CHAIN: H, L;
(IMMUNOGLOBULIN/AUTOANTIGEN)

COMPLEX

(IMMUNOGLOBULIN/AUTOANTIGEN),

RHEUMATOID FACTOR 2 AUTO-

ANTIBODY COMPLEX

332
1adq
L
57
268
6e−98

301.73
IGG4 REA; CHAIN: A; RF-AN
COMPLEX

IGM/LAMBDA; CHAIN: H, L;
(IMMUNOGLOBULIN/AUTOANTIGEN)

COMPLEX

(IMMUNOGLOBULIN/AUTOANTIGEN),

RHEUMATOID FACTOR 2 AUTO-

ANTIBODY COMPLEX

332
1aqk
L
56
268
6.8e−88

318.27
FAB B7-15A2; CHAIN: L, H;
IMMUNOGLOBULIN HUMAN FAB,

ANTI-TETANUS TOXOID, HIGH

AFFINITY, CRYSTAL 2 PACKING

MOTIF, PROGRAMMING

PROPENSITY TO CRYSTALLIZE. 3

IMMUNOGLOBULIN

332
1b2w
L
55
267
5.1e−90
0.76
1.00

ANTIBODY (LIGHT CHAIN);
IMMUNE SYSTEM

CHAIN: L; ANTIBODY (HEAVY
IMMUNOGLOBULIN;

CHAIN); CHAIN: H;
IMMUNOGLOBULIN ANTIBODY

ENGINEERING, HUMANIZED AND

CHIMERIC ANTIBODY, FAB, 2 X-RAY

STRUCTURE, THREE-DIMENSIONAL

STRYCTURE, GAMMA-3

INTERFERON, IMMUNE SYSTEM

332
1bjm
A
55
268
3.4e−85

322.11
LOC-LAMBDA 1 TYPE LIGHT-
IMMUNOGLOBULIN BENCE-JONES

CHAIN DIMER; 1BJM 6 CHAIN: A,
PROTEIN; 1BJM 8 BENCE JONES,

B; 1BJM 7
ANTIBODY, MULTIPLE

QUATERNARY STRUCTURES 1BJM 13

332
1bwm
A
7
161
3.4e−21
−0.07
0.33

ALPHA-BETA T CELL RECEPTOR
IMMUNE SYSTEM

(TCR) (D10); CHAIN: A;
IMMUNOGLOBULIN,

IMMUNORECEPTOR, IMMUNE

SYSTEM

332
1dee
A
55
267
1e−90
0.84
1.00

IGM RF 2A2; CHAIN: A, C, E; IGM
IMMUNE SYSTEM FAB-IBP COMPLEX

RF 2A2; CHAIN: B, D, F;
CRYSTAL STRUCTURE 2.7A

IMMUNOGLOBULIN G BINDING
RESOLUTION BINDING 2 OUTSIDE

PROTEIN A; CHAIN: G, H;
THE ANTIGEN COMBINING SITE

SUPERANTIGEN FAB VH3 3

SPECIFICITY

332
1dzb
A
1
162
5.1e−60
0.09
0.46

SCFV FRAGMENT IF9; CHAIN: A,
COMPLEX (ANTIBODY ANTIGEN) 1,4-

B; TURKEY EGG-WHITE
BETA-N-ACETYLMURAMIDASE C;

LYSOZYME C; CHAIN: X, Y;
SINGLE-DOMAIN ANTIBODY,

TURKEY EGG-WHITE LYSOZYME, 2

ANTIBODY-PROTEIN COMPLEX,

SINGLE-CHAIN FV FRAGMENT

332
1f3r
B
1
164
1.4e−61
0.14
0.98

ACETYLCHOLINE RECEPTOR
IMMUNE SYSTEM IG-FOLD, IMMUNO

ALPHA: CHAIN: A; FV ANTIBODY
COMPLEX, ANTIBODY-ANTIGEN.

FRAGMENT; CHAIN: B;
BETA-TURN

332
1igl
A
55
267
1.2e−89
0.68
1.00

IGG2A INTACT ANTIBODY-
IMMUNOGLOBULIN INTACT

MAB231; CHAIN: A, B, C, D
IMMUNOGLOBULIN V REGION C

REGION, IMMUNOGLOBULIN

332
1lil
A
57
268
4.5e−99
086
1.00

LAMBDA III BENCE JONES
IMMUNOGLOBULIN

PROTEIN CLE; CHAIN: A, B
IMMUNOGLOBULIN, BENCE JONES

PROTEIN

332
1lil
A
58
268
4.5e−99

299.68
LAMBDA III BENCE JONES
IMMUNOGLOBULIN

PROTEIN CLE; CHAIN: A, B
IMMUNOGLOBULIN, BENCE JONES

PROTEIN

332
1lmk
A
1
162
3.4e−59
0.12
0.92

IMMUNOGLOBULIN ANTI-

PHOSPHATIDYLINOSITOL

SPECIFIC PHOSPHOLIPASE C

DIABODY 1LMK 3 SYNONYMS:

L5MK16 DIABODY, SINGLE-

CHAIN FV DIMER 1LMK 4

332
1mcp
L
55
267
3.4e−91
0.79
1.00

IMMUNOGLOBULIN

IMMUNOGLOBULIN FAB

FRAGMENT (MC/PC$603) 1MCP 4

332
1mcp
L
55
267
3.4e−91

202.00
IMMUNOGLOBULIN

IMMUNOGLOBULIN FAB

FRAGMENT (MC/PC$603) 1MCP 4

332
1mcw
W
55
268
1e−82

294.22
IMMUNOGLOBULIN

IMMUNOGLOBULIN

HETEROLOGOUS LIGHT CHAIN

DIMER IMCW 3 (/MCG$-/WEIR$

HYBRID) 1MCW 4

332
1mfa

1
161
3.4e−21
−0.34
0.01

IMMUNOGLOBULIN FV

FRAGMENT (MURINE SE155-4)

COMPLEX WITH THE

TRISACCHARIDE: 1MFA 3

ALPHA-D-GALACTOSE(1-2)

[ALPHA-D-ABEQUOSE(1-3)]

ALPHA-1MFA 4 D-MANNOSE

(PI-OME) (PART OF THE CELL-

SURFACE CARBOHYDRATE

1MFA 5 OF PATHOGENIC

SALMONELLA) 1MFA 6

332
1nca
L
55
267
5.1e−91
0.78
1.00

HYDROLASE(O-GLYCOSYL)N9

NEURAMINIDASE-NC4I

(E.C.3.2.1.18) COMPLEX WITH FAB

1NCA 3

332
1nqb
A
1
163
5.1e−61
0.17
0.53

SINGLE-CHAIN ANTIBODY
IMMUNOGLOBULIN VARIABLE

FRAGMENT; CHAIN: A, C;
HEAVY (VH) DOMAIN, VARIABLE

LIGHT (VL) ANTIBODY FRAGMENT,

MULTIVALENT ANTIBODY,

DIABODY, DOMAIN 2 SWAPPING,

IMMUNOGLOBULIN

332
1qlr
A
55
267
1.5e−89
0.65
1.00

IGM KAPPA CHAIN V-III (KAU
IMMUNOGLOBULIN

COLD AGGLUTININ); CHAIN: A,
IMMUNOGLOBULIN,

C; IGM FAB REGION IV-J(H4)-C
AUTOANTIBODY, COLD

(KAU COLD AGGLUTININ);
AGGLUTININ, HUMAN IGM 2 FAB

CHAIN: B, D;
FRAGMENT

332
1qok
A
1
162
1.7e−61
0.45
0.42

MFE-23 RECOMBINANT
IMMUNOGLOBULIN

ANTIBODY FRAGMENT; CHAIN:
IMMUNOGLOBULIN, SINGLE-CHAIN

A;
FV, ANTI-CARCINOEMBRYONIC 2

ANTIGEN

332
1sbs
L
55
267
3.4e−92
0.89
1.00

MONOCLONAL ANTIBODY 3A2;
MONOCLONAL ANTIBODY

CHAIN: H, L;
MONOCLONAL ANTIBODY, FAB-

FRAGMENT, REPRODUCTION

332
2fb4
L
55
268
6.8e−87

326.11
IMMUNOGLOBULIN

IMMUNOGLOBULIN FAB 2FB4 4

332
2mcg
L
55
268
1.7e−86

304.84
IMMUNOGLOBULIN

IMMUNOGLOBULIN LAMBDA

LIGHT CHAIN DIMER (/MCG$)

2MCG 3 (TRIGONAL FORM) 2MCG 4

332
7fab
L
55
264
3e−95

290.47
IMMUNOGLOBULIN

IMMUNOGLOBULIN FAB' NEW

(LAMBDA LIGHT CHAIN) 7FAB 3

332
7fab
L
56
264
3e−95
0.85
1.00

IMMUNOGLOBULIN

IMMUNOGLOBULIN FAB' NEW

(LAMBDA LIGHT CHAIN) 7FAB 3

332
8fab
A
58
264
5.1e−87

291.96
IMMUNOGLOBULIN FAB

FRAGMENT FROM HUMAN

IMMUNOGLOBULIN IGGI

(LAMBDA, HIL) 8FAB 3

338
1fl3
L
39
117
0.00034
−0.04
0.22

BLUE FLUORESCENT ANTIBODY
IMMUNE SYSTEM

(19G2)-HEAVY CHAIN; CHAIN: H,
IMMUNOGLOBULIN FOLD

A; BLUE FLUORESCENT

ANTIBODY (19G2)-LIGHT CHAIN;

CHAIN: L, B;

342
1ekl
A
225
349
3.4e−14
−0.04
0.19

EPOXIDE HYDROLASE; CHAIN: A,
HYDROLASE HOMODIMER,

B;
ALPHA/BETA HYDROLASE FOLD,

DISUBSTITUTED UREA 2 INHIBITOR

342
1ek1
B
132
349
1.5e−17
0.25
0.54

EPOXIDE HYDROLASE; CHAIN: A,
HYDROLASE HOMODIMER,

B;
ALPHA/BETA HYDROLASE FOLD,

DISUBSTITUTED UREA 2 INHIBITOR

342
1fez
A
130
330
4.5e−29
0.37
0.82

PHOSPHONOACETALDEHYDE
HYDROLASE HAD-FAMILY

HYDROLASE; CHAIN: A, B, C, D;
ALPHA/BETA CORE DOMAIN, MG(II)

BINDING SITE, 5-2 HELIX BUNDLE

342
1fez
A
130
366
1.5e−23
0.56
1.00

PHOSPHONOACETALDEHYDE
HYDROLASE HAD-FAMILY

HYDROLASE; CHAIN: A, B, C, D;
ALPHA/BETA CORE DOMAIN, MG(II)

BINDING SITE, 5-2 HELIX BUNDLE

342
1qq5
A
130
386
3.4e−26

51.58
L-2-HALOACID DEHALOGENASE;
HYDROLASE L-2-HALOACID

CHAIN: A, B;
DEHALOGENASE, HYDROLASE

342
1qq5
A
131
362
3.4e−26
0.32
0.65

L-2-HALOACID DEHALOGENASE;
HYDROLASE L-2-HALOACID

CHAIN: A, B;
DEHALOGENASE, HYDROLASE

342
1zrn

130
362
1.7e−28

57.26
L-2-HALOACID DEHALOGENASE;
DEHALOGENASE DEHALOGENASE,

CHAIN: NULL;
HYDROLASE

342
1zrn

131
361
1.7e−28
0.29
0.76

L-2-HALOACID DEHALOGENASE;
DEHALOGENASE DEHALOGENASE,

CHAIN: NULL;
HYDROLASE

343
1alh
A
129
213
8.5e−24
0.05
−0.05

QGSR ZINC FINGER PEPTIDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

343
1alh
A
161
241
3.4e−30
0.13
0.12

QGSR ZINC FINGER PEPTlDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

343
1mey
C
145
213
3.4e−38
−0.21
0.10

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN: CHAIN; C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

343
1mey
C
160
241
6.8e−50
0.09
0.54

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

343
1mey
C
188
269
5.1e−50
−0.08
0.89

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

343
1mey
C
216
297
5.1e−50
0.20
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

343
1mey
C
244
325
3.4e−50
0.22
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

343
1mey
C
272
353
1.4e−49
0.47
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G:
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE COMPLEX

(ZINC FINGER/DNA)

343
1mey
C
272
354
3.4e−50

103.55
DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

343
1mey
C
300
357
3.4e−33
0.42
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

343
1mey
C
39
142
5.1e−43
−0.12
0.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

343
1mey
G
158
185
1.2e−12
0.50
0.71

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

343
1mey
G
37
64
1.7e−11
−0.39
0.13

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

343
1tf6
A
161
313
8.5e−38
−0.20
0.66

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

343
1tf6
A
187
353
8.5e−38

89.34
TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

343
1tf6
A
217
355
3.4e−35
0.13
1.00

TFIIIA: CHAIN: A, D: 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE: CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

343
1ubd
C
168
269
5.1e−35
−0.19
0.69

YY1: CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1:

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

343
1ubd
C
214
325
1.2e−52
−0.09
0.93

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

343
1ubd
C
242
353
6e−53
0.03
0.99

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

343
1ubd
C
244
354
6e−53

86.36
YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

343
1ubd
C
252
353
6.8e−34
0.09
1.00

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

343
2gli
A
157
268
1.2e−31
0.00
0.27

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

343
2gli
A
188
327
1.2e−61
0.41
1.00

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

343
2gli
A
216
353
1.5e−67
0.42
0.99

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

343
2gli
A
216
355
1.5e−67

95.61
ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

343
2gli
A
224
352
3.4e−33
0.43
0.98

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

343
2gli
A
40
243
3e−23
−0.10
0.00

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A: DNA: CHAIN: C. D:
PROTEIN/DNA) FIVE-FINGER GL1;

GL1, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

345
1bbz
A
7
63
4.5e−15
−0.10
0.72

ABL TYROSINEKINASE; CHAIN:
COMPLEX (TRANSFERASE/PEPTIDE)

A, C, E, G; PEPTIDE P41; CHAIN: B,
COMPLEX (TRANSFERASE/PEPTIDE),

D, F, H;
SIGNAL TRANSDUCTION, 2 SH3

DOMAIN

345
1gbq
A
8
63
3e−16
−0.22
0.88

GRB2; CHAIN: A; SOS-1; CHAIN: B;
COMPLEX (SIGNAL

TRANSDUCTION/PEPTIDE) COMPLEX

(SIGNAL TRANSDUCTION/PEPTIDE),

SH3 DOMAIN

345
1gbr
A
8
65
3e−16
−0.04
0.98

SIGNAL TRANSDUCTION

PROTEIN GROWTH FACTOR

RECEPTOR-BOUND PROTEIN 2

(GRB2, N-TERMINAL 1GBR 3 SH3

DOMAIN) COMPLEXED WITH

SOS-A PEPTIDE 1GBR 4 (NMR, 29

STRUCTURES) 1GBR 5

345
1gfc

8
63
3e−15
0.27
0.89

ADAPTOR PROTEIN CONTAINING

SH2 AND SH3 GROWTH FACTOR

RECEPTOR-BOUND PROTEIN 2

(GRB2) 1GFC 3 (C-TERMINAL SH3

DOMAIN) (NMR, MINIMIZED

MEAN STRUCTURE) 1GFC 4

345
1pht

8
71
1.2e−15
−0.32
0.33

PHOSPHATIDYLINOSITOL 3-
PHOSPHOTRANSFERASE P13K SH3;

KINASE P85-ALPHA SUBUNIT;
1PHT 9 PHOSPHATIDYLINOSITOL 3-

1PHT 6 CHAIN: NULL; 1PHT 7
KINASE, P85-ALPHA SUBUNIT, SH3

DOMAIN 1PHT 21

345
1pks

8
63
1.5e−14
−0.24
0.30

PHOSPHOTRANSFERASE

PHOSPHATIDYLINOSITOL 3-

KINASE (E.C.2.7.1.137) (P13K) 1PKS

3 (SH3 DOMAIN) (NMR,

MINIMIZED AVERAGE

STRUCTURE) 1PKS 4

345
1pwt

1
63
7.5e−16
−0.09
0.99

ALPHA SPECTRIN; CHAIN: NULL;
CIRCULAR PERMUTANT PWT;

CIRCULAR PERMUTANT, SH3

DOMAIN, CYTOSKELETON

345
1qkw
A
8
63
7.5e−16
0.13
0.98

ALPHA II SPECTRIN; CHAIN: A;
CYTOSKELETON CYTOSKELETON,

MEMBRANE, SH3 DOMAIN

345
1sem
A
8
58
6e−15
0.30
0.92

SEM-5; 1SEM 3 CHAIN: A, B; 1SEM
SIGNAL TRANSDUCTION PROTEIN

5 10-RESIDUE PROLINE-RICH
SRC-HOMOLOGY 3 (SH3) DOMAIN,

PEPTIDE FROM MSOS 1SEM 8
PEPTIDE-BINDING PROTEIN, 1SEM 18

CHAIN: C, D 1SEM 10
2 GUANINE NUCLEOTIDE

EXCHANGE FACTOR 1SEM 19

348
2occ
K
30
78
8.5e−27
−0.76
0.60

CYTOCHROME C OXIDASE;
OXIDOREDUCTASE

CHAIN: A, B, C, D, E, F, G, H, I, J, K,
FERROCYTOCHROME C\:OXYGEN

L, M, N, O, P, Q,
OXIDOREDUCTASE;

OXIDOREDUCTASE,

CYTOCHROME(C)-OXYGEN,

CYTOCHROME C 2 OXIDASE

348
2occ
K
30
78
8.5e−27

69.07
CYTOCHROME C OXIDASE;
OXIDOREDUCTASE

CHAIN: A, B, C, D, E, F, G, H, I, J, K,
FERROCYTOCHROME C\:OXYGEN

L, M, N, O, P, Q,
OXIDOREDUCTASE;

OXIDOREDUCTASE,

CYTOCHROME(C)-OXYGEN,

CYTOCHROME C 2 OXIDASE

355
1bxe
A
66
175
5.1e−43
0.90
1.00

RIBOSOMAL PROTEIN L22;
RNA BINDING PROTEIN RIBOSOMAL

CHAIN: A:
PROTEIN, PROTEIN SYNTHESIS, RNA

BINDING, 2 ANTIBIOTICS

RESISTANCE, RNA BINDING

PROTEIN

355
1ffk
O
54
174
3.4e−23
0.21
0.60

23S RRNA; CHAIN: 0; 5S RRNA;
RIBOSOME 50S RIBOSOMAL

CHAIN: 9; RIBOSOMAL PROTEIN
PROTEIN L2P, HMAL2, HL4: 50S

L2; CHAIN: A; RIBOSOMAL
RIBOSOMAL PROTEIN L3P, HMAL3.

PROTEIN L3; CHAIN: B;
HL1; 50S RIBOSOMAL PROTEIN L4E,

RIBOSOMAL PROTEIN L4; CHAIN:
HMAL4, HL6; 50S RIBOSOMAL

C: RIBOSOMAL PROTEIN L5;
PROTEIN L5P, HMAL5, HL13; 30S

CHAIN: D; RIBOSOMAL PROTEIN
RIBOSOMAL PROTEIN HS6; 50S

L7AE; CHAIN: E; RIBOSOMAL
RIBOSOMAL PROTEIN L13P, HMAL13;

PROTEIN L10E; CHAIN: F;
50S RIBOSOMAL PROTEIN L14P,

RIBOSOMAL PROTEIN L13;
HMAL14, HL27; 50S RIBOSOMAL

CHAIN: G; RIBOSOMAL PROTEIN
PROTEIN L15P, HMAL15, HL9; 50S

L14; CHAIN: H; RIBOSOMAL
RIBOSOMAL PROTEIN L18P, HMAL18,

PROTEIN L15E, CHAIN: I;
HL12; 50S RIBOSOMAL PROTEIN

RIBOSOMAL PROTEIN L15;
L18E, HL29, L19; 50S RIBOSOMAL

CHAIN: J; RIBOSOMAL PROTEIN
PROTEIN L19E, HMAL19, HL24; 50S

L18; CHAIN: K; RIBOSOMAL
RIBOSOMAL PROTEIN L21E, HL31;

PROTEIN L18E; CHAIN: L;
50S RIBOSOMAL PROTEIN L22P,

RIBOSOMAL PROTEIN L19;
HMAL22, HL23; 50S RIBOSOMAL

CHAIN: M; RIBOSOMAL PROTEIN
PROTEIN L23P, HMAL23, HL25, L21;

L21E; CHAIN: N; RIBOSOMAL
50S RIBOSOMAL PROTEIN L24P,

PROTEIN L22; CHAIN: O;
HMAL24, HL16, HL15; 50S

RIBOSOMAL PROTEIN L23;
RIBOSOMAL PROTEIN L24E,

CHAIN: P; RIBOSOMAL PROTEIN
HL21/HL22; 50S RIBOSOMAL

L24; CHAIN: Q; RIBOSOMAL
PROTEIN L29P, HMAL29, HL33; 50S

PROTEIN L24E; CHAIN: R;
RIBOSOMAL PROTEIN L30P, HMAL30,

RIBOSOMAL PROTEIN L29;
HL20, HL16; 50S RIBOSOMAL

CHAIN: S; RIBOSOMAL PROTEIN
PROTEIN L31E, L34, HL30; 50S

L30; CHAIN: T; RIBOSOMAL
RIBOSOMAL PROTEIN L32E, HL5; 50S

PROTEIN L31E; CHAIN: U;
RIBOSOMAL PROTEIN L37E, L35E;

RIBOSOMAL PROTEIN L32E;
50S RIBOSOMAL PROTEINS L39E,

CHAIN: V; RIBOSOMAL PROTEIN
HL39E, HL46E; 50S RIBOSOMAL

L37AE; CHAIN: W; RIBOSOMAL
PROTEIN L44E, LA, HLA; 50S

PROTEIN L37E; CHAIN: X;
RIBOSOMAL PROTEIN L6P, HMAL6,

RIBOSOMAL PROTEIN L39E;
HL10 RIBOSOME ASSEMBLY, RNA-

CHAIN: Y; RIBOSOMAL PROTEIN
RNA, PROTEIN-RNA, PROTEIN-

L44E; CHAIN: Z; RIBOSOMAL
PROTEIN

PROTEIN L6; CHAIN: 1;

369
1d2h
A
70
190
1.2e−14
0.20
0.17

GLYCINE N-
TRANSFERASE

METHYLTRANSFERASE; CHAIN:
METHYLTRANSFERASE

A, B, C, D;

369
2adm
A
66
209
6.8e−13
0.14
−0.11

ADENINE-N6-DNA-
METHYLTRANSFERASE

METHYLTRANSFERASE TAQ1;
TRANSFERASE,

CHAIN: A, B;
METHYLTRANSFERASE,

RESTRICTION SYSTEM

371
1a02
F
108
160
4.5e−13
−0.36
0.17

NFAT; CHAIN: N; C-FOS; CHAIN:
COMPLEX

F; C-JUN; CHAIN: J; DNA; CHAIN:
(TRANSCRIPTION/NUCLEAR/NUCLEAR)

A, B;
AR) NF-AT; TRANSCRIPTION

FACTOR, PROTEIN-DNA COMPLEX,

NFAT, NF-AT, 2 AP-I, FOS-JUN,

QUATERNARY PROTEIN-DNA

COMPLEX, CRYSTAL 3 STRUCTURE,

TRANSCRIPTION SYNERGY,

COMBINATORIAL GENE 4

REGULATION, COMPLEX

(TRANSCRIPTION/NUCLEAR/NUCLEAR)

371
1a02
F
108
160
4.5e−13

62.39
NFAT; CHAIN: N; C-FOS; CHAIN:
COMPLEX

F; C-JUN; CHAIN: J; DNA; CHAIN:
(TRANSCRIPTION/NUCLEAR/NUCLEAR)

A, B;
NF-AT; TRANSCRIPTION

FACTOR, PROTEIN-DNA COMPLEX,

NFAT, NF-AT, 2 AP-1, FOS-JUN,

QUATERNARY PROTEIN-DNA

COMPLEX, CRYSTAL 3 STRUCTURE,

TRANSCRIPTION SYNERGY,

COMBINATORIAL GENE 4

REGULATION, COMPLEX

(TRANSCRIPTION/NUCLEAR/NUCLEAR)

371
1a02
F
115
146
3.4e−10
−0.05
0.69

NFAT; CHAIN: N; C-FOS; CHAIN;
COMPLEX

F; C-JUN; CHAIN: J; DNA; CHAIN:
(TRANSCRIPTION/NUCLEAR/NUCLEAR)

A, B;
NF-AT; TRANSCRIPTION

FACTOR, PROTEIN-DNA COMPLEX,

NFAT, NF-AT, 2 AP-1, FOS-JUN.

QUATERNARY PROTEIN-DNA

COMPLEX, CRYSTAL 3 STRUCTURE,

TRANSCRIPTION SYNERGY,

COMBINATORIAL GENE 4

REGULATION, COMPLEX

(TRANSCRIPTION/NUCLEAR/NUCLEAR)

371
1fos
E
107
166
3.4e−10

70.24
COMPLEX (GENE-REGULATORY

PROTEIN/DNA) C-JUN PROTO-

ONCOGENE (TRANSCRIPTION

FACTOR AP-1) DIMERIZED IFOS 4

WITH C-FOS AND COMPLEXED

WITH DNA IFOS 5 COILED-COIL,

DNA-BINDING PROTEIN,

HETERODIMER 1FOS 19

371
1fos
E
115
146
3.4e−10
−0.39
0.76

COMPLEX(GENE-REGULATORY

PROTEIN/DNA) C-JUN PROTO-

ONCOGENE (TRANSCRIPTION

FACTOR AP-1) DIMERIZED 1FOS 4

WITH C-FOS AND COMPLEXED

WITH DNA 1FOS 5 COILED-COIL,

DNA-BINDlNG PROTEIN,

HETERODIMER IFOS 19

373
1d5t
A
166
598
0
0.32
1.00

GUANINE NUCLEOTIDE
HYDROLASE INHIBITOR ULTRA-

DISSOCIATION INHIBITOR:
HIGH RESOLUTION

CHAIN: A;

373
1qo8
A
8
46
0.0045
0.01
0.17

FLAVOCYTOCHROME C3
OXIDOREDUCTASE

FUMARATE REDUCTASE; CHAIN:
OXIDOREDUCTASE

A, D;

373
3lad
A
8
48
0.006
−0.12
0.36

OXIDOREDUCTASE

DIHYDROLIPOAMIDE

DEHYDROGENASE (E.C.1.8.1.4)

3LAD 3

374
1alh
A
168
252
5.1e−15
0.00
0.05

QGSR ZINC FINGER PEPTIDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

374
1alh
A
188
280
6.8e−22
−0.03
0.30

QGSR ZINC FINGER PEPTIDE:
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

374
1alh
A
228
304
3.4e−23
0.60
0.12

QGSR ZINC FINGER PEPTIDE:
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

374
1alh
A
308
388
1.2e−29
−0.01
1.00

QGSR ZINC FINGER PEPTIDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

374
1alh
A
308
389
1.2e−32
−0.32
1.00

QGSR ZINC FINGER PEPTIDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

374
1alh
A
336
416
1e−30
0.03
0.92

QGSR ZINC FINGER PEPTIDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

374
1alh
A
393
472
1.2e−37
0.64
1.00

QGSR ZINC FINGER PEPTIDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

374
1alh
A
420
502
1.2e−37

86.81
QGSR ZINC FINGER PEPTIDE:
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

374
1alh
A
476
556
1.2e−34
0.57
1.00

QGSR ZINC FINGER PEPTIDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

374
1alh
A
476
556
1.7e−31
0.43
1.00

QGSR ZINC FINGER PEPTIDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

374
1mey
C
186
280
3.4e−38
0.45
0.75

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

374
1mey
C
227
304
8.5e−41
0.40
0.84

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

374
1mey
C
255
360
1e−43
−0.15
0.35

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN: CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

374
1mey
C
307
388
1e−48
0.06
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN: CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

374
1mey
C
335
416
5.1e−50
−0.05
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

374
1mey
C
363
444
1e−50
0.39
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

374
1mey
C
391
472
1.7e−51
0.48
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

374
1mey
C
419
500
6.8e−51
0.55
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

374
1mey
C
447
528
1.2e−50
0.51
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

374
1mey
C
447
529
6.8e−51

106.37
DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

374
1mey
C
475
556
1.7e−50
0.37
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

374
1mey
G
225
252
1.5e−10
−0.12
0.69

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

374
1tf3
A
187
276
6.8e−14
0.06
−0.06

TRANSCRIPTION FACTOR IIIA;
COMPLEX (TRANSCRIPTION

CHAIN: A; 5S RNA GENE; CHAIN:
REGULATION/DNA) TFIIIA; 5S GENE;

E, F;
NMR, TFIIIA, PROTEIN, DNA,

TRANSCRIPTION FACTOR, 5S RNA 2

GENE, DNA BINDING PROTEIN, ZINC

FINGER, COMPLEX 3

(TRANSCRIPTION

REGULATION/DNA)

374
1tf6
A
187
341
5.1e−29
0.05
−0.07

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN;
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

374
1tf6
A
307
470
8.5e−39

117.85
TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

374
1tf6
A
308
453
6.8e−38
0.01
0.98

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

374
1tf6
A
336
481
1.7e−38
0.12
1.00

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

374
1tf6
A
392
538
8.5e−39
0.13
0.96

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

374
1tf6
A
448
556
3.4e−30
0.18
0.46

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE: CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

374
1ubd
C
166
280
8.5e−25
0.10
0.05

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

374
1ubd
C
190
304
3.4e−27
0.28
0.60

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

374
1ubd
C
263
360
8.5e−29
−0.15
0.19

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

374
1ubd
C
287
388
5.1e−34
0.12
0.94

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

374
1ubd
C
312
444
9e−41
0.13
1.00

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

374
1ubd
C
315
416
1.5e−34
0.01
0.99

YY1; CHAIN: C: ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

374
1ubd
C
343
444
1.5e−34
0.30
1.00

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

374
1ubd
C
399
500
5.1e−36
0.23
1.00

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

374
1ubd
C
418
529
1.5e−51
0.18
1.00

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

374
1ubd
C
421
529
1.5e−51

98.87
YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

374
1ubd
C
445
556
1.5e−46
0.20
0.98

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

374
1ubd
C
455
556
1.5e−34
0.21
1.00

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

374
1zfd

532
558
6.8e−05
0.06
0.30

SWI5; CHAIN: NULL;
ZINC FINGER DNA BINDING DOMAIN

DNA BINDING MOTIF, ZINC FINGER

DNA BINDING DOMAIN

374
2adr

189
254
3.4e−11
−0.04
0.06

ADR1; CHAIN: NULL;
TRANSCRIPTION REGULATION

TRANSCRIPTION REGULATION,

ADRI, ZINC FINGER, NMR

374
2gli
A
161
303
8.5e−24
0.07
−0.11

ZINC FINGER PROTEIN GLII;
COMPLEX (DNA-BINDING

CHAIN: A; DNA: CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

374
2gli
A
287
415
1.2e−34
0.18
0.87

ZINC FINGER PROTEIN GLII;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

374
2gli
A
335
474
1.2e−61

106.08
ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

374
2gli
A
393
530
1.2e−61
0.49
1.00

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

374
2gli
A
420
557
4.5e−58
0.36
1.00

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C. D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

375
1c3t
A
1
76
1e−31
0.68
1.00

ID8 UBIQUITIN; CHAIN: A;
DE NOVO PROTEIN PROTEIN

DESIGN, HYDROPHOBIC CORE,

PACKING, ROTAMERS, ROC, 2

UBIQUITIN, DE NOVO PROTEIN,

UBIQUITIN

375
1c3t
A
1
76
1e−31

102.61
ID8 UBIQUITIN; CHAIN: A;
DE NOVO PROTEIN PROTEIN

DESIGN, HYDROPHOBIC CORE,

PACKING, ROTAMERS, ROC, 2

UBIQUITIN, DE NOVO PROTEIN,

UBIQUITIN

375
1tbe
B
1
72
1.2e−32
0.97
1.00

UBIQUITIN TETRAUBIQUITIN

1TBE 3

375
1tbe
B
1
72
1.2e−32

97.63
UBIQUITIN TETRAUBIQUITIN

1TBE 3

375
1ubi

1
76
1e−33
1.07
1.00

CHROMOSOMAL PROTEIN

UBIQUITIN 1UBI 3

375
1ubi

1
76
7.5e−36

105.89
CHROMOSOMAL PROTEIN

UBIQUITIN 1UBI 3

375
1ubi

1
76
7.5e−36
1.07
1.00

CHROMOSOMAL PROTEIN

UBIQUITIN 1UBI 3

375
1ud7
A
1
76
1.2e−32
0.96
1.00

UBIQUITIN CORE MUTANT ID7:
UBIQUITIN UBIQUITIN, DESIGNED

CHAIN: A;
CORE MUTANT

375
1ud7
A
1
76
1.2e−32

102.60
UBIQUITIN CORE MUTANT ID7:
UBIQUITIN UBIQUITIN, DESIGNED

CHAIN: A;
CORE MUTANT

377
1cdm
A
5
144
1.2e−62
0.90
1.00

CALCIUM-BINDING PROTEIN

CALMODULIN COMPLEXED

WITH CALMODULIN-BINDING

DOMAIN OF 1CDM 3

CALMODULIN-DEPENDENT

PROTEIN KINASE II 1CDM 4

377
1cdm
A
5
144
1.2e−62

149.72
CALCIUM-BINDING PROTEIN

CALMODULIN COMPLEXED

WITH CALMODULIN-BINDING

DOMAIN OF ICDM 3

CALMODULIN-DEPENDENT

PROTEIN KINASE II 1CDM 4

377
1cll

5
144
3.4e−66
1.07
1.00

CALCIUM-BINDING PROTEIN

CALMODULIN (VERTEBRATE)

1CLL 3

377
1cll

5
145
3.4e−66

156.05
CALCIUM-BINDING PROTEIN

CALMODULIN (VERTEBRATE)

1CLL 3

377
1cmf

74
146
1.5e−23

79.20
CALMODULIN (VERTEBRATE);
CALCIUM-BINDING PROTEIN

1CMF 6 CHAIN: NULL; 1CMF 7
CALMODULIN APO TR2C-DOMAIN;

1CMF 9

377
1cmf

81
143
1.5e−23
0.90
1.00

CALMODULIN (VERTEBRATE);
CALCIUM-BINDING PROTEIN

1CMF 6 CHAIN: NULL; 1CMF 7
CALMODULIN APO TR2C-DOMAIN;

1CMF 9

377
1exr
A
3
143
5.1e−64
0.96
1.00

CALMODULIN; CHAIN: A;
METAL TRANSPORT CALMODULIN,

HIGH RESOLUTION, DISORDER

377
1t71
A
81
143
1.5e−23
1.14
1.00

CALMODULIN; CHAIN: A;
TRANSPORT PROTEIN CALCIUM

BINDING, EF HAND, FOUR-HELIX

BUNDLE

377
1tnx

1
143
3.4e−50

127.27
TROPONIN C; 1TNX 4 CHAIN:
CALCIUM-BINDING PROTEIN EF-

NULL; 1TNX 5
HAND 1TNX 14

377
1tnx

5
143
3.4e−50
0.85
1.00

TROPONIN C; 1TNX 4 CHAIN:
CALCIUM-BINDING PROTEIN EF-

NULL; 1TNX 5
HAND 1TNX 14

377
1vrk
A
2
146
1.5e−66
1.08
1.00

CALMODULIN; CHAIN: A; RS20;
CALMODULIN, CALCIUM BINDING,

CHAIN: B;
HELIX-LOOP-HELIX, SIGNALLING, 2

COMPLEX(CALCIUM-BINDING

PROTEIN/PEPTIDE)

377
1vrk
A
2
146
1.5e−66

156.22
CALMODULIN; CHAIN: A; RS20;
CALMODULIN, CALCIUM BINDING,

CHAIN: B;
HELIX-LOOP-HELIX, SIGNALLING, 2

COMPLEX(CALCIUM-BINDING

PROTEIN/PEPTIDE)

384
1b7f
A
2
113
1.7e−21
0.43
0.99

SXL-LETHAL PROTEIN; CHAIN: A,
RNA-BINDING PROTEIN/RNA TRA

B; RNA (5′-
PRE-MRNA; SPLICING REGULATION,

R(P*GP*UP*UP*GP*UP*UP*UP*UP
RNP DOMAIN, RNA COMPLEX

*UP*UP*UP*U)-CHAIN: P, Q:

384
1b7f
A
33
205
3.4e−43
1.07
1.00

SXL-LETHAL PROTEIN; CHAIN: A,
RNA-BINDING PROTEIN/RNA TRA

B; RNA (5′-
PRE-MRNA; SPLICING REGULATION,

R(P*GP*UP*UP*GP*UP*UP*UP*UP
RNP DOMAIN, RNA COMPLEX

*UP*UP*UP*U)-CHAIN: P, Q;

384
1b7f
A
33
205
3.4e−43

84.87
SXL-LETHAL PROTEIN; CHAIN: A,
RNA-BINDING PROTEIN/RNA TRA

B; RNA (5′-
PRE-MRNA; SPLICING REGULATION,

R(P*GP*UP*UP*GP*UP*UP*UP*UP
RNP DOMAIN, RNA COMPLEX

*UP*UP*UP*U)-CHAIN: P, Q;

384
1cvj
A
2
119
1.5e−31
0.42
1.00

POLYDENYLATE BINDING
GENE REGULATION/RNA POLY(A)

PROTEIN 1; CHAIN: A, B, C, D, E,
BINDING PROTEIN 1, PABP 1; RRM,

F, G, H; RNA (5′-
PROTEIN-RNA COMPLEX, GENE

R(*AP*AP*AP*AP*AP*AP*AP*AP*
REGULATION/RNA

AP*AP*A)-3′); CHAIN: M, N, O, P,

Q, R, S, T;

384
1cvj
A
37
211
1.4e−43
0.72
1.00

POLYDENYLATE BINDING
GENE REGULATION/RNA POLY(A)

PROTEIN 1; CHAIN: A, B, C, D, E,
BINDING PROTEIN 1, PABP 1; RRM,

F, G, H; RNA (5′-
PROTEIN-RNA COMPLEX, GENE

R(*AP*AP*AP*AP*AP*AP*AP*AP*
REGULATION/RNA

AP*AP*A)-3′); CHAIN: M, N, O, P,

Q, R, S, T;

384
1cvj
A
378
500
3.4e−23
0.16
1.00

POLYDENYLATE BINDING
GENE REGULATION/RNA POLY(A)

PROTEIN 1; CHAIN: A, B, C, D, E,
BINDING PROTEIN 1, PABP 1; RRM,

F, G, H: RNA(5′-
PROTEIN-RNA COMPLEX, GENE

R(*AP*AP*AP*AP*AP*AP*AP*AP*
REGULATION/RNA

AP*AP*A)-3′); CHAIN: M, N, O, P,

Q, R, S, T;

384
1cvj
B
2
99
6.8e−26
0.31
1.00

POLYDENYLATE BINDING
GENE REGULATION/RNA POLY(A)

PROTEIN 1; CHAIN: A, B, C, D, E,
BINDING PROTEIN 1, PABP 1; RRM,

F, G, H; RNA (5′-
PROTEIN-RNA COMPLEX, GENE

R(*AP*AP*AP*AP*AP*AP*AP*AP*
REGULATION/RNA

AP*AP*A)-3′); CHAIN: M, N, O, P,

Q, R, S, T;

384
1cvj
B
37
188
1.7e−37
0.57
1.00

POLYDENYLATE BINDING
GENE REGULATION/RNA POLY(A)

PROTEIN 1; CHAIN: A, B, C, D, E,
BINDING PROTEIN 1, PABP 1; RRM,

F, G, H; RNA (5′-
PROTEIN-RNA COMPLEX, GENE

R(*AP*AP*AP*AP*AP*AP*AP*AP*
REGULATION/RNA

AP*AP*A)-3′); CHAIN: M, N, O, P,

Q, R, S, T;

384
1cvj
F
37
178
8.5e−28
0.33
1.00

POLYDENYLATE BINDING
GENE REGULATION/RNA POLY(A)

PROTEIN 1; CHAIN: A, B, C, D, E,
BINDING PROTEIN 1, PABP 1; RRM,

F, G, H; RNA (5′-
PROTEIN-RNA COMPLEX, GENE

R(*AP*AP*AP*AP*AP*AP*AP*AP*
REGULATION/RNA

AP*AP*A)-3′); CHAIN: M, N, O, P,

Q, R, S, T;

384
1cvj
H
37
181
1.4e−28
0.46
1.00

POLYDENYLATE BINDING
GENE REGULATION/RNA POLY(A)

PROTEIN 1; CHAIN: A, B, C, D, E,
BINDING PROTEIN 1, PABP 1; RRM,

F, G, H; RNA (5′-
PROTEIN-RNA COMPLEX, GENE

R(*AP*AP*AP*AP*AP*AP*AP*AP*
REGULATION/RNA

AP*AP*A)-3′); CHAIN: M, N, O, P,

Q, R, S, T;

384
1d8z
A
32
117
5.1e−22
0.61
1.00

HU ANTIGEN C; CHAIN: A;
RNA BINDING PROTEIN RNA-

BINDING DOMAIN

384
1d8z
A
419
501
4.5e−24
0.83
1.00

HU ANTIGEN C; CHAIN: A;
RNA BINDING PROTEIN RNA-

BINDING DOMAIN

384
1d9a
A
36
120
1.5e−17
0.77
1.00

HU ANTIGEN C; CHAIN: A;
RNA BINDING PROTEIN RNA-

BINDING DOMAIN

384
1d9a
A
418
501
4.5e−23
0.72
1.00

HU ANTIGEN C; CHAIN: A;
RNA BINDING PROTEIN RNA-

BINDING DOMAIN

384
1hal

30
205
1.7e−51
0.70
1.00

HNRNP A1; CHAIN: NULL;
NUCLEAR PROTEIN

HETEROGENEOUS NUCLEAR

RIBONUCLEOPROTEIN A1, NUCLEAR

PROTEIN, HNRNP, RBD, RRM, RNP,

RNA BINDING, 2

RIBONUCLEOPROTEIN

384
1hal

31
204
1.7e−51

74.92
HNRNP A1; CHAIN: NULL;
NUCLEAR PROTEIN

HETEROGENEOUS NUCLEAR

RIBONUCLEOPROTEIN A1, NUCLEAR

PROTEIN, HNRNP, RBD, RRM, RNP,

RNA BINDING, 2

RIBONUCLEOPROTEIN

384
1hal

376
494
1e−23
0.63
−0.05

HNRNP A1; CHAIN: NULL;
NUCLEAR PROTEIN

HETEROGENEOUS NUCLEAR

RIBONUCLEOPROTEIN A1, NUCLEAR

PROTEIN, HNRNP, RBD, RRM, RNP,

RNA BINDING, 2

RIBONUCLEOPROTEIN

384
1hal

4
113
6.8e−22
0.33
0.63

HNRNP A1; CHAIN: NULL;
NUCLEAR PROTEIN

HETEROGENEOUS NUCLEAR

RIBONUCLEOPROTEIN A1, NUCLEAR

PROTEIN, HNRNP, RBD, RRM, RNP,

RNA BINDING, 2

RIBONUCLEOPROTEIN

384
1hal

413
498
3.4e−28
0.70
1.00

HNRNP A1; CHAIN: NULL;
NUCLEAR PROTEIN

HETEROGENEOUS NUCLEAR

RIBONUCLEOPROTEIN A1, NUCLEAR

PROTEIN, HNRNP, RBD, RRM, RNP,

RNA BINDING, 2

RIBONUCLEOPROTEIN

384
1hdl
A
36
113
1e−22
0.91
1.00

HETEROGENEOUS NUCLEAR
RNA BINDING PROTEIN RNA-

RIBONUCLEOPROTEIN D0;
BINDING DOMAIN

CHAIN: A;

384
1hdl
A
419
494
8.5e−24
1.02
0.99

HETEROGENEOUS NUCLEAR
RNA BINDING PROTEIN RNA-

RIBONUCLEOPROTEIN D0;
BINDING DOMAIN

CHAIN: A;

384
1sxl

406
501
6e−25
0.48
0.99

RNA-BINDING PROTEIN SEX-

LETHAL PROTEIN (C-TERMINUS,

OR SECOND RNA-BINDING

DOMAIN 1SXL 3 (RBD-2),

RESIDUES 199-294 PLUS N-

TERMINAL MET) 1SXL 4 (NMR, 17

STRUCTURES) ISXL 5

384
2mss
A
36
113
6.8e−18
0.50
0.58

MUSASHI1; CHAIN: A;
RNA BINDING PROTEIN RNA-

BINDING DOMAIN

384
2sxl

33
118
3.4e−20
0.63
1.00

SEX-LETHAL PROTEIN; CHAIN:
RNA-BINDING DOMAIN RNA-

NULL;
BINDING DOMAIN, ALTERNATIVE

SPLICING

384
2upl
A
29
210
1.4e−53
0.69
1.00

HETEROGENEOUS NUCLEAR
COMPLEX

RIBONUCLEOPROTEIN A1;
(RIBONUCLEOPROTEIN/DNA) HNRNP

CHAIN: A; 12-NUCLEOTIDE
AI, UPI; COMPLEX

SINGLE-STRANDED TELOMETRIC
(RIBONUCLEOPROTEIN/DNA),

DNA; CHAIN: B;
HETEROGENEOUS NUCLEAR 2

RIBONUCLEOPROTEIN A1

384
2upl
A
30
213
1.4e−53

77.86
HETEROGENEOUS NUCLEAR
COMPLEX

RIBONUCLEOPROTEIN A1;
(RIBONUCLEOPROTEIN/DNA) HNRNP

CHAIN: A; 12-NUCLEOTIDE
AI, UPI; COMPLEX

SINGLE-STRANDED TELOMETRIC
(RIBONUCLEOPROTEIN/DNA),

DNA; CHAIN: B;
HETEROGENEOUS NUCLEAR 2

RIBONUCLEOPROTEIN A1

384
2upl
A
376
499
1e−24
−0.07
0.06

HETEROGENEOUS NUCLEAR
COMPLEX

RIBONUCLEOPROTEIN A1;
(RIBONUCLEOPROTEIN/DNA) HNRNP

CHAIN: A; 12-NUCLEOTIDE
AI, UPI; COMPLEX

SINGLE-STRANDED TELOMETRIC
(RIBONUCLEOPROTEIN/DNA),

DNA; CHAIN: B;
HETEROGENEOUS NUCLEAR 2

RIBONUCLEOPROTEIN A1

384
2upl
A
4
119
5.1e−23
0.44
0.63

HETEROGENEOUS NUCLEAR
COMPLEX

RIBONUCLEOPROTEIN A1;
(RIBONUCLEOPROTEIN/DNA) HNRNP

CHAIN: A; 12-NUCLEOTIDE
AI, UPI; COMPLEX

SINGLE-STRANDED TELOMETRIC
(RIBONUCLEOPROTEIN/DNA),

DNA; CHAIN: B;
HETEROGENEOUS NUCLEAR 2

RIBONUCLEOPROTEIN AI

384
2up1
A
412
501
1.5e−29
0.87
1.00

HETEROGENEOUS NUCLEAR
COMPLEX

RIBONUCLEOPROTEIN AI;
(RIBONUCLEOPROTEIN/DNA) HNRNP

CHAIN: A; 12-NUCLEOTIDE
AI, UPI; COMPLEX

SINGLE-STRANDED TELOMETRIC
(RIBONUCLEOPROTEIN/DNA),

DNA; CHAIN: B;
HETEROGENEOUS NUCLEAR 2

RIBONUCLEOPROTEIN AI

384
3sx1
A
2
106
1.2e−20
0.47
0.99

SEX-LETHAL; CHAIN: A, B, C;
RNA BINDING DOMAIN RNA

BINDING DOMAIN, RBD, RNA

RECOGNITION MOTIF, RRM, 2

SPLICING INHIBITOR,

TRANSLATIONAL INHIBITOR, SEX 3

DETERMINATION, X CHROMOSOME

DOSAGE COMPENSATION

384
3sx1
A
35
189
3.4e−41
0.72
1.00

SEX-LETHAL; CHAIN: A, B, C;
RNA BINDING DOMAIN RNA

BINDING DOMAIN, RBD, RNA

RECOGNITION MOTIF, RRM, 2

SPLICING INHIBITOR,

TRANSLATIONAL INHIBITOR, SEX 3

DETERMINATION, X CHROMOSOME

DOSAGE COMPENSATION

391
1a06

1
327
1.7e−63

98.83
CALCIUM/CALMODULIN-
KINASE KINASE, SIGNAL

DEPENDENT PROTEIN KINASE;
TRANSDUCTION,

CHAIN: NULL;
CALCIUM/CALMODULIN

391
1a6o

1
296
1.2e−81

153.21
PROTEIN KINASE CK2/ALPHA-
TRANSFERASE TRANSFERASE,

SUBUNIT; CHAIN: NULL;
SERINE/THREONINE-PROTEIN

KINASE, CASEIN KINASE, 2 SER/THR

KINASE

391
1a6o

3
295
1.2e−81
0.30
1.00

PROTEIN KINASE CK2/ALPHA-
TRANSFERASE TRANSFERASE,

SUBUNIT; CHAIN: NULL;
SERINE/THREONINE-PROTEIN

KINASE, CASEIN KINASE, 2 SER/THR

KINASE

391
1apm
E
1
324
6e−55

116.50
TRANSFERASE(PHOSPHOTRANSFERASE)

$C-/AMP$-DEPENDENT

PROTEIN KINASE (E.C.2.7.1.37)

($C/APK$) 1APM 3 (CATALYTIC

SUBUNIT) ALPHA ISOENZYME

MUTANT WITH SER 139 1APM 4

REPLACED BY ALA (/S139A$)

COMPLEX WITH THE PEPTIDE

1APM 5 INHIBITOR PKI(5-24) AND

THE DETERGENT MEGA-8 1APM 6

391
1apm
E
2
288
1e−53
0.45
1.00

TRANSFERASE(PHOSPHOTRANSFERASE)

$C-/AMP$-DEPENDENT

PROTEIN KINASE (E.C.2.7.1.37)

($C/APK$) 1APM 3 (CATALYTIC

SUBUNIT) ALPHA ISOENZYME

MUTANT WITH SER 139 1APM 4

REPLACED BY ALA (/S139A$)

COMPLEX WITH THE PEPTIDE

1APM 5 INHIBITOR PKI(5-24) AND

THE DETERGENT MEGA-8 1APM 6

391
1apm
E
2
304
6e−55
0.31
1.00

TRANSFERASE(PHOSPHOTRANSFERASE)

$C-/AMP$-DEPENDENT

PROTElN KINASE (E.C.2.7.1.37)

($C/APK$) 1APM 3 (CATALYTIC

SUBUNIT) ALPHA ISOENZYME

MUTANT WITH SER 139 1APM 4

REPLACED BY ALA (/S139A$)

COMPLEX WITH THE PEPTIDE

1APM 5 INHIBITOR PKI(5-24) AND

THE DETERGENT MEGA-8 1APM 6

391
1aql

2
294
0
0.37
1.00

CYCLIN-DEPENDENT PROTEIN
PROTEIN KINASE CDK2; PROTEIN

KINASE 2; CHAIN: NULL;
KINASE, CELL CYCLE,

PHOSPHORYLATION,

STAUROSPORINE, 2 CELL DIVISION,

MITOSIS, INHIBITION

391
1aql

2
298
0

212.68
CYCLIN-DEPENDENT PROTEIN
PROTEIN KINASE CDK2; PROTEIN

KINASE 2; CHAIN: NULL;
KINASE, CELL CYCLE,

PHOSPHORYLATION,

STAUROSPORINE, 2 CELL DIVISION,

MITOSIS, INHIBITION

391
1bi8
A
3
289
3.4e−91

182.71
CYCLIN-DEPENDENT KINASE 6;
COMPLEX (KINASE/INHIBITOR)

CHAIN: A, C; CYCLIN-
CDK6; P19INK4D; CYCLIN

DEPENDENT KINASE INHIBITOR;
DEPENDENT KINASE, CYCLIN

CHAIN: B, D;
DEPENDENT KINASE INHIBITORY 2

PROTEIN, CDK, INK4, CELL CYCLE,

COMPLEX (KINASE/INHIBITOR)

HEADER HELIX

391
1bi8
A
4
289
3.4e−91
0.04
1.00

CYCLIN-DEPENDENT KINASE 6;
COMPLEX (KINASE/INHIBITOR)

CHAIN: A, C; CYCLIN-
CDK6; P19INK4D; CYCLIN

DEPENDENT KINASE INHIBITOR;
DEPENDENT KINASE, CYCLIN

CHAIN: B, D;
DEPENDENT KINASE INHIBITORY 2

PROTEIN, CDK, INK4, CELL CYCLE,

COMPLEX (KINASE/INHIBITOR)

HEADER HELIX

391
1blx
A
1
296
1.7e−99

202.88
CYCLIN-DEPENDENT KINASE 6;
COMPLEX (INHIBITOR

CHAIN: A; P19INK4D; CHAIN: B;
PROTEIN/KINASE) INHIBITOR

PROTEIN, CYCLIN-DEPENDENT

KINASE, CELL CYCLE 2 CONTROL,

ALPHA/BETA, COMPLEX (INHIBITOR

PROTEIN/KINASE)

391
1blx
A
4
291
1.7e−99
0.27
1.00

CYCLIN-DEPENDENT KINASE 6;
COMPLEX (INHIBITOR

CHAIN: A; P19INK4D; CHAIN: B;
PROTEIN/KINASE) INHIBITOR

PROTEIN, CYCLIN-DEPENDENT

KINASE, CELL CYCLE 2 CONTROL,

ALPHA/BETA, COMPLEX (INHIBITOR

PROTEIN/KINASE)

391
1byg
A
1
303
3e−34

74.19
C-TERMINAL SRC KINASE;
TRANSFERASE CSK; PROTEIN

CHAIN: A;
KINASE, C-TERMINAL SRC KINASE,

PHOSPHORYLATION, 2

STAUROSPORINE, TRANSFERASE

391
1cki
A
2
281
3e−55

68.61
CASEIN KINASE 1 DELTA; 1CKI 6
PHOSPHOTRANSFERASE PROTEIN

CHAIN: A, B; 1CKI 7
KINASE 1CKI 18

391
1cki
A
4
288
3e−55
0.17
0.89

CASEIN KINASE 1 DELTA; 1CKI 6
PHOSPHOTRANSFERASE PROTEIN

CHAIN: A, B; 1CKI 7
KINASE 1CKI 18

391
1cm8
A
1
326
0
0.42
1.00

PHOSPHORYLATED MAP KINASE
TRANSFERASE STRESS-ACTIVATED

P38-GAMMA; CHAIN: A, B;
PROTEIN KINASE-3, ERK6, ERK5: P38-

GAMMA, GAMMA,

PHOSPHORYLATION, MAP KINASE

391
1cmk
E
1
324
6.8e−56

111.92
PHOSPHOTRANSFERASE CAMP-

DEPENDENT PROTEIN KINASE

CATALYTIC SUBUNIT 1CMK 3

(E.C.2.7.1.37) 1CMK 4

391
1cmk
E
2
288
6.8e−56
0.46
1.00

PHOSPHOTRANSFERASE CAMP-

DEPENDENT PROTEIN KINASE

CATALYTIC SUBUNIT 1CMK 3

(E.C.2.7.1.37) 1CMK 4

391
1csn

1
284
5.1e−18

77.16
CASEIN KINASE-1; 1CSN 4
PHOSPHOTRANSFERASE

391
1ctp
E
1
311
1.5e−56

109.28
TRANSFERASE(PHOSPHOTRANSFERASE)

CAMP-DEPENDENT

PROTEIN KINASE (E.C.2.7.1.37)

(CAPK) 1CTP 3 (CATALYTIC

SUBUNIT) 1CTP 4

391
1f3m
C
3
297
7.5e−67
0.41
1.00

SERINE/THREONINE-PROTEIN
TRANSFERASE KINASE DOMAIN,

KINASE PAK-ALPHA; CHAIN: A,
AUTOINHIBITORY FRAGMENT,

B; SERINE/THREONINE-PROTEIN
HOMODIMER

KINASE PAK-ALPHA; CHAIN: C,

D;

391
1fgk
A
1
299
1.5e−38

95.41
FGF RECEPTOR I; CHAIN: A, B;
PHOSPHOTRANSFERASE FGFRIK,

FIBROBLAST GROWTH FACTOR

RECEPTOR 1; TRANSFERASE,

TYROSINE-PROTEIN KINASE, ATP-

BINDING, 2 PHOSPHORYLATION,

RECEPTOR, PHOSPHOTRANSFERASE

391
1fgk
B
1
298
7.5e−37

101.29
FGF RECEPTOR 1; CHAIN: A, B;
PHOSPHOTRANSFERASE FGFRIK,

FIBROBLAST GROWTH FACTOR

RECEPTOR 1; TRANSFERASE,

TYROSINE-PROTEIN KINASE, ATP-

BINDING, 2 PHOSPHORYLATION,

RECEPTOR, PHOSPHOTRANSFERASE

391
1hcl

2
294
0
0.67
1.00

HUMAN CYCLIN-DEPENDENT
PROTEIN KINASE CDK2;

KINASE 2; CHAIN: NULL;
TRANSFERASE, SERINE/THREONINE

PROTEIN KINASE, ATP-BINDING, 2

CELL CYCLE, CELL DIVISION,

MITOSIS, PHOSPHORYLATION

391
1hcl

2
298
0

239.66
HUMAN CYCLIN-DEPENDENT
PROTEIN KINASE CDK2;

KINASE 2; CHAIN: NULL;
TRANSFERASE, SERINE/THREONINE

PROTEIN KINASE, ATP-BINDING, 2

CELL CYCLE, CELL DIVISION,

MITOSIS, PHOSPHORYLATION

391
1ian

1
328
0
0.12
1.00

P38 MAP KINASE; CHAIN: NULL;
SERINE/THREONINE-PROTEIN

KINASE CSBP, RK, P38; PROTEIN

SER/THR-KINASE,

SERINE/THREONINE-PROTEIN

KINASE

391
1ian

1
328
0

163.36
P38 MAP KINASE; CHAIN: NULL;
SERINE/THREONINE-PROTEIN

KINASE CSBP, RK, P38; PROTEIN

SER/THR-KINASE,

SERINE/THREONINE-PROTEIN

KINASE

391
1ir3
A
1
275
4.5e−37

79.01
INSULIN RECEPTOR; CHAIN: A;
COMPLEX

PEPTIDE SUBSTRATE; CHAIN: B;
(TRANSFERASE/SUBSTRATE)

TYROSINE KINASE, SIGNAL

TRANSDUCTION,

PHOSPHOTRANSFERASE, 2

COMPLEX (KINASE/PEPTIDE

SUBSTRATE/ATP ANALOG),

ENZYME, 3 COMPLEX

(TRANSFERASE/SUBSTRATE)

391
1jnk

1
323
0
0.46
1.00

C-JUN N-TERMINAL KINASE;
TRANSFERASE JNK3; TRANSFERASE,

CHAIN: NULL;
JNK3 MAP KINASE,

SERINE/THREONINE PROTEIN 2

KINASE

391
1jnk

1
331
0

161.78
C-JUN N-TERMINAL KINASE;
TRANSFERASE JNK3; TRANSFERASE,

CHAIN: NULL;
JNK3 MAP KINASE,

SERINE/THREONINE PROTEIN 2

KINASE

391
1koa

1
302
1e−57
0.26
1.00

TWITCHIN; CHAIN: NULL;
KINASE KINASE, TWITCHIN,

INTRASTERIC REGULATION

391
1koa

1
358
1e−57

86.80
TWITCHIN; CHAIN: NULL;
KINASE KINASE, TWITCHIN,

INTRASTERIC REGULATION

391
1kob
A
1
292
1.7e−57
0.26
1.00

TWITCHIN: CHAIN: A, B;
KINASE KINASE, TWITCHIN,

INTRASTERIC REGULATION

391
1kob
A
1
357
1.7e−57

124.22
TWITCHIN; CHAIN: A, B;
KINASE KINASE, TWITCHIN,

INTRASTERIC REGULATION

391
1p38

1
328
0
0.47
1.00

MAP KINASE P38; CHAIN: NULL;
TRANSFERASE MITOGEN

ACTIVATED PROTEIN KINASE;

TRANSFERASE, MAP KINASE,

SERINE/THREONINE-PROTEIN

KINASE, 2 P38

391
1p38

1
332
0

191.19
MAP KINASE P38; CHAIN: NULL;
TRANSFERASE MITOGEN

ACTIVATED PROTEIN KINASE;

TRANSFERASE, MAP KINASE,

SERINE/THREONINE-PROTEIN

KINASE, 2 P38

391
1phk

1
291
1.7e−66

123.81
PHOSPHORYLASE KINASE;
KINASE RABBIT MUSCLE

CHAIN: NULL;
PHOSPHORYLASE KINASE;

GLYCOGEN METABOLISM,

TRANSFERASE, SERINE/THREONINE-

PROTEIN, 2 KINASE, ATP-BINDING,

CALMODULIN-BINDING

391
1phk

3
291
1.7e−66
0.37
1.00

PHOSPHORYLASE KINASE;
KINASE RABBIT MUSCLE

CHAIN: NULL;
PHOSPHORYLASE KINASE;

GLYCOGEN METABOLISM,

TRANSFERASE, SERINE/THREONINE-

PROTEIN, 2 KINASE, ATP-BINDING,

CALMODULIN-BINDING

391
1pme

1
330
0
0.53
1.00

ERK2: CHAIN: NULL;
TRANSFERASE MAP KINASE,

SERINE/THREONINE PROTEIN

KINASE, TRANSFERASE

391
1pme

1
331
0

183.19
ERK2; CHAIN: NULL;
TRANSFERASE MAP KINASE,

SERINE/THREONINE PROTEIN

KINASE, TRANSFERASE

391
1tki
A
1
358
1.7e−45

114.84
TITIN; CHAIN: A, B;
SERINE KINASE SERINE KINASE,

TITIN, MUSCLE, AUTOINHIBITION

391
3erk

1
325
0

187.32
EXTRACELLULAR REGULATED
TRANSFERASE MITOGEN

KINASE 2; CHAIN: NULL;
ACTIVATED PROTEIN KINASE, MAP

2, ERK2; TRANSFERASE,

SERINE/THREONINE-PROTEIN

KINASE, MAP KINASE, 2 ERK2

391
3erk

1
326
0
0.54
1.00

EXTRACELLULAR REGULATED
TRANSFERASE MITOGEN

KINASE 2; CHAIN: NULL;
ACTIVATED PROTEIN KINASE, MAP

2, ERK2; TRANSFERASE,

SERINE/THREONINE-PROTEIN

KINASE, MAP KINASE, 2 ERK2

393
1apq

120
154
1.5e−11
−0.02
1.00

COMPLEMENT PROTEASE CIR:
COMPLEMENT COMPLEMENT, EGF,

CHAIN: NULL;
CALCIUM BINDING, SERINE

PROTEASE

393
1ek4
A
5
111
6e−25
0.51
1.00

INTEGRIN ALPHA-1; CHAIN: A, B;
STRUCTURAL PROTEIN I-DOMAIN,

METAL BINDING, COLLAGEN,

ADHESION

393
1ek4
A
527
709
1e−46
1.12
1.00

INTEGRIN ALPHA-1; CHAIN: A, B;
STRUCTURAL PROTEIN I-DOMAIN,

METAL BINDING, COLLAGEN,

ADHESION

393
1dan
L
116
205
4.5e−20
−0.44
0.65

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

393
1dan
L
124
246
3e−32
−0.30
0.10

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

393
1dan
L
168
287
4.5e−31
−0.15
0.55

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

393
1dan
L
207
328
6e−31
−0.25
0.57

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

393
1dan
L
248
369
3e−25
−0.40
0.11

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

393
1dan
L
276
358
6.8e−16
−0.17
0.84

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

393
1dan
L
317
397
3.4e−16
−0.32
0.47

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

393
1dan
L
332
451
9e−25
−0.23
0.17

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

393
1dan
L
336
447
1.7e−18
−0.42
0.00

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

393
1dan
L
372
492
9e−26
−0.12
0.05

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

393
1dan
L
412
535
1.2e−30
0.20
0.22

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

393
1dan
L
439
528
1.7e−17
−0.09
0.94

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
(GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

393
1dqb
A
438
525
7.5e−17
0.40
0.98

THROMBOMODULIN; CHAIN: A;
MEMBRANE PROTEIN NMR,

THROMBIN, EGF MODULE,

ANTICOAGULANT,

GLYCOSYLATION

393
1dva
L
317
397
3.4e−16
−0.62
0.58

DES-GLA FACTOR VIIA (HEAVY
HYDROLASE/HYDROLASE

CHAIN); CHAIN: H, I; DES-GLA
INHIBITOR PROTEIN-PEPTIDE

FACTOR VIIA (LIGHT CHAIN);
COMPLEX

CHAIN: L, M; (DPN)-PHE-ARG;

CHAIN: C, D; PEPTIDE E-76;

CHAIN: X, Y;

393
1dva
L
439
528
1.7e−17
0.21
0.84

DES-GLA FACTOR VIIA (HEAVY
HYDROLASE/HYDROLASE

CHAIN); CHAIN: H, I; DES-GLA
INHIBITOR PROTEIN-PEPTIDE

FACTOR VIIA (LIGHT CHAIN);
COMPLEX

CHAIN: L, M; (DPN)-PHE-ARG;

CHAIN: C, D; PEPTIDE E-76;

CHAIN: X, Y;

393
1dx5
I
121
233
1e−23
0.04
1.00

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

393
1dx5
I
153
274
3e−25
0.09
0.55

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

393
1dx5
I
195
315
4.5e−27
0.30
1.00

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

393
1dx5
I
235
346
1.2e−17
0.02
0.99

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

393
1dx5
I
236
356
1.5e−26
−0.04
1.00

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

393
1dx5
I
318
438
1.5e−22
0.19
0.93

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

393
1dx5
I
359
479
3e−24
0.41
1.00

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

393
1dx5
I
401
520
3e−24
0.61
1.00

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

393
1dx5
I
79
188
6.8e−15
−0.40
0.05

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

393
1emn

273
347
5.1e−19
0.06
0.78

FIBRILLIN; CHAIN: NULL;
MATRIX PROTEIN EXTRACELLULAR

MATRIX, CALCIUM-BINDING,

GLYCOPROTEIN, 2 REPEAT, SIGNAL,

MULTIGENE FAMILY, DISEASE

MUTATION, 3 EGF-LIKE DOMAIN,

HUMAN FIBRILLIN-I FRAGMENT,

MATRIX PROTEIN

393
1emn

317
388
3.4e−18
−0.20
0.99

FIBRILLIN; CHAIN: NULL;
MATRIX PROTEIN EXTRACELLULAR

MATRIX, CALCIUM-BINDING,

GLYCOPROTEIN, 2 REPEAT, SIGNAL,

MULTIGENE FAMILY, DISEASE

MUTATION, 3 EGF-LIKE DOMAIN,

HUMAN FIBRILLIN-I FRAGMENT,

MATRIX PROTEIN

393
1emn

440
511
5.1e−18
0.32
1.00

FIBRILLIN; CHAIN: NULL;
MATRIX PROTEIN EXTRACELLULAR

MATRIX, CALCIUM-BINDING,

GLYCOPROTEIN, 2 REPEAT, SIGNAL,

MULTIGENE FAMILY, DISEASE

MUTATION, 3 EGF-LIKE DOMAIN,

HUMAN FIBRILLIN-I FRAGMENT,

MATRIX PROTEIN

393
1fak
L
150
246
7.5e−22
−0.23
0.10

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

393
1fak
L
192
287
1.5e−21
−0.05
0.24

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

393
1fak
L
232
328
3e−23
0.08
0.80

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

393
1fak
L
273
369
3e−18
−0.27
0.15

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

393
1fak
L
276
358
6.8e−16
0.01
0.90

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

393
1fak
L
317
397
3.4e−16
−0.41
0.35

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

393
1fak
L
355
451
6e−19
0.35
0.23

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

393
1fak
L
396
492
4.5e−19
0.09
0.10

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

393
1fak
L
437
527
3e−21
0.44
0.76

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

393
1fak
L
439
528
1.7e−17
0.22
0.98

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

393
1ido

1
109
4.5e−24
0.33
0.84

INTEGRIN; CHAIN: NULL;
CELL ADHESION PROTEIN A-

DOMAIN INTEGRIN, CELL ADHESION

PROTEIN, GLYCOPROTEIN,

EXTRACELLULAR 2 MATRIX,

CYTOSKELETON

393
1ido

527
707
4.5e−46

98.35
INTEGRIN; CHAIN: NULL;
CELL ADHESION PROTEIN A-

DOMAIN INTEGRIN, CELL ADHESION

PROTEIN, GLYCOPROTEIN,

EXTRACELLULAR 2 MATRIX,

CYTOSKELETON

393
1ido

529
706
4.5e−46
1.04
1.00

INTEGRIN; CHAIN: NULL;
CELL ADHESION PROTEIN A-

DOMAIN INTEGRIN, CELL ADHESION

PROTEIN, GLYCOPROTEIN,

EXTRACELLULAR 2 MATRIX,

CYTOSKELETON

393
1jia
A
205
321
1.5e−19
0.01
−0.02

PHOSPHOLIPASE A2; CHAIN: A, B;
PHOSPHOLIPASE PHOSPHOLIPASE

A2, AGKISTRODON HALYS PALLAS

CRYSTAL 2 STRUCTURE

393
1lfa
A
1
112
1.5e−24
0.01
0.89

CD11A; 1LFA 5 CHAIN: A, B; 1LFA 6
CELL ADHESION LFA-1, ALPHA-

L\, BETA-2 INTEGRIN, A-DOMAIN;

1LFA 8

393
1lfa
A
526
711
1.5e−53

93.64
CD11A; 1LFA 5 CHAIN: A, B; 1LFA 6
CELL ADHESION LFA-1, ALPHA-

L\, BETA-2 INTEGRIN, A-DOMAIN;

1LFA 8

393
1lfa
A
526
713
1.5e−53
1.12
1.00

CD11A; 1LFA 5 CHAIN: A, B; 1LFA 6
CELL ADHESION LFA-1, ALPHA-

L\, BETA-2 INTEGRIN, A-DOMAIN;

1LFA 8

393
1pfx
L
157
301
4.5e−30
−0.01
0.07

FACTOR IXA; CHAIN: C, L,; D-
COMPLEX (BLOOD

PHE-PRO-ARG; CHAIN: I;
COAGULATION/INHIBITOR)

CHRISTMAS FACTOR; COMPLEX,

INHIBITOR, HEMOPHILIA/EGF,

BLOOD COAGULATION, 2 PLASMA,

SERINE PROTEASE, CALCIUM-

BINDING, HYDROLASE, 3

GLYCOPROTEIN

393
1pfx
L
197
341
3e−29
−0.15
0.81

FACTOR IXA; CHAIN: C, L,; D-
COMPLEX (BLOOD

PHE-PRO-ARG; CHAIN: I;
COAGULATION/INHIBITOR)

CHRISTMAS FACTOR; COMPLEX,

INHIBITOR, HEMOPHILIA/EGF,

BLOOD COAGULATION, 2 PLASMA,

SERINE PROTEASE, CALCIUM-

BINDING, HYDROLASE, 3

GLYCOPROTEIN

393
1pfx
L
286
423
3e−23
−0.10
0.06

FACTOR IXA; CHAIN: C, L,; D-
COMPLEX (BLOOD

PHE-PRO-ARG; CHAIN: I;
COAGULATION/INHIBITOR)

CHRISTMAS FACTOR; COMPLEX,

INHIBITOR, HEMOPHILIA/EGF,

BLOOD COAGULATION, 2 PLASMA,

SERINE PROTEASE, CALCIUM-

BINDING, HYDROLASE, 3

GLYCOPROTEIN

393
1pfx
L
403
527
6e−25
0.06
0.41

FACTOR IXA; CHAIN: C, L,; D-
COMPLEX (BLOOD

PHE-PRO-ARG; CHAIN: I;
COAGULATION/INHIBITOR)

CHRISTMAS FACTOR; COMPLEX,

INHIBITOR, HEMOPHILIA/EGF,

BLOOD COAGULATION, 2 PLASMA,

SERINE PROTEASE, CALCIUM-

BINDING, HYDROLASE, 3

GLYCOPROTEIN

393
1pfx
L
440
538
1.2e−15
−0.13
0.11

FACTOR IXA; CHAIN: C, L,; D-
COMPLEX (BLOOD

PHE-PRO-ARG; CHAIN: I;
COAGULATION/INHIBITOR)

CHRISTMAS FACTOR; COMPLEX,

INHIBITOR, HEMOPHILIA/EGF,

BLOOD COAGULATION, 2 PLASMA,

SERINE PROTEASE, CALCIUM-

BINDING, HYDROLASE, 3

GLYCOPROTEIN

393
1qfk
L
444
528
1.7e−16
0.30
0.86

COAGULATION FACTOR VIIA
SERINE PROTEASE FVIIA; FVIIA;

(LIGHT CHAIN); CHAIN: L;
BLOOD COAGULATION, SERINE

COAGULATION FACTOR VIIA
PROTEASE

(HEAVY CHAIN); CHAIN: H;

TRIPEPTIDYL INHIBITOR; CHAIN:

C;

393
1xka
L
444
528
1.7e−14
0.33
0.64

BLOOD COAGULATION FACTOR
BLOOD COAGULATION FACTOR

XA; CHAIN: L, C;
STUART FACTOR; BLOOD

COAGULATION FACTOR, SERINE

PROTEINASE, EPIDERMAL 2

GROWTH FACTOR LIKE DOMAIN

393
1apq

120
154
1.5e−11
−0.02
1.00

COMPLEMENT PROTEASE CIR;
COMPLEMENT COMPLEMENT, EGF,

CHAIN: NULL;
CALCIUM BINDING, SERINE

PROTEASE

393
1aut
L
80
151
1.2e−10
−0.62
0.05

ACTIVATED PROTEIN C; CHAIN:
COMPLEX (BLOOD

C, L; D-PHE-PRO-MAI; CHAIN: P;
COAGULATION/INHIBITOR)

AUTOPROTHROMBIN IIA;

HYDROLASE, SERINE PROTEINASE),

PLASMA CALCIUM BINDING, 2

GLYCOPROTEIN, COMPLEX (BLOOD

COAGULATION/INHIBITOR)

393
1ck4
A
5
111
6e−25
0.51
1.00

INTEGRIN ALPHA-I; CHAIN: A, B;
STRUCTURAL PROTEIN I-DOMAIN,

METAL BINDING, COLLAGEN,

ADHESION

393
1ck4
A
527
709
1e−46
1.12
1.00

INTEGRIN ALPHA-I; CHAIN: A, B;
STRUCTURAL PROTEIN I-DOMAIN,

METAL BINDING, COLLAGEN,

ADHESION

393
1dan
L
116
205
4.5e−20
−0.44
0.65

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

393
1dan
L
124
246
3e−32
−0.30
0.10

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA, CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

393
1dan
L
168
287
4.5e−31
−0.15
0.55

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

393
1dan
L
207
328
6e−31
−0.25
0.57

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

393
1dan
L
248
369
3e−25
−0.40
0.11

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

393
1dan
L
273
365
1.2e−16
0.02
0.23

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

393
1dan
L
332
451
9e−25
−0.23
0.17

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

393
1dan
L
372
492
9e−26
−0.12
0.05

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

393
1dan
L
412
535
1.2e−30
0.20
0.22

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

393
1dan
L
439
528
1.7e−18
0.18
0.89

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINI:

VIIA: CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

393
1dqb
A
315
401
1.1e−15
0.05
0.69

THROMBOMODULIN; CHAIN: A;
MEMBRANE PROTEIN NMR,

THROMBIN, EGF MODULE,

ANTICOAGULANT,

GLYCOSYLATION

393
1dqb
A
438
525
7.5e−17
0.40
0.98

THROMBOMODULIN; CHAIN: A;
MEMBRANE PROTEIN NMR,

THROMBIN, EGF MODULE,

ANTICOAGULANT,

GLYCOSYLATION

393
1dva
L
273
365
1.2e−16
−0.09
0.63

DES-GLA FACTOR VIIA (HEAVY
HYDROLASE/HYDROLASE

CHAIN); CHAIN: H, I; DES-GLA
INHIBITOR PROTEIN-PEPTIDE

FACTOR VIIA (LIGHT CHAIN);
COMPLEX

CHAIN: L, M; (DPN)-PHE-ARG;

CHAIN: C, D; PEPTIDE E-76;

CHAIN: X, Y;

393
1dva
L
439
528
1.7e−18
0.32
0.92

DES-GLA FACTOR VIIA (HEAVY
HYDROLASE/HYDROLASE

CHAIN); CHAIN: H, 1; DES-GLA
INHIBITOR PROTEIN-PEPTIDE

FACTOR VIIA (LIGHT CHAIN);
COMPLEX

CHAIN: L, M; (DPN)-PHE-ARG;

CHAIN: C, D: PEPTIDE E-76;

CHAIN: X, Y;

393
1dx5
I
121
233
1e−23
0.04
1.00

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN: EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

393
1dx5
I
153
274
3e−25
0.09
0.55

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

393
1dx5
I
195
315
4.5e−27
0.30
1.00

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

393
1dx5
I
236
356
1.5e−26
−0.04
1.00

THROMBIN LIGHT CHAIN:
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D: THROMBIN
FACTOR II: COAGULATION FACTOR

HEAVY CHAIN: CHAIN: M, N, O, P:
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

393
1dx5
I
316
438
3.4e−17
−0.08
0.99

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

393
1dx5
I
318
438
1.5e−22
0.19
0.93

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

393
1dx5
I
359
479
3e−24
0.41
1.00

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

393
1dx5
I
401
520
3e−24
0.61
1.00

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D: THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

393
1dx5
I
442
525
1.5e−13
0.45
0.78

THROMBIN LIGHT CHAIN:
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II: FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L: THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

393
1dx5
I
77
188
3.4e−15
−0.52
0.18

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

393
1emn

112
187
3.4e−16
0.12
0.96

FIBRILLIN; CHAIN: NULL;
MATRIX PROTEIN EXTRACELLULAR

MATRIX, CALCIUM-BINDING.

GLYCOPROTEIN, 2 REPEAT, SIGNAL,

MULTIGENE FAMILY, DISEASE

MUTATION, 3 EGF-LIKE DOMAIN,

HUMAN FIBRILLIN-I FRAGMENT,

MATRIX PROTEIN

393
1emn

235
306
1.7e−18
0.27
0.81

FIBRILLIN; CHAIN: NULL;
MATRIX PROTEIN EXTRACELLULAR

MATRIX, CALCIUM-BINDING,

GLYCOPROTEIN, 2 REPEAT, SIGNAL,

MULTIGENE FAMILY, DISEASE

MUTATION, 3 EGF-LIKE DOMAIN,

HUMAN FIBRILLIN-I FRAGMENT,

MATRIX PROTEIN

393
1emn

273
347
1.7e−17
0.10
0.88

FIBRILLIN; CHAIN: NULL;
MATRIX PROTEIN EXTRACELLULAR

MATRIX, CALCIUM-BINDING,

GLYCOPROTEIN, 2 REPEAT, SIGNAL,

MULTIGENE FAMILY, DISEASE

MUTATION, 3 EGF-LIKE DOMAIN,

HUMAN FIBRILLIN-I FRAGMENT,

MATRIX PROTEIN

393
1emn

317
392
1e−17
−0.34
0.80

FIBRILLIN; CHAIN: NULL;
MATRIX PROTEIN EXTRACELLULAR

MATRIX, CALCIUM-BINDING,

GLYCOPROTEIN, 2 REPEAT, SIGNAL,

MULTIGENE FAMILY, DISEASE

MUTATION, 3 EGF-LIKE DOMAIN,

HUMAN FIBRILLIN-I FRAGMENT,

MATRIX PROTEIN

393
1emn

710
779
6.8e−15
0.06
−0.19

FIBRILLIN; CHAIN: NULL;
MATRIX PROTEIN EXTRACELLULAR

MATRIX, CALCIUM-BINDING,

GLYCOPROTEIN, 2 REPEAT, SIGNAL,

MULTIGENE FAMILY, DISEASE

MUTATION, 3 EGF-LIKE DOMAIN,

HUMAN FIBRILLIN-I FRAGMENT,

MATRIX PROTEIN

393
1fak
L
107
164
6e−11
−0.12
0.31

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX (SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

393
1fak
L
150
246
7.5e−22
−0.23
0.10

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

393
1fak
L
192
287
1.5e−21
−0.05
0.24

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND).

BLOOD CLOTTING

393
1fak
L
232
328
3e−23
0.08
0.80

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA:
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

393
1fak
L
273
365
1.2e−16
−0.05
0.21

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND).

BLOOD CLOTTING

393
1fak
L
273
369
3e−18
−0.27
0.15

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA:
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T: 5LI5; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

393
1fak
L
355
451
6e−19
0.35
0.23

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

393
1fak
L
396
492
4.5e−19
0.09
0.10

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

393
1fak
L
437
527
3e−21
0.44
0.76

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA: CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H: SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

1;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

393
1fak
L
439
528
1.7e−18
0.13
0.94

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR.

1;
RECEPTOR ENZYME, 3 INHIBITOR.

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

393
1ido

1
109
4.5e−24
0.33
0.84

INTEGRIN; CHAIN: NULL;
CELL ADHESION PROTEIN A-

DOMAIN INTEGRIN, CELL ADHESION

PROTEIN, GLYCOPROTEIN,

EXTRACELLULAR 2 MATRIX,

CYTOSKELETON

393
1ido

527
707
4.5e−46

98.35
INTEGRIN; CHAIN: NULL;
CELL ADHESION PROTEIN A-

DOMAIN INTEGRIN, CELL ADHESION

PROTEIN, GLYCOPROTEIN,

EXTRACELLULAR 2 MATRIX,

CYTOSKELETON

393
1ido

529
706
4.5e−46
1.04
1.00

INTEGRIN; CHAIN: NULL;
CELL ADHESION PROTEIN A-

DOMAIN INTEGRIN, CELL ADHESION

PROTEIN, GLYCOPROTEIN,

EXTRACELLULAR 2 MATRIX,

CYTOSKELETON

393
1jia
A
205
321
1.5e−19
0.01
−0.02

PHOSPHOLIPASE A2; CHAIN: A, B;
PHOSPHOLIPASE PHOSPHOLIPASE

A2, AGKISTRODON HALYS PALLAS

CRYSTAL 2 STRUCTURE

393
1lfa
A
1
112
1.5e−24
0.01
0.89

CDIIA; ILFA 5 CHAIN: A, B; ILFA 6
CELL ADHESION LFA-1, ALPHA-

L\,BETA-2 INTEGRIN, A-DOMAIN;

ILFA 8

393
1lfa
A
526
711
1.5e−53

93.74
CDIIA; ILFA 5 CHAIN: A, B; ILFA 6
CELL ADHESION LFA-1, ALPHA-

L\,BETA-2 INTEGRIN, A-DOMAIN;

ILFA 8

393
1lfa
A
526
713
1.5e−53
1.12
1.00

CDIIA; ILFA 5 CHAIN: A, B; ILFA 6
CELL ADHESION LFA-1, ALPHA-

L\,BETA-2 INTEGRIN, A-DOMAIN;

1LFA 8

393
1pfx
L
157
301
4.5e−30
−0.01
0.07

FACTOR IXA; CHAIN: C, L,; D-
COMPLEX (BLOOD

PHE-PRO-ARG; CHAIN: 1;
COAGULATION/INHIBITOR)

CHRISTMAS FACTOR; COMPLEX,

INHIBITOR, HEMOPHILIA/EGF,

BLOOD COAGULATION, 2 PLASMA,

SERINE PROTEASE, CALCIUM-

BINDING, HYDROLASE, 3

GLYCOPROTEIN

393
1pfx
L
197
341
3e−29
−0.15
0.81

FACTOR IXA; CHAIN: C, L,; D-
COMPLEX (BLOOD

PHE-PRO-ARG; CHAIN: 1;
COAGULATION/INHIBITOR)

CHRISTMAS FACTOR; COMPLEX,

INHIBITOR, HEMOPHILIA/EGF,

BLOOD COAGULATION, 2 PLASMA,

SERINE PROTEASE, CALCIUM-

BINDING, HYDROLASE, 3

GLYCOPROTEIN

393
1pfx
L
286
423
3e−23
−0.10
0.06

FACTOR IXA; CHAIN: C, L,; D-
COMPLEX (BLOOD

PHE-PRO-ARG; CHAIN: 1;
COAGULATION/INHIBITOR)

CHRISTMAS FACTOR; COMPLEX,

INHIBITOR, HEMOPHILIA/EGF,

BLOOD COAGULATION, 2 PLASMA,

SERINE PROTEASE, CALCIUM-

BINDING, HYDROLASE, 3

GLYCOPROTEIN

393
1pfx
L
403
527
6e−25
0.06
0.41

FACTOR IXA: CHAIN: C, L,; D-
COMPLEX (BLOOD

PHE-PRO-ARG; CHAIN: 1;
COAGULATION/INHIBITOR)

CHRISTMAS FACTOR; COMPLEX,

INHIBITOR, HEMOPHILIA/EGF,

BLOOD COAGULATION, 2 PLASMA,

SERINE PROTEASE, CALCIUM-

BINDING, HYDROLASE, 3

GLYCOPROTEIN

393
1pfx
L
440
536
8.5e−15
0.30
0.94

FACTOR IXA; CHAIN: C, L,; D-
COMPLEX (BLOOD

PHE-PRO-ARG; CHAIN: 1;
COAGULATION/INHIBITOR)

CHRISTMAS FACTOR; COMPLEX,

INHIBITOR, HEMOPHILIA/EGF,

BLOOD COAGULATION, 2 PLASMA,

SERINE PROTEASE, CALCIUM-

BINDING, HYDROLASE, 3

GLYCOPROTEIN

393
1qfk
L
444
528
3.4e−17
0.06
0.92

COAGULATION FACTOR VIIA
SERINE PROTEASE FVIIA; FVIIA;

(LIGHT CHAIN); CHAIN: L;
BLOOD COAGULATION, SERINE

COAGULATION FACTOR VIIA
PROTEASE

(HEAVY CHAIN); CHAIN: H;

TRIPEPTIDYL INHIBITOR; CHAIN:

C;

393
1xka
L
444
528
1.5e−14
0.33
0.64

BLOOD COAGULATION FACTOR
BLOOD COAGULATION FACTOR

XA; CHAIN: L, C;
STUART FACTOR; BLOOD

COAGULATION FACTOR, SERINE

PROTEINASE, EPIDERMAL 2

GROWTH FACTOR LIKE DOMAIN

394
1apq

120
154
1.5e−11
−0.02
1.00

COMPLEMENT PROTEASE CIR;
COMPLEMENT COMPLEMENT, EGF,

CHAIN: NULL;
CALCIUM BINDING, SERINE

PROTEASE

394
1ck4
A
5
111
6e−25
0.51
1.00

INTEGRIN ALPHA-1; CHAIN: A, B;
STRUCTURAL PROTEIN 1-DOMAIN,

METAL BINDING, COLLAGEN,

ADHESION

394
1ck4
A
527
709
1e−46
1.12
1.00

INTEGRIN ALPHA-1; CHAIN: A, B;
STRUCTURAL PROTEIN 1-DOMAIN,

METAL BINDING, COLLAGEN,

ADHESION

394
1dan
L
116
205
4.5e−20
−0.44
0.65

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

DFFRCMK) WITH CHAIN: C;

394
1dan
L
124
246
3e−32
−0.30
0.10

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR: CHAIN: T, U: D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

394
1dan
L
168
287
4.5e−31
−0.15
0.55

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

394
1dan
L
207
328
6e−31
−0.25
0.57

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

394
1dan
L
248
369
3e−25
−0.40
0.11

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

394
1dan
L
276
358
6.8e−16
−0.17
0.84

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

394
1dan
L
317
397
3.4e−16
−0.32
0.47

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

394
1dan
L
332
451
9e−25
−0.23
0.17

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

394
1dan
L
336
447
1.7e−18
−0.42
0.00

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

394
1dan
L
372
492
9e−26
−0.12
0.05

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

394
1dan
L
412
535
1.2e−30
0.20
0.22

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

394
1dan
L
439
528
1.7e−17
−0.09
0.94

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

394
1dqb
A
438
525
7.5e−17
0.40
0.98

THROMBOMODULIN; CHAIN: A;
MEMBRANE PROTEIN NMR,

THROMBIN, EGF MODULE,

ANTICOAGULANT,

GLYCOSYLATION

394
1dva
L
317
397
3.4e−16
−0.62
0.58

DES-GLA FACTOR VIIA (HEAVY
HYDROLASE/HYDROLASE

CHAIN); CHAIN: H, I; DES-GLA
INHIBITOR PROTEIN-PEPTIDE

FACTOR VIIA (LIGHT CHAIN);
COMPLEX

CHAIN: L, M; (DPN)-PHE-ARG;

CHAIN: C, D; PEPTIDE E-76;

CHAIN: X, Y;

394
1dva
L
439
528
1.7e−17
0.21
0.84

DES-GLA FACTOR VIIA (HEAVY
HYDROLASE/HYDROLASE

CHAIN): CHAIN: H, I; DES-GLA
INHIBITOR PROTEIN-PEPTIDE

FACTOR VIIA (LIGHT CHAIN);
COMPLEX

CHAIN: L, M; (DPN)-PHE-ARG;

CHAIN: C, D; PEPTIDE E-76;

CHAIN: X, Y;

394
1dx5
I
121
233
1e−23
0.04
1.00

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

394
1dx5
I
153
274
3e−25
0.09
0.55

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, 0, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

394
1dx5
I
195
315
4.5e−27
0.30
1.00

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F;
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

394
1dx5
I
235
346
1.2e−17
0.02
0.99

THROMBIN LIGHT CHAIN:
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CDI41

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

394
1dx5
I
236
356
1.5e−26
−0.04
1.00

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CDI41

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

394
1dx5
I
318
438
1.5e−22
0.19
0.93

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CDI41

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

394
1dx5
I
359
479
3e−24
0.41
1.00

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CDI41

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN: EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS.

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

394
1dx5
I
401
520
3e−24
0.61
1.00

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CDI41

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

394
1dx5
I
79
188
6.8e−15
−0.40
0.05

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CDI41

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

394
1emn

273
347
5.1e−19
0.06
0.78

FIBRILLIN; CHAIN: NULL;
MATRIX PROTEIN EXTRACELLULAR

MATRIX, CALCIUM-BINDING,

GLYCOPROTEIN, 2 REPEAT, SIGNAL,

MULTIGENE FAMILY, DISEASE

MUTATION, 3 EGF-LIKE DOMAIN,

HUMAN FIBRILLIN-1 FRAGMENT,

MATRIX PROTEIN

394
1emn

317
388
3.4e−18
−0.20
0.99

FIBRILLIN; CHAIN: NULL;
MATRIX PROTEIN EXTRACELLULAR

MATRIX, CALCIUM-BINDING,

GLYCOPROTEIN, 2 REPEAT, SIGNAL,

MULTIGENE FAMILY, DISEASE

MUTATION, 3 EGF-LIKE DOMAIN,

HUMAN FIBRILLIN-1 FRAGMENT,

MATRIX PROTEIN

394
1emn

440
511
5.1e−18
0.32
1.00

FIBRILLIN; CHAIN: NULL;
MATRIX PROTEIN EXTRACELLULAR

MATRIX, CALCIUM-BINDING,

GLYCOPROTEIN, 2 REPEAT, SIGNAL,

MULTIGENE FAMILY, DISEASE

MUTATION, 3 EGF-LIKE DOMAIN,

HUMAN FIBRILLIN-1 FRAGMENT,

MATRIX PROTEIN

394
1fak
L
150
246
7.5e−22
−0.23
0.10

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

1;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

394
1fak
L
192
287
1.5e−21
−0.05
0.24

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

1;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

394
1fak
L
232
328
3e−23
0.08
0.80

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

1;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

394
1fak
L
273
369
3e−18
−0.27
0.15

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

1;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

394
1fak
L
276
358
6.8e−16
0.01
0.90

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

1;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

394
1fak
L
317
397
3.4e−16
−0.41
0.35

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

1;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

394
1fak
L
355
451
6e−19
0.35
0.23

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

1;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

394
1 fak
L
396
492
4.5e−19
0.09
0.10

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

1;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

394
1fak
L
437
527
3e−21
0.44
0.76

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

1;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

394
1fak
L
439
528
1.7e−17
0.22
0.98

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

1;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

394
1ido

1
109
4.5e−24
0.33
0.84

INTEGRIN; CHAIN: NULL;
CELL ADHESION PROTEIN A-

DOMAIN INTEGRIN, CELL ADHESION

PROTEIN, GLYCOPROTEIN,

EXTRACELLULAR 2 MATRIX,

CYTOSKELETON

394
1ido

527
707
4.5e−46

98.35
INTEGRIN; CHAIN: NULL;
CELL ADHESION PROTEIN A-

DOMAIN INTEGRIN, CELL ADHESION

PROTEIN, GLYCOPROTEIN,

EXTRACELLULAR 2 MATRIX,

CYTOSKELETON

394
1ido

529
706
4.5e−46
1.04
1.00

INTEGRIN; CHAIN: NULL;
CELL ADHESION PROTEIN A-

DOMAIN INTEGRIN, CELL ADHESION

PROTEIN, GLYCOPROTEIN,

EXTRACELLULAR 2 MATRIX,

CYTOSKELETON

394
1jia
A
205
321
1.5e−19
0.01
−0.02

PHOSPHOLIPASE A2; CHAIN: A, B;
PHOSPHOLIPASE PHOSPHOLIPASE

A2, AGKISTRODON HALYS PALLAS

CRYSTAL 2 STRUCTURE

394
1lfa
A
1
112
1.5e−24
0.01
0.89

CD11A; ILFA 5 CHAIN: A, B; ILFA 6
CELL ADHESION LFA-1, ALPHA-

L\, BETA-2 INTEGRIN, A-DOMAIN;

ILFA 8

394
1lfa
A
526
711
1.5e−53

93.64
CD11A; ILFA 5 CHAIN: A, B; ILFA 6
CELL ADHESION LFA-1, ALPHA-

L\, BETA-2 INTEGRIN, A-DOMAIN;

ILFA 8

394
1lfa
A
526
713
1.5e−53
1.12
1.00

CD11A; ILFA 5 CHAIN: A, B; ILFA 6
CELL ADHESION LFA-1, ALPHA-

L\, BETA-2 INTEGRIN, A-DOMAIN;

ILFA 8

394
1pfx
L
157
301
4.5e−30
−0.01
0.07

FACTOR IXA; CHAIN: C, L,; D-
COMPLEX (BLOOD

PHE-PRO-ARG; CHAIN: 1;
COAGULATION/INHIBITOR)

CHRISTMAS FACTOR; COMPLEX,

INHIBITOR, HEMOPHILIA/EGF,

BLOOD COAGULATION, 2 PLASMA,

SERINE PROTEASE, CALCIUM-

BINDING, HYDROLASE, 3

GLYCOPROTEIN

394
1pfx
L
197
341
3e−29
−0.15
0.81

FACTOR IXA; CHAIN: C, L,; D-
COMPLEX (BLOOD

PHE-PRO-ARG; CHAIN: 1;
COAGULATION/INHIBITOR)

CHRISTMAS FACTOR; COMPLEX,

INHIBITOR, HEMOPHILIA/EGF,

BLOOD COAGULATION, 2 PLASMA,

SERINE PROTEASE, CALCIUM-

BINDING, HYDROLASE, 3

GLYCOPROTEIN

394
1pfx
L
286
423
3e−23
−0.10
0.06

FACTOR IXA; CHAIN: C, L,; D-
COMPLEX (BLOOD

PHE-PRO-ARG; CHAIN: 1;
COAGULATION/INHIBITOR)

CHRISTMAS FACTOR; COMPLEX,

INHIBITOR, HEMOPHILIA/EGF,

BLOOD COAGULATION, 2 PLASMA,

SERINE PROTEASE, CALCIUM-

BINDING, HYDROLASE, 3

GLYCOPROTEIN

394
1pfx
L
403
527
6e−25
0.06
0.41

FACTOR IXA; CHAIN: C, L,; D-
COMPLEX (BLOOD

PHE-PRO-ARG; CHAIN: 1;
COAGULATION/INHIBITOR)

CHRISTMAS FACTOR; COMPLEX,

INHIBITOR, HEMOPHILIA/EGF,

BLOOD COAGULATION, 2 PLASMA,

SERINE PROTEASE, CALCIUM-

BINDING, HYDROLASE, 3

GLYCOPROTEIN

394
1pfx
L
440
538
1.2e−15
−0.13
0.11

FACTOR IXA; CHAIN: C, L,; D-
COMPLEX (BLOOD

PHE-PRO-ARG; CHAIN: 1;
COAGULATION/INHIBITOR)

CHRISTMAS FACTOR; COMPLEX,

INHIBITOR, HEMOPHILIA/EGF,

BLOOD COAGULATION, 2 PLASMA,

SERINE PROTEASE, CALCIUM-

BINDING, HYDROLASE, 3

GLYCOPROTEIN

394
1qfk
L
444
528
1.7e−16
0.30
0.86

COAGULATION FACTOR VIIA
SERINE PROTEASE FVIIA; FVIIA;

(LIGHT CHAIN); CHAIN: L;
BLOOD COAGULATION, SERINE

COAGULATION FACTOR VIIA
PROTEASE

(HEAVY CHAIN); CHAIN: H;

TRIPEPTIDYL INHIBITOR; CHAIN:

C;

394
1xka
L
444
528
1.7e−14
0.33
0.64

BLOOD COAGULATION FACTOR
BLOOD COAGULATION FACTOR

XA; CHAIN: L, C;
STUART FACTOR; BLOOD

COAGULATION FACTOR, SERINE

PROTEINASE, EPIDERMAL 2

GROWTH FACTOR LIKE DOMAIN

394
1apq

120
154
1.5e−11
−0.02
1.00

COMPLEMENT PROTEASE CIR;
COMPLEMENT COMPLEMENT, EGF,

CHAIN: NULL;
CALCIUM BINDING, SERINE

PROTEASE

394
1aut
L
80
151
1.2e−10
−0.62
0.05

ACTIVATED PROTEIN C; CHAIN:
COMPLEX (BLOOD

C, L; D-PHE-PRO-MAI; CHAIN: P;
COAGULATION/INHIBITOR)

AUTOPROTHROMBIN IIA;

HYDROLASE, SERINE PROTEINASE).

PLASMA CALCIUM BINDING, 2

GLYCOPROTEIN, COMPLEX (BLOOD

COAGULATION/INHIBITOR)

394
1ck4
A
5
111
6e−25
0.51
1.00

INTEGRIN ALPHA-1; CHAIN: A, B;
STRUCTURAL PROTEIN I-DOMAIN,

METAL BINDING, COLLAGEN,

ADHESION

394
1ck4
A
527
709
1e−46
1.12
1.00

INTEGRIN ALPHA-1; CHAIN: A, B;
STRUCTURAL PROTEIN I-DOMAIN,

METAL BINDING, COLLAGEN,

ADHESION

394
1dan
L
116
205
4.5e−20
−0.44
0.65

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

394
1dan
L
124
246
3e−32
−0.30
0.10

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

394
1dan
L
168
287
4.5e−31
-0.15
0.55

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H: SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

394
1dan
L
207
328
6e−31
−0.25
0.57

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

394
1dan
L
248
369
3e−25
−0.40
0.11

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

394
1dan
L
273
365
1.2e−16
0.02
0.23

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

394
1dan
L
332
451
9e−25
−0.23
0.17

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

394
1dan
L
372
492
9e−26
−0.12
0.05

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

394
1dan
L
412
535
1.2e−30
0.20
0.22

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

394
1dan
L
439
528
1.7e−18
0.18
0.89

BLOOD COAGULATION FACTOR
BLOOD COAGULATION, SERINE

VIIA; CHAIN: L, H; SOLUBLE
PROTEASE, COMPLEX, CO-FACTOR,

TISSUE FACTOR; CHAIN: T, U; D-
2 RECEPTOR ENZYME, INHIBITOR,

PHE-PHE-ARG-
GLA, EGF, 3 COMPLEX (SERINE

CHLOROMETHYLKETONE
PROTEASE/COFACTOR/LIGAND)

(DFFRCMK) WITH CHAIN: C;

394
1dqb
A
315
401
1.1e−15
0.05
0.69

THROMBOMODULIN; CHAIN: A;
MEMBRANE PROTEIN NMR,

THROMBIN, EGF MODULE,

ANTICOAGULANT,

GLYCOSYLATION

394
1dqb
A
438
525
7.5e−17
0.40
0.98

THROMBOMODULIN; CHAIN: A;
MEMBRANE PROTEIN NMR,

THROMBIN, EGF MODULE,

ANTICOAGULANT,

GLYCOSYLATION

394
1dva
L
273
365
1.2e−16
−0.09
0.63

DES-GLA FACTOR VIIA (HEAVY
HYDROLASE/HYDROLASE

CHAIN); CHAIN: H, 1; DES-GLA
INHIBITOR PROTEIN-PEPTIDE

FACTOR VIIA (LIGHT CHAIN);
COMPLEX

CHAIN: L, M; (DPN)-PHE-ARG;

CHAIN: C, D; PEPTIDE E-76;

CHAIN: X, Y;

394
1dva
L
439
528
1.7e−18
0.32
0.92

DES-GLA FACTOR VIIA (HEAVY
HYDROLASE/HYDROLASE

CHAIN); CHAIN: H, I; DES-GLA
INHIBITOR PROTEIN-PEPTIDE

FACTOR VIIA (LIGHT CHAIN);
COMPLEX

CHAIN: L, M; (DPN)-PHE-ARG;

CHAIN: C, D; PEPTIDE E-76;

CHAIN: X, Y;

394
1dx5
I
121
233
1e−23
0.04
1.00

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

394
1dx5
I
153
274
3e−25
0.09
0.55

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

394
1dx5
I
195
315
4.5e−27
0.30
1.00

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

394
1dx5
I
236
356
1.5e−26
−0.04
1.00

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

394
1dx5
I
316
438
3.4e−17
−0.08
0.99

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATlON FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P:
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

394
1dx5
I
318
438
1.5e−22
0.19
0.93

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

394
1dx5
I
359
479
3e−24
0.41
1.00

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

394
1dx5
I
401
520
3e−24
0.61
1.00

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

394
1dx5
I
442
525
1.5e−13
0.45
0.78

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

394
1dx5
I
77
188
3.4e−15
−0.52
0.18

THROMBIN LIGHT CHAIN;
SERINE PROTEINASE COAGULATION

CHAIN: A, B, C, D; THROMBIN
FACTOR II; COAGULATION FACTOR

HEAVY CHAIN; CHAIN: M, N, O, P;
II; FETOMODULIN, TM, CD141

THROMBOMODULIN; CHAIN: I, J,
ANTIGEN; EGR-CMK SERINE

K, L; THROMBIN INHIBITOR L-
PROTEINASE, EGF-LIKE DOMAINS,

GLU-L-GLY-L-ARM; CHAIN: E, F,
ANTICOAGULANT COMPLEX, 2

G, H;
ANTIFIBRINOLYTIC COMPLEX

394
1emn

112
187
3.4e−16
0.12
0.96

FIBRILLIN; CHAIN: NULL;
MATRIX PROTEIN EXTRACELLULAR

MATRIX, CALCIUM-BINDING,

GLYCOPROTEIN, 2 REPEAT, SIGNAL,

MULTIGENE FAMILY, DISEASE

MUTATION, 3 EGF-LIKE DOMAIN,

HUMAN FIBRILLIN-I FRAGMENT,

MATRIX PROTEIN

394
1emn

235
306
1.7e−18
0.27
0.81

FIBRILLIN; CHAIN: NULL;
MATRIX PROTEIN EXTRACELLULAR

MATRIX, CALCIUM-BINDING,

GLYCOPROTEIN, 2 REPEAT, SIGNAL,

MULTIGENE FAMILY, DISEASE

MUTATION, 3 EGF-LIKE DOMAIN,

HUMAN FIBRILLIN-I FRAGMENT,

MATRIX PROTEIN

394
1emn

273
347
1.7e−17
0.10
0.88

FIBRILLIN; CHAIN: NULL;
MATRIX PROTEIN EXTRACELLULAR

MATRIX, CALCIUM-BINDING,

GLYCOPROTEIN, 2 REPEAT, SIGNAL,

MULTIGENE FAMILY, DISEASE

MUTATION, 3 EGF-LIKE DOMAIN,

HUMAN FIBRILLIN-I FRAGMENT,

MATRIX PROTEIN

394
1emn

317
392
1e−17
−0.34
0.80

FIBRILLIN; CHAIN: NULL;
MATRIX PROTEIN EXTRACELLULAR

MATRIX, CALClUM-BINDlNG,

GLYCOPROTEIN, 2 REPEAT, SIGNAL,

MULTIGENE FAMILY, DISEASE

MUTATION, 3 EGF-LIKE DOMAIN,

HUMAN FIBRILLIN-I FRAGMENT,

MATRIX PROTEIN

394
1emn

710
779
6.8e−15
0.06
−0.19

FIBRILLIN; CHAIN: NULL;
MATRIX PROTEIN EXTRACELLULAR

MATRIX, CALCIUM-BINDING,

GLYCOPROTEIN, 2 REPEAT, SIGNAL,

MULTIGENE FAMILY, DISEASE

MUTATION, 3 EGF-LIKE DOMAIN,

HUMAN FIBRILLIN-I FRAGMENT,

MATRIX PROTEIN

394
1fak
L
107
164
6e−11
−0.12
0.31

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

394
1fak
L
150
246
7.5e−22
−0.23
0.10

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

394
1fak
L
192
287
1.5e−21
−0.05
0.24

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

394
1fak
L
232
328
3e−23
0.08
0.80

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

394
1fak
L
273
365
1.2e−16
−0.05
0.21

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

394
1fak
L
273
369
3e−18
−0.27
0.15

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

394
1fak
L
355
451
6e−19
0.35
0.23

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

394
1fak
L
396
492
4.5e−19
0.09
0.10

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

394
1fak
L
437
527
3e−21
0.44
0.76

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

394
1fak
L
439
528
1.7e−18
0.13
0.94

BLOOD COAGULATION FACTOR
BLOOD CLOTTING

VIIA; CHAIN: L; BLOOD
COMPLEX(SERINE

COAGULATION FACTOR VIIA;
PROTEASE/COFACTOR/LIGAND),

CHAIN: H; SOLUBLE TISSUE
BLOOD COAGULATION, 2 SERINE

FACTOR; CHAIN: T; 5L15; CHAIN:
PROTEASE, COMPLEX, CO-FACTOR,

I;
RECEPTOR ENZYME, 3 INHIBITOR,

GLA, EGF, COMPLEX (SERINE 4

PROTEASE/COFACTOR/LIGAND),

BLOOD CLOTTING

394
1ido

1
109
4.5e−24
0.33
0.84

INTEGRIN; CHAIN: NULL;
CELL ADHESION PROTEIN A-

DOMAIN INTEGRIN, CELL ADHESION

PROTEIN, GLYCOPROTEIN,

EXTRACELLULAR 2 MATRIX,

CYTOSKELETON

394
1ido

527
707
4.5e−46

98.35
INTEGRIN; CHAIN: NULL;
CELL ADHESION PROTEIN A-

DOMAIN INTEGRIN, CELL ADHESION

PROTEIN, GLYCOPROTEIN,

EXTRACELLULAR 2 MATRIX,

CYTOSKELETON

394
1ido

529
706
4.5e−46
1.04
1.00

INTEGRIN; CHAIN: NULL;
CELL ADHESION PROTEIN A-

DOMAIN INTEGRIN, CELL ADHESION

PROTEIN, GLYCOPROTEIN,

EXTRACELLULAR 2 MATRIX,

CYTOSKELETON

394
1jia
A
205
321
1.5e−19
0.01
−0.02

PHOSPHOLIPASE A2; CHAIN: A, B;
PHOSPHOLIPASE PHOSPHOLIPASE

A2, AGKISTRODON HALYS PALLAS

CRYSTAL 2 STRUCTURE

394
1lfa
A
1
112
1.5e−24
0.01
0.89

CDIIA; ILFA 5 CHAIN: A, B; ILFA 6
CELL ADHESION LFA-I, ALPHA-

L\,BETA-2 INTEGRIN, A-DOMAIN;

ILFA 8

394
1lfa
A
526
711
1.5e−53

93.74
CDIIA; ILFA 5 CHAIN: A, B; ILFA 6
CELL ADHESION LFA-I, ALPHA-

L\,BETA-2 INTEGRIN, A-DOMAIN;

ILFA 8

394
1lfa
A
526
713
1.5e−53
1.12
1.00

CDIIA; ILFA 5 CHAIN: A, B; ILFA 6
CELL ADHESION LFA-I, ALPHA-

L\,BETA-2 INTEGRIN, A-DOMAIN;

ILFA 8

394
1pfx
L
157
301
4.5e−30
−0.01
0.07

FACTOR IXA; CHAIN: C, L,; D-
COMPLEX (BLOOD

PHE-PRO-ARG; CHAIN: I;
COAGULATION/INHIBITOR)

CHRISTMAS FACTOR; COMPLEX,

INHIBITOR, HEMOPHILIA/EGF,

BLOOD COAGULATION, 2 PLASMA,

SERINE PROTEASE, CALCIUM-

BINDING, HYDROLASE, 3

GLYCOPROTEIN

394
1pfx
L
197
341
3e−29
−0.15
0.81

FACTOR IXA; CHAIN: C, L,; D-
COMPLEX (BLOOD

PHE-PRO-ARG; CHAIN: I;
COAGULATION/INHIBITOR)

CHRISTMAS FACTOR; COMPLEX,

INHIBITOR, HEMOPHILIA/EGF,

BLOOD COAGULATION, 2 PLASMA,

SERINE PROTEASE, CALCIUM-

BINDING, HYDROLASE, 3

GLYCOPROTEIN

394
1pfx
L
286
423
3e−23
−0.10
0.06

FACTOR IXA; CHAIN: C, L,; D-
COMPLEX (BLOOD

PHE-PRO-ARG; CHAIN: I;
COAGULATION/INHIBITOR)

CHRISTMAS FACTOR; COMPLEX,

INHIBITOR, HEMOPHILIA/EGF,

BLOOD COAGULATION, 2 PLASMA,

SERINE PROTEASE, CALCIUM-

BINDING, HYDROLASE, 3

GLYCOPROTEIN

394
1pfx
L
403
527
6e−25
0.06
0.41

FACTOR IXA; CHAIN: C, L,; D-
COMPLEX (BLOOD

PHE-PRO-ARG; CHAIN: I;
COAGULATION/INHIBITOR)

CHRISTMAS FACTOR; COMPLEX,

INHIBITOR, HEMOPHILIA/EGF,

BLOOD COAGULATION, 2 PLASMA,

SERINE PROTEASE, CALCIUM-

BINDING, HYDROLASE, 3

GLYCOPROTEIN

394
1pfx
L
440
536
8.5e−15
0.30
0.94

FACTOR IXA; CHAIN: C, L,; D-
COMPLEX (BLOOD

PHE-PRO-ARG; CHAIN: I;
COAGULATION/INHIBITOR)

CHRISTMAS FACTOR; COMPLEX,

INHIBITOR, HEMOPHILIA/EGF,

BLOOD COAGULATION, 2 PLASMA,

SERINE PROTEASE, CALCIUM-

BINDING, HYDROLASE, 3

GLYCOPROTEIN

394
1qfk
L
444
528
3.4e−17
0.06
0.92

COAGULATION FACTOR VIIA
SERINE PROTEASE FVIIA; FVIIA;

(LIGHT CHAIN); CHAIN: L;
BLOOD COAGULATION, SERINE

COAGULATION FACTOR VIIA
PROTEASE

(HEAVY CHAIN); CHAIN: H;

TRIPEPTIDYL INHIBITOR; CHAIN:

C;

394
1xka
L
444
528
1.5e−14
0.33
0.64

BLOOD COAGULATION FACTOR
BLOOD COAGULATION FACTOR

XA; CHAIN: L, C;
STUART FACTOR; BLOOD

COAGULATION FACTOR, SERINE

PROTEINASE, EPIDERMAL 2

GROWTH FACTOR LIKE DOMAIN

399
1aip
A
183
403
3.4e−67
−0.15
0.17

ELONGATION FACTOR TU;
COMPLEX OF TWO ELONGATION

CHAIN: A, B, E, F; ELONGATION
FACTORS EF-TU; EF-TS;

FACTOR TS; CHAIN: C, D, G, H;
ELONGATION FACTOR,

NUCLEOTIDE EXCHANGE, GTP-

BINDING, 2 COMPLEX OF TWO

ELONGATION FACTORS

399
1efc
A
183
403
3.4e−71
−0.23
0.01

ELONGATION FACTOR; CHAIN:
RNA BINDING PROTEIN EFTU;

A, B;
TRANSPORT AND PROTECTION

PROTEIN, RNA BINDING PROTEIN

399
1efu
A
183
403
5.1e−65
−0.21
0.09

ELONGATION FACTOR TU;
COMPLEX (TWO ELONGATION

CHAIN: A, C; ELONGATION
FACTORS) ELONGATION FACTOR

FACTOR TS; CHAIN: B, D;
FOR TRANSFER, HEAT UNSTABLE,

ELONGATION FACTOR FOR

TRANSFER, HEAT STABLE,

ELONGATION FACTOR, COMPLEX

(TWO ELONGATION FACTORS)

399
1ega
A
184
388
6.8e−38
−0.11
0.13

GTP-BINDING PROTEIN ERA;
HYDROLASE ERA, GTPASE, RNA-

CHAIN: A, B;
BINDING, RAS-LIKE, HYDROLASE

399
1etu

183
343
5.1e−47
0.07
0.41

TRANSPORT AND PROTECTION

PROTEIN ELONGATION FACTOR

TU (DOMAIN I) —*GUANOSINE

DIPHOSPHATE IETU 4 COMPLEX

IETU 5

399
1exm
A
183
403
1.7e−73
−0.28
0.10

ELONGATION FACTOR TU (EF-
TRANSLATION EF-TU; GTPASE,

TU); CHAIN: A;
MOLECULAR SWITCH, TRNA,

RIBOSOME, Q-BETA REPLICASE, 2

CHAPERONE, DISULFIDE

ISOMERASE

399
1f60
A
183
400
1e−73
−0.34
0.07

ELONGATION FACTOR EEFIA;
TRANSLATION PROTEIN-PROTEIN

CHAIN: A; ELONGATION FACTOR
COMPLEX

EEFIBA; CHAIN: B;

399
1kao

184
342
1.7e−05
−0.06
0.13

RAP2A; CHAIN: NULL;
GTP-BINDING PROTEIN GTP-

BINDING PROTEIN, SMALL G

PROTEIN, RAP2, GDP, RAS

402
1alh
A
167
239
1.5e−20
−0.09
0.27

QGSR ZINC FINGER PEPTIDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

402
1alh
A
186
271
1.5e−20

58.92
QGSR ZINC FINGER PEPTIDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

402
1alh
A
243
310
3.4e−24
0.08
1.00

QGSR ZINC FINGER PEPTIDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

402
1mey
C
166
239
5.1e−37
−0.10
0.30

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

402
1mey
C
185
269
1.4e−44
−0.23
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

402
1mey
C
214
300
1.4e−44

67.85
DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

402
1mey
C
242
310
1e−37
−0.09
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

402
1spl

273
301
0.00015
−0.17
0.99

SPIF3; CHAIN: NULL;
ZINC FINGER TRANSCRIPTION

FACTOR SPI; ZINC FINGER,

TRANSCRIPTION ACTIVATION, SPI

402
1tf3
A
214
303
3.4e−20

67.04
TRANSCRIPTION FACTOR IIIA;
COMPLEX (TRANSCRIPTION

CHAIN: A; 5S RNA GENE; CHAIN:
REGULATION/DNA) TFIIIA; 5S GENE;

E, F;
NMR, TFIIIA, PROTEIN, DNA,

TRANSCRIPTION FACTOR, 5S RNA 2

GENE, DNA BINDING PROTEIN, ZINC

FINGER, COMPLEX 3

(TRANSCRIPTION

REGULATION/DNA)

402
1tf3
A
243
307
3.4e−20
0.06
0.48

TRANSCRIPTION FACTOR IIIA;
COMPLEX (TRANSCRIPTION

CHAIN: A; 5S RNA GENE; CHAIN:
REGULATION/DNA) TFIIIA; 5S GENE;

E, F;
NMR, TFIIIA, PROTEIN, DNA,

TRANSCRIPTION FACTOR, 5S RNA 2

GENE, DNA BINDING PROTEIN, ZINC

FINGER, COMPLEX 3

(TRANSCRIPTION

REGULATION/DNA)

402
1tf6
A
108
295
5.1e−39

78.75
TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

402
1tf6
A
167
306
5.1e−39
−0.11
0.39

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

402
1ubd
C
167
269
1.7e−33
−0.23
0.31

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

402
1ubd
C
187
300
5.1e−49

165.14
YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

402
1ubd
C
190
299
5.1e−49
0.13
1.00

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

402
1ubd
C
222
310
1.7e−30
−0.28
0.98

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

402
2gli
A
149
301
8.5e−38

82.64
ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

402
2gli
A
167
298
8.5e−38
−0.15
0.94

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GL1, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

404
1fjg
Q
71
147
1.5e−28
0.12
0.99

16S RIBOSOMAL RNA; CHAIN: A;
RIBOSOME 30S RIBOSOMAL

FRAGMENT OF MESSENGER
SUBUNIT, RIBOSOME, ANTIBIOTIC,

RNA; CHAIN: X; 30S RIBOSOMAL
STREPTOMYCIN, 2 SPECTINOMYCIN,

PROTEIN S2; CHAIN: B; 30S
PAROMOMYCIN

RIBOSOMAL PROTEIN S3; CHAIN:

C; 30S RIBOSOMAL PROTEIN S4;

CHAIN: D; 30S RIBOSOMAL

PROTEIN S5; CHAIN: E; 30S

RIBOSOMAL PROTEIN S6; CHAIN:

F; 30S RIBOSOMAL PROTEIN S7;

CHAIN: G; 30S RIBOSOMAL

PROTEIN S8; CHAIN: H; 30S

RIBOSOMAL PROTEIN S9; CHAIN:

I; 30S RIBOSOMAL PROTEIN S10;

CHAIN: J; 30S RIBOSOMAL

PROTEIN S11; CHAIN: K; 30S

RIBOSOMAL PROTEIN S12;

CHAIN: L; 30S RIBOSOMAL

PROTEIN S13; CHAIN: M; 30S

RIBOSOMAL PROTEIN S14;

CHAIN: N; 30S RIBOSOMAL

PROTEIN S15; CHAIN: O; 30S

RIBOSOMAL PROTEIN S16;

CHAIN: P; 30S RIBOSOMAL

PROTEIN S17; CHAIN: Q; 30S

RIBOSOMAL PROTEIN S18;

CHAIN: R; 30S RIBOSOMAL

PROTEIN S19; CHAIN: S; 30S

RIBOSOMAL PROTEIN S20;

CHAIN: T; 30S RIBOSOMAL

PROTEIN THX; CHAIN: V

404
1qd7
I
69
151
3.4e−32
−0.76
0.00

CENTRAL FRAGMENT OF 16S
RIBOSOME 30S RIBOSOMAL

RNA; CHAIN: A; END FRAGMENT
SUBUNIT, LOW RESOLUTION MODEL

OF 16 S RNA; CHAIN: B; S4

RIBOSOMAL PROTEIN; CHAIN: C;

S5 RIBOSOMAL PROTEIN; CHAIN:

D; S6 RIBOSOMAL PROTEIN;

CHAIN: E; S7 RIBOSOMAL

PROTEIN; CHAIN: F; S8

RIBOSOMAL PROTEIN; CHAIN: G;

S15 RIBOSOMAL PROTEIN;

CHAIN: H; S17 RIBOSOMAL

PROTEIN; CHAIN: I; S20

RIBOSOMAL PROTEIN; CHAIN: J

406
1aps

2
98
1.4e−33
0.96
1.00

HYDROLASE(ACTING ON ACID

ANHYDRIDES)

ACYLPHOSPHATASE (E.C.3.6.1.7)

(NMR, 5 STRUCTURES) 1APS 3

406
1aps

2
99
1.4e−33

102.47
HYDROLASE(ACTING ON ACID

ANHYDRIDES)

ACYLPHOSPHATASE (E.C.3.6.1.7)

(NMR, 5 STRUCTURES) 1APS 3

406
2acy

2
99
3.4e−33
0.79
1.00

ACYLPHOSPHATASE; CHAIN:
ACYLPHOSPHATASE ACP;

NULL;
ACYLPHOSPHATASE, PHOSPHORIC

MONOESTER HYDROLASE

406
2acy

2
99
3.4e−33

139.55
ACYLPHOSPHATASE; CHAIN:
ACYLPHOSPHATASE ACP;

NULL;
ACYLPHOSPHATASE, PHOSPHORIC

MONOESTER HYDROLASE

407
1a17

622
730
1.5e−11
0.15
0.77

SERINE/THREONINE PROTEIN
HYDROLASE TETRATRICOPEPTIDE,

PHOSPHATASE 5; CHAIN: NULL;
TRP; HYDROLASE, PHOSPHATASE,

PROTEIN-PROTEIN INTERACTIONS,

TPR, 2 SUPER-HELIX, X-RAY

STRUCTURE

407
1a17

661
728
5.1e−06
0.09
0.98

SERINE/THREONINE PROTEIN
HYDROLASE TETRATRICOPEPTIDE,

PHOSPHATASE 5; CHAIN: NULL;
TRP; HYDROLASE, PHOSPHATASE,

PROTEIN-PROTEIN INTERACTIONS,

TPR, 2 SUPER-HELIX, X-RAY

STRUCTURE

407
1elr
A
263
376
1.2e−07
−0.04
0.12

TPR2A-DOMAIN OF HOP; CHAIN:
CHAPERONE HOP, TPR-DOMAIN,

A; HSP90-PEPTIDE MEEVD;
PEPTIDE-COMPLEX, HELICAL

CHAIN: B;
REPEAT, HSP90, 2 PROTEIN BINDING

407
1elr
A
620
727
9e−10
−0.47
0.00

TPR2A-DOMAIN OF HOP; CHAIN:
CHAPERONE HOP, TPR-DOMAIN,

A; HSP90-PEPTIDE MEEVD;
PEPTIDE-COMPLEX, HELICAL

CHAIN: B;
REPEAT, HSP90, 2 PROTEIN BINDING

407
1elr
A
660
733
6.8e−05
−0.38
0.40

TPR2A-DOMAIN OF HOP; CHAIN:
CHAPERONE HOP, TPR-DOMAIN,

A; HSP90-PEPTIDE MEEVD;
PEPTIDE-COMPLEX, HELICAL

CHAIN: B;
REPEAT, HSP90, 2 PROTEIN BINDING

407
1elw
A
658
758
1.2e−07
−0.23
0.21

TPR1-DOMAIN OF HOP; CHAIN: A,
CHAPERONE HOP, TPR-DOMAIN,

B; HSC70-PEPTIDE; CHAIN: C, D;
PEPTIDE-COMPLEX, HELICAL

REPEAT, HSC70, 2 HSP70, PROTEIN

BINDING

407
1fch
A
192
386
6e−12
−0.22
0.24

PEROXISOMAL TARGETING
SIGNALING PROTEIN PEROXISMORE

SIGNAL 1 RECEPTOR; CHAIN: A,
RECEPTOR 1, PTS1-BP, PEROXIN-5,

B; PTS1-CONTAINING PEPTIDE:
PTS1 PROTEIN-PEPTIDE COMPLEX,

CHAIN: C, D;
TETRATRICOPEPTIDE REPEAT, TPR,

2 HELICAL REPEAT

407
1fch
A
510
749
5.1e−12
−0.31
0.09

PEROXISOMAL TARGETING
SIGNALING PROTEIN PEROXISMORE

SIGNAL 1 RECEPTOR; CHAIN: A,
RECEPTOR 1, PTS1-BP, PEROXIN-5,

B; PTS1-CONTAINING PEPTIDE;
PTS1 PROTEIN-PEPTIDE COMPLEX,

CHAIN: C, D;
TETRATRICOPEPTIDE REPEAT, TPR,

2 HELICAL REPEAT

407
1fch
A
550
840
5.1e−15
−0.44
0.07

PEROXISOMAL TARGETING
SIGNALING PROTEIN PEROXISMORE

SIGNAL 1 RECEPTOR; CHAIN: A,
RECEPTOR 1, PTS1-BP, PEROXIN-5,

B; PTS1-CONTAINING PEPTIDE;
PTS1 PROTEIN-PEPTIDE COMPLEX,

CHAIN: C, D;
TETRATRICOPEPTIDE REPEAT, TPR,

2 HELICAL REPEAT

407
4hb1

703
744
0.0036
−0.01
0.10

DHP1; CHAIN: NULL;
DESIGNED HELICAL BUNDLE

DESIGNED HELICAL BUNDLE

414
1a5j

112
146
0.00075
−0.08
0.62

B-MYB; CHAIN: NULL;
DNA-BINDING PROTEIN DNA-

BINDING PROTEIN,

PROTOONCOGENE PRODUCT

414
1ak2

749
973
1.7e−52

304.37
ADENYLATE KINASE
PHOSPHOTRANSFERASE ATP\;AMP

ISOENZYME-2; CHAIN: NULL;
PHOSPHOTRANSFERASE,

MYOKINASE; NUCLEOSIDE

MONOPHOSPHATE KINASE,

PHOSPHOTRANSFERASE

414
1ak2

756
972
1.7e−52
0.84
1.00

ADENYLATE KINASE
PHOSPHOTRANSFERASE ATP\:AMP

ISOENZYME-2; CHAIN: NULL;
PHOSPHOTRANSFERASE,

MYOKINASE; NUCLEOSIDE

MONOPHOSPHATE KINASE,

PHOSPHOTRANSFERASE

414
1aky

751
971
4.5e−78

212.52
ADENYLATE KINASE; 1AKY 4
TRANSFERASE

CHAIN: NULL; 1AKY 5
(PHOSPHOTRANSFERASE) ATP\:AMP

PHOSPHOTRANSFERASE,

MYOKINASE; 1AKY 6 ATP:AMP

PHOSPHOTRANSFERASE,

MYOKINASE 1AKY 15

414
1aky

767
970
4.5e−78
0.66
1.00

ADENYLATE KINASE; 1AKY 4
TRANSFERASE

CHAIN: NULL; 1AKY 5
(PHOSPHOTRANSFERASE) ATP\:AMP

PHOSPHOTRANSFERASE,

MYOKINASE; 1AKY 6 ATP:AMP

PHOSPHOTRANSFERASE,

MYOKINASE 1AKY 15

414
1e4v
A
767
967
1.5e−74
0.13
1.00

ADENYLATE KINASE; CHAIN: A;
TRANSFERASE(PHOSPHOTRANSFERASE)

TRANSFERASE(PHOSPHOTRANSFERASE)

414
1mbj

113
146
7.5e−05
−0.18
0.51

MYB PROTO-ONCOGENE
DNA BINDING PROTEIN

PROTEIN; 1MBJ 4
PROTOONCOGENE PRODUCT 1MBJ

12

414
1mse
C
113
146
0.0015
−0.06
0.55

COMPLEX (BINDING

PROTEIN/DNA) C-MYB DNA-

BINDING DOMAIN COMPLEXED

WITH DNA 1MSE 3 (NMR,

MINIMIZED AVERAGE

STRUCTURE) 1MSE 4 1MSE 84

415
1e7u
A
3501
3986
1e−68
0.10
0.86

PHOSPHATIDYLINOSITOL 3-
PHOSPHOINOSITIDE 3-KINASE

KINASE CATALYTIC SUBUNIT;
GAMMA PTDINS-3-KINASE P110,

CHAIN: A;
P13K, P1 3K; PHOSPHOINOSITIDE 3-

KINASE GAMMA, SECONDARY

MESSENGER 2 GENERATION, P13K, P1

3K, WORTMANNIN

415
1e8y
A
3501
3986
3.4e−68
0.02
1.00

PHOSPHATIDYLINOSITOL 3-
PHOSPHOINOSITIDE 3-KINASE

KINASE CATALYTIC SUBUNIT;
GAMMA PTDINS-3-KINASE P110,

CHAIN: A;
P13K; PHOSPHOINOSITIDE 3-KINASE

GAMMA, SECONDARY MESSENGER 2

GENERATION, P13K, P1 3K

415
3fap
B
3581
3674
1.4e−24
0.05
−0.18

FK506-BINDING PROTEIN; CHAIN:
CELL CYCLE FKBP12; FRAP FKBP12,

A; FKBP12-RAPAMYCIN
FRAP, RAPAMYCIN, COMPLEX, GENE

ASSOCIATED PROTEIN; CHAIN:
THERAPY

B;

415
1e7u
A
3480
4043
8.5e−83
−0.12
0.37

PHOSPHATIDYLINOSITOL 3-
PHOSPHOINOSITIDE 3-KINASE

KINASE CATALYTIC SUBUNIT;
GAMMA PTDINS-3-KINASE P110,

CHAIN: A;
P13K, P1 3K; PHOSPHOINOSITIDE 3-

KINASE GAMMA, SECONDARY

MESSENGER 2 GENERATION, P13K, P1

3K, WORTMANNIN

415
1e8y
A
3480
4043
1e−77
0.13
0.94

PHOSPHATIDYLINOSITOL 3-
PHOSPHOINOSITIDE 3-KINASE

KINASE CATALYTIC SUBUNIT;
GAMMA PTDINS-3-KINASE P110,

CHAIN: A;
P13K; PHOSPHOINOSITIDE 3-KINASE

GAMMA, SECONDARY MESSENGER 2

GENERATION, P13K, P1 3K

415
3fap
B
3581
3673
1.5e−21
0.07
−0.18

FK506-BINDING PROTEIN; CHAIN:
CELL CYCLE FKBP12; FRAP FKBP12,

A; FKBP12-RAPAMYCIN
FRAP, RAPAMYCIN, COMPLEX, GENE

ASSOCIATED PROTEIN; CHAIN:
THERAPY

B;

416
1e7u
A
3501
3986
1e−68
0.10
0.86

PHOSPHATIDYLINOSITOL 3-
PHOSPHOINOSITIDE 3-KINASE

KINASE CATALYTIC SUBUNIT;
GAMMA PTDINS-3-KINASE P110,

CHAIN: A;
P13K, P1 3K; PHOSPHOINOSITIDE 3-

KINASE GAMMA, SECONDARY

MESSENGER 2 GENERATION, P13K, P1

3K, WORTMANNIN

416
1e8y
A
3501
3986
3.4e−68
0.02
1.00

PHOSPHATIDYLINOSITOL 3-
PHOSPHOINOSITIDE 3-KINASE

KINASE CATALYTIC SUBUNIT;
GAMMA PTDINS-3-KINASE P110,

CHAIN: A;
P13K; PHOSPHOINOSITIDE 3-KINASE

GAMMA, SECONDARY MESSENGER 2

GENERATION, P13K, P1 3K

416
3fap
B
3581
3674
1.4e−24
0.05
−0.18

FK506-BINDING PROTEIN; CHAIN:
CELL CYCLE FKBP12; FRAP FKBP12,

A; FKBP12-RAPAMYCIN
FRAP, RAPAMYCIN, COMPLEX, GENE

ASSOCIATED PROTEIN; CHAIN:
THERAPY

B;

416
1e7u
A
3480
4043
8.5e−83
−0.12
0.37

PHOSPHATIDYLINOSITOL 3-
PHOSPHOINOSITIDE 3-KINASE

KINASE CATALYTIC SUBUNIT;
GAMMA PTDINS-3-KINASE P110,

CHAIN: A;
P13K, P1 3K; PHOSPHOINOSITIDE 3-

KINASE GAMMA, SECONDARY

MESSENGER 2 GENERATION, P13K, P1

3K, WORTMANNIN

416
1e8y
A
3480
4043
1e−77
0.13
0.94

PHOSPHATIDYLINOSITOL 3-
PHOSPHOINOSITIDE 3-KINASE

KINASE CATALYTIC SUBUNIT;
GAMMA PTDINS-3-KINASE P110,

CHAIN: A;
P13K; PHOSPHOINOSITIDE 3-KINASE

GAMMA, SECONDARY MESSENGER 2

GENERATION, P13K, P1 3K

416
3fap
B
3581
3673
1.5e−21
0.07
−0.18

FK506-BINDING PROTEIN; CHAIN:
CELL CYCLE FKBP12; FRAP FKBP12,

A; FKBP12-RAPAMYCIN
FRAP, RAPAMYCIN, COMPLEX GENE

ASSOCIATED PROTEIN; CHAIN:
THERAPY

B;

418
1aip
A
181
384
1.7e−46
0.07
−0.15

ELONGATION FACTOR TU;
COMPLEX OF TWO ELONGATION

CHAIN: A, B, E, F; ELONGATION
FACTORS EF-TU; EF-TS;

FACTOR TS; CHAIN: C, D, G, H;
ELONGATION FACTOR,

NUCLEOTIDE EXCHANGE, GTP-

BINDING, 2 COMPLEX OF TWO

ELONGATION FACTORS

418
1d2e
A
181
386
1.7e−44
0.32
−0.17

ELONGATION FACTOR TU (EF-
RNA BINDING PROTEIN G-PROTEIN,

TU); CHAIN: A, B, C, D
BETA-BARREL

418
1e0s
A
185
312
3e−05
0.05
0.07

ADP-RIBOSYLATION FACTOR 6;
G PROTEIN G PROTEIN, RAS, ARF,

CHAIN: A;
ARF6, MEMBRANE TRAFFIC

418
1efe
A
181
386
3.4e−50
0.20
−0.17

ELONGATION FACTOR; CHAIN:
RNA BINDING PROTEIN EFTU;

A, B;
TRANSPORT AND PROTECTION

PROTEIN, RNA BINDING PROTEIN

418
1efu
A
181
386
5.1e−46
0.15
−0.17

ELONGATION FACTOR TU;
COMPLEX (TWO ELONGATION

CHAIN: A, C; ELONGATION
FACTORS) ELONGATION FACTOR

FACTOR TS; CHAIN: B, D;
FOR TRANSFER, HEAT UNSTABLE,

ELONGATION FACTOR FOR

TRANSFER, HEAT STABLE,

ELONGATION FACTOR, COMPLEX

(TWO ELONGATION FACTORS)

418
1ega
A
186
381
3.4e−36
0.10
0.01

GTP-BINDING PROTEIN ERA;
HYDROLASE ERA, GTPASE, RNA-

CHAIN: A, B;
BINDING, RAS-LIKE, HYDROLASE

418
1ega
A
34
185
8.5e−13
0.23
−0.19

GTP-BINDING PROTEIN ERA;
HYDROLASE ERA, GTPASE, RNA-

CHAIN: A, B;
BINDING, RAS-LIKE, HYDROLASE

418
1exm
A
179
384
5.1e−52
0.23
−0.17

ELONGATION FACTOR TU (EF-
TRANSLATION EF-TU; GTPASE,

TU); CHAIN: A;
MOLECULAR SWITCH, TRNA,

RIBOSOME, Q-BETA REPLICASE, 2

CHAPERONE, DISULFIDE

ISOMERASE

418
1f60
A
179
386
3.4e−31
0.23
−0.12

ELONGATION FACTOR EEFIA;
TRANSLATION PROTEIN-PROTEIN

CHAIN: A; ELONGATION FACTOR
COMPLEX

EEFIBA; CHAIN: B;

418
1hur
A
185
312
9e−05
0.06
0.12

HUMAN ADP-RIBOSYLATION
PROTEIN TRANSPORT GDP-BINDING,

FACTOR 1; 1HUR 5 CHAIN: A, B;
MEMBRANE TRAFFICKIN, NON-

1HUR 7
MYRISTOYLATED 1HUR 16

421
1afh
A
201
281
1.2e−26
−0.10
0.99

QGSR ZINC FINGER PEPTIDE;
COMPLEX (ZINC FINGER/DNA)

CHAIN: A; DUPLEX
COMPLEX (ZINC FINGER/DNA), ZINC

OLIGONUCLEOTIDE BINDING
FINGER, DNA-BINDING PROTEIN

SITE; CHAIN: B, C;

421
1c2a
A
396
513
1e−09
0.14
−0.15

BOWMAN-BIRK TRYPSIN
HYDROLASE INHIBITOR ALL-BETA

INHIBITOR; CHAIN: A
STRUCTURE, HYDROLASE

INHIBITOR

421
1mey
C
172
253
6.8e−41
−0.21
0.58

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

421
1mey
C
200
281
6.8e−44
0.09
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

421
1mey
C
228
309
3.4e−46
0.64
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

421
1mey
C
256
337
1.4e−47
0.60
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

421
1mey
C
284
365
1.7e−48
0.55
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

421
1mey
C
312
393
3.4e−49
0.50
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

421
1mey
C
340
421
6.8e−49
0.61
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

421
1mey
C
368
449
5.1e−50
0.34
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

421
1mey
C
396
477
3.4e−51
0.56
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

421
1mey
C
424
505
5.1e−51
0.53
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

421
1mey
C
452
533
6.8e−51
0.42
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

421
1mey
C
452
534
5.1e−51

108.34
DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

421
1mey
C
480
561
1.7e−50
0.40
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

421
1mey
C
508
589
8.5e−51
0.63
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

421
1mey
C
536
617
1.5e−50
0.31
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

421
1mey
C
564
641
5.1e−46
0.13
1.00

DNA; CHAIN: A, B, D, E;
COMPLEX (ZINC FINGER/DNA) ZINC

CONSENSUS ZINC FINGER
FINGER, PROTEIN-DNA

PROTEIN; CHAIN: C, F, G;
INTERACTION, PROTEIN DESIGN, 2

CRYSTAL STRUCTURE, COMPLEX

(ZINC FINGER/DNA)

421
1tf6
A
201
346
5.1e−35
0.01
0.96

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

421
1tf6
A
257
402
1.4e−36
0.24
1.00

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

421
1tf6
A
369
514
1.7e−38
0.25
1.00

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

421
1tf6
A
396
559
1.7e−38

118.07
TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

421
1tf6
A
481
627
5.1e−38
0.04
1.00

TFIIIA; CHAIN: A, D; 5S
COMPLEX (TRANSCRIPTION

RIBOSOMAL RNA GENE; CHAIN:
REGULATION/DNA) COMPLEX

B, C, E, F;
(TRANSCRIPTION

REGULATION/DNA), RNA

POLYMERASE III, 2 TRANSCRIPTION

INITIATION, ZINC FINGER PROTEIN

421
1ubd
C
182
309
3e−26
−0.20
0.18

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION lNITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

421
1ubd
C
203
309
3.4e−31
0.06
1.00

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

421
1ubd
C
228
337
3e−51
0.33
1.00

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

421
1ubd
C
282
393
4.5e−53
0.48
1.00

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

421
1ubd
C
284
394
4.5e−53

92.65
YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

421
1ubd
C
320
421
1.2e−33
0.29
1.00

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

421
1ubd
C
348
449
1.7e−34
0.15
1.00

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

421
1ubd
C
366
477
3e−53
0.23
1.00

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

421
1ubd
C
376
477
3.4e−36
0.36
1.00

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

421
1ubd
C
401
505
8.5e−36
0.16
1.00

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

421
1ubd
C
422
533
6e−56
0.28
1.00

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

421
1ubd
C
450
562
3e−55
0.16
0.96

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

421
1ubd
C
460
561
1.7e−35
0.13
0.98

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTElN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

421
1ubd
C
478
589
3e−53
0.04
1.00

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

421
1ubd
C
506
617
3e−53
0.20
1.00

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

421
1ubd
C
516
617
5.1e−34
0.34
0.96

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPTION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INTIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

421
1ubd
C
534
641
1.1e−39
0.17
0.98

YY1; CHAIN: C; ADENO-
COMPLEX (TRANSCRIPlION

ASSOCIATED VIRUS P5
REGULATION/DNA) YING-YANG 1;

INITIATOR ELEMENT DNA;
TRANSCRIPTION INITIATION,

CHAIN: A, B;
INITIATOR ELEMENT, YY1, ZINC 2

FINGER PROTEIN, DNA-PROTEIN

RECOGNITION, 3 COMPLEX

(TRANSCRIPTION

REGULATION/DNA)

421
2gli
A
172
308
1.5e−31
−0.27
0.78

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

421
2gli
A
192
311
3e−41
0.06
0.98

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

421
2gli
A
228
367
1.4e−63
0.72
1.00

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER (GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

421
2gli
A
264
392
1.7e−33
0.54
1.00

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

421
2gli
A
284
423
1.4e−63

110.65
ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

421
2gli
A
312
535
1.5e−67
−0.12
0.75

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

421
2gli
A
320
448
3.4e−34
0.31
0.99

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GL1, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

421
2gli
A
404
532
3.4e−34
0.47
1.00

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

421
2gli
A
452
591
1.5e-70
0.39
1.00

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

421
2gli
A
508
626
7.5e−55
0.24
0.94

ZINC FINGER PROTEIN GLI1;
COMPLEX (DNA-BINDING

CHAIN: A; DNA; CHAIN: C, D;
PROTEIN/DNA) FIVE-FINGER GLI;

GLI, ZINC FINGER, COMPLEX (DNA-

BINDING PROTEIN/DNA)

423
1bcc
A
24
459
0
0.90
1.00

UBIQUINOL CYTOCHROME C
OXIDOREDUCTASE CYTOCHROME

OXIDOREDUCTASE; CHAIN: A, B,
BCI COMPLEX, COMPLEX III;

C, D, E, F, G, H, I, J;
UBIQUINONE, OXIDOREDUCTASE,

REDOX ENZYME, MEMBRANE

PROTEIN, 2 RESPIRATORY CHAIN,

ELECTRON TRANSPORT

423
1bcc
A
49
459
0

457.94
UBIQUINOL CYTOCHROME C
OXIDOREDUCTASE CYTOCHROME

OXIDOREDUCTASE; CHAIN: A, B,
BCI COMPLEX, COMPLEX III;

C, D, E, F, C, H, I, J;
UBIQUINONE, OXIDOREDUCTASE,

REDOX ENZYME, MEMBRANE

PROTEIN, 2 RESPIRATORY CHAIN,

ELECTRON TRANSPORT

423
1qcr
A
24
459
0
0.41
1.00

UBIQUINOL CYTOCHROME C
OXIDOREDUCTASE CYTOCHROME

OXIDOREDUCTASE; CHAIN: A, B,
BC1, QCR; BCI, QCR, MEMBRANE

C, D, E, F, G, H, I, J, K;
PROTEIN, PROTON

TRANSLOCATION, ELECTRON 2

TRANSFER, PROTEASE, MPP,

MITOCHONDRIAL PROCESSING 3

PEPTIDASE, STRUCTURE,

CYTOCHROME CI, CYTOCHROME B,

RIESKE, 4 IRON SULFER PROTEIN,

OXIDOREDUCTASE

426
1deq
B
122
285
1.4e−52
−0.25
0.62

FIBRINOGEN (ALPHA CHAIN);
BLOOD CLOTTING COILED-COIL

CHAIN: A, D, N, Q; FIBRINOGEN

(BETA CHAIN); CHAIN: B, E, O, R;

FIBRINOGEN (GAMMA CHAIN);

CHAIN: C, F, P, S; FIBRINOGEN;

CHAIN: M, Z;

426
1deq
C
53
276
4.2e−89
−0.52
1.00

FIBRINOGEN (ALPHA CHAIN);
BLOOD CLOTTING COIELD-COIL

CHAIN: A, D, N, Q; FIBRINOGEN

(BETA CHAIN); CHAIN: B, E, O, R;

FIBRINOGEN (GAMMA CHAIN);

CHAIN: C, F, P, S; FIBRINOGEN;

CHAIN: M, Z;

426
1deq
C
53
286
8.5e−45
−0.58
1.00

FIBRINOGEN (ALPHA CHAIN);
BLOOD CLOTTING COILED-COIL

CHAIN: A, D, N, Q; FIBRINOGEN

(BETA CHAIN); CHAIN: B, E, O, R;

FIBRINOGEN (GAMMA CHAIN);

CHAIN: C, F, P, S; FIBRINOGEN;

CHAIN: M, Z;

426
1ei3
C
29
286
3.4e−52
−0.58
1.00

FIBRINOGEN; CHAIN: A, D;
BLOOD CLOTTING COILED COILS,

FIBRINOGEN; CHAIN: B, E;
DISULFIDE RINGS, FIBRIN FORMING

FIBRINOGEN; CHAIN: C, F;
ENTITIES

426
1fzc
C
123
286
3.4e−39
0.19
1.00

FIBRIN; CHAIN: A, B, C, D, E, F, G,
BLOOD COAGULATION BLOOD

H, I, J;
COAGULATION, PLASMA PROTEIN,

CROSSLINKING

426
1fzc
C
123
288
3.4e−39

175.96
FIBRIN; CHAIN: A, B, C, D, E, F, G,
BLOOD COAGULATION BLOOD

H, I, J;
COAGULATION, PLASMA PROTEIN,

CROSSLINKING

426
1fzg
C
128
288
1e−38

174.90
FIBRINOGEN; CHAIN: A, B, C, D,
BLOOD COAGULATION BLOOD

E, F, S, T, M, N;
COAGULATION, PLASMA,

PLATELET, FIBRINOGEN, FIBRIN

426
1fzg
C
129
286
1e−38
0.22
1.00

FIBRINOGEN; CHAIN: A, B, C, D,
BLOOD COAGULATION BLOOD

E, F, S, T, M, N;
COAGULATION, PLASMA,

PLATELET, FIBRINOGEN, FIBRIN

432
2dnj
A
21
251
3.4e−100
0.93
1.00

ENDONUCLEASE

DEOXYRIBONUCLEASE I (DNASE

I) (E.C.3.1.21.1) COMPLEXED

WITH 2DNJ 3 DNA (5′-

D(*GP*CP*GP*AP*TP*CP*GP*CP)-

3′) 2DNJ 4

432
2dnj
A
21
252
3.4e−100

202.60
ENDONUCLEASE

DEOXYRIBONUCLEASE I (DNASE

I) (F.C.3.1.21.1) COMPLEXED

WITH 2DNJ 3 DNA (5′-

D(*GP*CP*GP*AP*TP*CP*GP*CP)-

3′) 2DNJ 4

433
1b50
A
25
92
1.1e−28

90.96
MIP-1A; CHAIN: A, B;
CHEMOKINE CHEMOKINE,

CYTOKINE, CHEMOTAXIS

433
1b50
A
26
92
1.1e−28
0.01
1.00

MIP-1A; CHAIN: A, B;
CHEMOKINE CHEMOKINE,

CYTOKINE, CHEMOTAXIS

433
1b50
A
27
92
5.1e−25
0.29
1.00

MIP-1A; CHAIN: A, B;
CHEMOKINE CHEMOKINE,

CYTOKINE, CHEMOTAXIS

433
1hum
A
24
92
6.8e−25

114.82
CYTOKINE(CHEMOTACTIC)

HUMAN MACROPHAGE

INFLAMMATORY PROTEIN 1

BETA (HMIP-1B) 1HUM 3 (NMR,

MINIMIZED AVERAGE

STRUCTURE) 1HUM 4

433
1hum
A
25
92
6.8e−25
0.28
1.00

CYTOKINE(CHEMOTACTIC)

HUMAN MACROPHAGE

INFLAMMATORY PROTEIN 1

BETA (HMIP-1B) 1HUM 3 (NMR,

MINIMIZED AVERAGE

STRUCTURE) 1HUM 4

433
1ncv
A
24
92
1.7e−25

61.57
MONOCYTE
CYTOKINE NMR, STRUCTURE, MCP-

CHEMOATTRACTANT PROTEIN 3;
3, BETA-CHEMOKINE, CYTOKINE,

CHAIN: A, B;
CHEMOTAXIS, 2 HEPARIN-BINDING,

GLYCOPROTEIN

433
1ncv
A
25
91
1.7e−25
−0.04
0.98

MONOCYTE
CYTOKINE NMR, STRUCTURE, MCP-

CHEMOATTRACTANT PROTEIN 3;
3, BETA-CHEMOKINE, CYTOKINE,

CHAIN: A, B;
CHEMOTAXIS, 2 HEPARIN-BINDING,

GLYCOPROTEIN

449
1awc
B
114
270
1.7e−39

61.04
GA BINDING PROTEIN ALPHA;
COMPLEX (TRANSCRIPTION

CHAIN: A; GA BINDING PROTEIN
REGULATION/DNA) GABPALPHA;

BETA 1; CHAIN: B; DNA; CHAIN:
GABPBETA1; COMPLEX

D, E;
(TRANSCRIPTION

REGULATION/DNA), DNA-BINDING, 2

NUCLEAR PROTEIN, ETS DOMAIN,

ANKYRIN REPEATS,

TRANSCRIPTION 3 FACTOR

449
1bd8

116
273
8.4e−33

57.66
P191NK4D CDK4/6 INHIBITOR;
TUMOR SUPPRESSOR TUMOR

CHAIN: NULL;
SUPPRESSOR, CDK4/6 INHIBITOR,

ANKYRIN MOTIF

449
1blx
B
115
276
1.4e−32

53.46
CYCLIN-DEPENDENT KINASE 6;
COMPLEX (INHIBITOR

CHAIN: A; P191NK4D; CHAIN: B;
PROTEIN/KINASE) INHIBITOR

PROTEIN, CYCLIN-DEPENDENT

KINASE, CELL CYCLE 2 CONTROL,

ALPHA/BETA, COMPLEX (INHIBITOR

PROTEIN/KINASE)

449
1bu9
A
113
280
3.4e−33

51.20
CYCLIN-DEPENDENT KINASE 6
HORMONE/GROWTH FACTOR P18-

INHIBITOR; CHAIN: A;
1NK4C; CELL CYCLE INHIBITOR,

P181NK4C, TUMOR, SUPPRESSOR,

CYCLIN-2 DEPENDENT KINASE,

HORMONE/GROWTH FACTOR

449
1ibb
A
122
273
1.5e−32

53.58
CYCLIN-DEPENDENT KINASE 6
CELL CYCLE INHIBITOR P18-

INHIBITOR; CHAIN: A, B;
1NK4C(1NK6); CELL CYCLE

INHIBITOR, P18-1NK4C(1NK6),

ANKYRIN REPEAT, 2 CDK 4/6

INHIBITOR

449
1ikn
D
81
293
2.8e−44

62.44
NF-KAPPA-B P65 SUBUNIT;
TRANSCRIPTION FACTOR P65; P50D;

CHAIN: A; NF-KAPPA-B P50D
TRANSCRIPTION FACTOR, IKB/NFKB

SUBUNIT; CHAIN: C; I-KAPPA-B-
COMPLEX

ALPHA; CHAIN: D;

449
1myo

48
166
9.8e−27

54.85
MYOTROPHIN; CHAIN: NULL
ANK-REPEAT MYOTROPHIN,

ACETYLATION, NMR, ANK-REPEAT

449
1nfl
E
78
282
2.8e−44

63.92
NF-KAPPA-B P65; CHAIN: A, C;
COMPLEX (TRANSCRIPTION

NF-KAPPA-B P50; CHAIN: B, D; I-
REG/ANK REPEAT) COMPLEX

KAPPA-B-ALPHA; CHAIN: E, F;
(TRANSCRIPTION REGULATION/AN K

REPEAT), ANKYRIN 2 REPEAT HELIX

451
1ndh

36
305
5.1e−79

366.08
ELECTRON TRANSPORT (FLAVO

PROTEIN) CYTOCHROME B = 5 =

REDUCTASE (E.C.1.6.2.2) 1NDH 3

456
1tub
A
2
440
0

308.77
TUBULIN; CHAIN: A, B;
MICROTUBULES MICROTUBULES,

ALPHA-TUBULIN, BETA-TUBULIN,

GTPASE HELIX

456
1tub
B
2
440
0

353.89
TUBULIN; CHAIN: A, B;
MICROTUBULES MICROTUBULES,

ALPHA-TUBULIN, BETA-TUBULIN,

GTPASE HELIX

457
1klo

82
239
2.8e−34

138.52
LAMININ; CHAIN: NULL;
GLYCOPROTEIN GLYCOPROTEIN

458
1bih
A
1
327
6.8e−47

77.74
HEMOLIN; CHAIN: A, B;
INSECT IMMUNITY INSECT

IMMUNITY, LPS-BINDING,

HOMOPHILIC ADHESION

458
1fig
H
54
276
0.00034

61.84
IMMUNOGLOBULIN

IMMUNOGLOBULIN GI (KAPPA

LIGHT CHAIN) FAB' FRAGMENT

1FIG 3

458
1for
H
64
278
0.0019

60.01
IMMUNOGLOBULIN IGG2A FAB

FRAGMENT (FAB17-1A)

(ORTHORHOMBIC CRYSTAL

FORM) 1FOR 3

458
1igc
H
58
279
0.00017

61.96
COMPLEX (ANTIBODY/BINDING

PROTEIN) IGG1 FAB FRAGMENT

COMPLEXED WITH PROTEIN G

(DOMAIN III) HGC 5 PROTEIN G.

STREPTOCOCCUS HGC 15

458
1itb
B
1
279
4.2e−25

62.51
INTERLEUKIN-I BETA; CHAIN: A;
COMPLEX

TYPE 1 INTERLEUKIN-1
(IMMUNOGLOBULIN/RECEPTOR)

RECEPTOR; CHAIN: B;
IMMUNOGLOBULIN FOLD,

TRANSMEMBRANE, GLYCOPROTEIN,

RECEPTOR, 2 SIGNAL, COMPLEX

(IMMUNOGLOBULIN/RECEPTOR)

458
1kb5
H
54
278
0.0024

63.34
KB5-C20 T-CELL ANTIGEN
COMPLEX

RECEPTOR; CHAIN: A, B;
(IMMUNOGLOBULIN/RECEPTOR)

ANTIBODY DESIRE-I; CHAIN: L,
TCR VAPLHA VBETA DOMAIN; T-

H;
CELL RECEPTOR, STRAND SWITCH,

FAB, ANTICLONOTYPIC, 2

(IMMUNOGLOBULIN/RECEPTOR)

458
2gfb
B
58
279
0.00034

67.09
IMMUNOGLOBULIN IGG2A FAB

FRAGMENT (CNJ206) 2GFB 3

458
7fab
L
65
260
1.5e−11

58.17
IMMUNOGLOBULIN

IMMUNOGLOBULIN FAB' NEW

(LAMBDA LIGHT CHAIN) 7FAB 3

462
1au7
A
143
289
3.4e−33

105.92
PIT-1; CHAIN: A, B; DNA; CHAIN:
COMPLEX (DNA-BINDING

C, D;
PROTEIN/DNA) GHF-I; COMPLEX

(DNA-BINDING PROTEIN/DNA),

PITUITARY, CPHD, 2 POU DOMAIN.

TRANSCRIPTION FACTOR

462
1ocp

223
289
2.8e−22

84.91
OCT-3; 1OCP 5 CHAIN: NULL;
DNA-BINDING PROTEIN

1OCP 6

462
1oct
C
143
290
1.3e−40

120.80
DNA-BINDING PROTEIN OCT-I

(POU DOMAIN) 1OCT 3

462
1pou

143
212
5.6e−32

79.90
DNA-BINDING PROTEIN OCT-I

(POU-SPECIFIC DOMAIN) (NMR,

20 STRUCTURES) 1POU 3

473
1fht

30
143
2.8e−16

53.05
U1 SMALL NUCLEAR
RIBONUCLEOPROTEIN U1A117;

RIBONUCLEOPROTEIN A; CHAIN:
RIBONUCLEOPROTEIN, RNP

NULL;
DOMAIN, SPLICEOSOME

476
1c96
A
82
963
0

253.82
MITOCHONDRIAL ACONITASE;
LYASE CITRATE HYDRO-LYASE;

CHAIN: A;
LYASE, TRICARBOXYLIC ACID

CYCLE, IRON-SULFUR,

MITOCHONDRION, 2 TRANSIT

PEPTIDE, 4FE-4S, 3D-STRUCTURE

477
1bab
B
2
140
6.8e−55

179.81
OXYGEN TRANSPORT

HEMOGLOBIN THIONVILLE

ALPHA CHAIN MUTANT WITH

VAL 1 1BAB 3 REPLACED BY GLU

AND AN ACETYLATED MET

BOUND TO THE 1BAB 4 AMINO

TERMINUS 1BAB 5

477
1ch4
A
2
140
1.7e−55

168.27
MODULE-SUBSTITUTED
OXYGEN TRANSPORT OXYGEN

CHIMERA HEMOGLOBIN BETA-
TRANSPORT, CHIMERA PROTEIN,

ALPHA; CHAIN: A, B, C, D;
RESPIRATORY PROTEIN, HEME

477
1fdh
G
3
140
1e−55

150.09
OXYGEN TRANSPORT

HEMOGLOBIN (DEOXY, HUMAN

FETAL F═/11$═) 1FDHG 1 1FDHH 2

477
1hda
B
3
140
8.5e−51

154.60
OXYGEN TRANSPORT

HEMOGLOBIN (DEOXY) 1HDA 3

477
1ibe
B
2
140
1e−52

154.97
HEMOGLOBIN (DEOXY); CHAIN:
OXYGEN TRANSPORT HEME,

A, B;
OXYGEN TRANSPORT,

RESPIRATORY PROTEIN,

ERYTHROCYTE

477
1qpw
B
2
140
1e−52

163.36
PORICINE HEMOGLOBIN (ALPHA
OXYGEN TRANSPORT X-RAY

SUBUNIT); CHAIN: A, C;
STUDY, PORCINE HEMOGLOBIN,

PORICINE HEMOGLOBIN (BETA
ARTIFICIAL HUMAN BLOOD, 2

SUBUNIT); CHAIN: B, D
OXYGEN TRANSPORT

480
1b6e

66
196
4.2e−29

81.88
CD94; CHAIN: NULL;
NK CELL NK CELL, RECEPTOR, C-

TYPE LECTIN, C-TYPE LECTIN-LIKE,

NKD

480
1bj3
A
67
193
3.4e−32

63.00
COAGULATION FACTOR IX-
COLLAGEN BINDING PROTEIN IX-BP;

BINDING PROTEIN A; CHAIN: A;
IX-BP; COAGULATION FACTOR IX-

COAGULATION FACTOR IX-
BINDING, HETERODIMER, VENOM,

BINDING PROTEIN B; CHAIN: B;
HABU 2 SNAKE, C-TYPE LECTIN

SUPERFAMILY, COLLAGEN BINDING

PROTEIN

480
1byf
A
77
194
5.1e−16

54.78
POLYANDROCARPA LECTIN;
SUGAR BINDING PROTEIN TC14; C-

CHAIN: A, B;
TYPE LECTIN, GALACTOSE-

SPECIFIC, SUGAR BINDING PROTEIN

480
1esl

78
197
8.5e−31

53.21
CELL ADHESION PROTEIN E-

SELECTIN (LECTIN AND EGF

DOMAINS, RESIDUES 1-157)

1ESL 3 (FORMERLY KNOWN AS

ELAM-1) 1ESL 4

480
1htn

46
196
1e−26

58.22
TETRANECTIN; CHAIN: NULL;
LECTIN TETRANECTIN,

PLASMINOGEN BINDING, KRINGLE

4, ALPHA-HELICAL 2 COILED COIL,

C-TYPE LECTIN, CARBOHYDRATE

RECOGNITION DOMAIN

480
1hup

46
194
1.7e−23

53.60
MANNOSE-BINDING PROTEIN;
C-TYPE LECTIN ALPHA-HELICAL

1HUP 4 CHAIN: NULL; 1HUP 5
COILED-COIL 1HUP 12

480
1ixx
A
67
193
5.1e−30

60.13
COAGULATION FACTORS IX/X-
COAGULATION FACTOR BINDING

BINDING PROTEIN; CHAIN: A, B,
IX/X-BP COAGULATION FACTOR

C, D, E, F;
BINDING, C-TYPE LECTIN, GLA-

DOMAIN 2 BINDING, C-TYPE CRD

MOTIF, LOOP EXCHANGED DIMER

480
1ixx
B
67
195
8.5e−32

69.01
COAGULATION FACTORS IX/X-
COAGULATION FACTOR BINDING

BINDING PROTEIN; CHAIN: A, B,
IX/X-BP COAGULATION FACTOR

C, D, E, F;
BINDING, C-TYPE LECTIN, GLA-

DOMAIN 2 BINDING, C-TYPE CRD

MOTIF, LOOP EXCHANGED DIMER

480
1lit

67
195
1.7e−33

77.94
LITHOSTATHINE; CHAIN: NULL
PANCREATIC STONE INHIBITOR

PANCREATIC STONE INHIBITOR,

LECTIN

480
1qdd
A
51
195
6.8e−35

84.76
LITHOSTATHINE; CHAIN: A;
METAL BINDING PROTEIN

PANCREATIC STONE PROTEIN, PSP:

PANCREATIC STONE INHIBITOR,

LITHOSTATHINE

480
1rtm
1
36
195
1e−22

50.50
LECTIN MANNOSE-BINDING

PROTEIN A (CLOSTRIPAIN

FRAGMENT) (CL-MBP-A) 1RTM 3

1RTM 96

480
1tn3

62
196
5.1e−25

59.09
TETRANECTIN; CHAIN: NULL;
LECTIN TETRANECTIN,

PLASMINOGEN BINDING, KRINGLE

4, C-TYPE LECTIN, 2

CARBOHYDRATE RECOGNITION

DOMAIN

480
2msh
A
77
193
1.2e−21

53.42
LECTIN MANNOSE-BINDING

PROTEIN A (LECTIN DOMAIN)

COMPLEX WITH 2MSB 3

CALCIUM AND GLYCOPEPTIDE

2MSB 4

489
1adq
L
21
235
3.4e−84

313.02
IGG4 REA; CHAIN: A; RF-AN
COMPLEX

IGM/LAMBDA; CHAIN: H, L;
(IMMUNOGLOBULIN/AUTOANTIGEN)

COMPLEX

(IMMUNOGLOBULIN/AUTOANTIGEN),

RHEUMATOID FACTOR 2 AUTO-

ANTIBODY COMPLEX

489
1aqk
L
22
235
5.1e−83

285.37
FAB B7-15A2; CHAIN: L, H;
IMMUNOGLOBULIN HUMAN FAB,

ANTI-TETANUS TOXOID, HIGH

AFFINITY, CRYSTAL 2 PACKING

MOTIF, PROGRAMMING

PROPENSITY TO CRYSTALLIZE, 3

IMMUNOGLOBULIN

489
1bjm
A
20
235
6.8e−79

287.81
LOC-LAMBDA I TYPE LIGHT-
IMMUNOGLOBULIN BENCE-JONES

CHAIN DIMER: 1BJM 6 CHAIN: A,
PROTEIN; 1BJM 8 BENCE JONES,

B: 1BJM 7
ANTIBODY, MULTIPLE

QUATERNARY STRUCTURES 1BJM 13

489
1lil
A
21
235
1.2e−80

311.90
LAMBDA III BENCE JONES
IMMUNOGLOBULIN

PROTEIN CLE: CHAIN: A, B
IMMUNOGLOBULIN, BENCE JONES

PROTEIN

489
1mew
W
20
235
8.5e−76

277.24
IMMUNOGLOBULIN

IMMUNOGLOBULIN

HETEROLOGOUS LIGHT CHAIN

DIMER 1MCW 3 (/MCG$-/WEIR$

HYBRID) 1MCW 4

489
1mfb
L
22
232
1.4e−96

225.27
IMMUNOGLOBULIN FAB

FRAGMENT (MURINE SE155-4)

COMPLEX WITH

HEPTASACCHARIDE 1MFB 3 B:

GAL(1-2)MAN(1-4)RAM(1-

3)GAL(1-2)[ABE(1-3)]MAN(1-

4)RAM 1MFB 4

489
2fb4
L
22
235
8.5e−83

298.26
IMMUNOGLOBULIN

IMMUNOGLOBULIN FAB 2FB4 4

489
2mcg
1
20
235
8.5e−81

292.66
IMMUNOGLOBULIN

IMMUNOGLOBULIN LAMBDA

LIGHT CHAIN DIMER (/MCG$)

2MCG 3 (TRIGONAL FORM) 2MCG 4

489
7fab
L
20
231
1.4e−89

252.72
IMMUNOGLOBULIN

IMMUNOGLOBULIN FAB′ NEW

(LAMBDA LIGHT CHAIN) 7FAB 3

489
8fab
A
22
231
1.7e−81

313.64
IMMUNOGLOBULIN FAB

FRAGMENT FROM HUMAN

IMMUNOGLOBULIN IGGI

(LAMBDA, HIL) 8FAB 3

[0450]

6

TABLE 6

Position Of the Last

Amino Acid Of Signal

SEQ ID NO:
Peptide
Maximum Score
Mean Score

246
23
0.948
0.886

247
20
0.954
0.900

249
19
0.992
0.946

252
35
0.906
0.594

255
20
0.943
0.601

256
18
0.895
0.587

257
26
0.966
0.902

258
20
0.974
0.942

262
44
0.967
0.702

273
20
0.954
0.900

291
19
0.992
0.946

296
26
0.965
0.852

309
16
0.885
0.571

328
18
0.939
0.693

338
18
0.988
0.897

340
13
0.887
0.839

355
21
0.895
0.558

356
18
0.906
0.614

357
19
0.966
0.927

362
26
0.994
0.899

376
35
0.906
0.594

379
23
0.989
0.919

405
20
0.943
0.601

418
18
0.895
0.587

426
26
0.966
0.902

428
22
0.970
0.910

430
14
0.941
0.861

432
20
0.974
0.942

433
23
0.994
0.967

451
26
0.978
0.885

457
27
0.980
0.853

482
27
0.989
0.918

484
18
0.996
0.953

489
19
0.981
0.914

[0451]

7

TABLE 7

SEQ ID NO:
Chromosomal location

1
6q27

2
4p16.3

3
4p16.3

4
1p21

5
8q13-q22

6
17

7
X

8
5

10
16

11
10

12
10

13
8pter-p23.3

15
17

16
X

17
11q23.2

18
19p13.3-p13.2

19
3p21.1

20
10

21
1

22
8

23
16

24
8

25
1

26
22q13.1

27
22q13.1

28
1

29
3

30
X

31
Xq27.3

32
Xq27.3

33
4

34
7q35-q36

35
11q12-1q22.2

36
11q23.1-q23.2

37
12

38
2q11.1-q11.2

39
17

40
7q32

41
22q13.2

42
1q42.13-q42.2

43
19q13.3

44
19p12

45
1q23.1-24.3

46
22q11.1-q11.2

48
17

49
8p22

50
22

51
3q23-q24

52
7p22-p21

53
16

54
12

55
21q22.3

56
18q

57
6

60
1

61
19

62
14

63
6q15-q16.1

64
13q12.3-q13.1

65
17q21-q22

66
7q11.2

67
12

68
12p13

69
19q13.13-q13.2

70
12

71
19

72
18

73
1p36.13-q31.3

74
14

75
7q21

76
7q21-q22

78
11p11.2-p11.1

80
22q13.31-q13.33

81
3p26-p25

82
2

84
22q13.2-q13.31

86
19

87
22q11.1-q11.2

88
17

89
7q11.21-q11.23

91
9

92
1p35.1-36.12

93
3q13.1-q13.2

94
15

95
19q13.2

96
1

97
20p11.1-11.22

98
19

100
6p12

101
3

102
3

103
X

104
3q29-qter

105
15

107
12

108
20p11.21-12.3

110
5

111
10

112
10

113
6p21.2-p21.3

114
12q15

115
22

118
19

119
Xp11.2

121
15

122
3

123
3

124
20

125
9

126
11q13

127
13

128
Xq21.1-Xq21.3

129
Xq28

130
19p13.1-p12

131
8q22-q23

133
17

134
1p36.3-p36.12

136
11p15.5

137
11p15.5

138
11p15.5

139
10p15-p13

140
3q29

141
11

142
20p12.2-13

143
20q13.3

144
19q13.3-q13.4

146
17

147
12p13.3

148
8q22

149
8q22

150
5

151
9q34

152
7q21

153
7p13-p12

154
Xp22.33

155
15

156
14

158
19q13.3

159
19q13.3

160
6

161
14q24.3

162
11

164
16

165
22q13.2-q13.31

166
19

167
11

168
5

169
1p34

170
8q11

171
8q11

172
17

173
19

176
19

177
11

178
7q22-q32

179
16q22.1

181
4q28

182
16p13.3

183
5

184
1

187
3p21.1-p14.3

188
17q21

189
7q21-q22

190
3p13-q26.1

191
17q21.2

192
3q27

193
22q13.2-13.3

194
11q22.2-q22.3

195
12q24.31-q24.32

196
19q13.4

197
17

198
17

199
16

200
20

201
20

202
5

203
17

204
11

205
20q11.2-q12

206
1q24-q41

207
17

208
14

209
11q13

210
6

211
17q21

212
6q21

214
16

216
17

217
6p21.31

219
Xp22

220
20

221
3

222
22q13.31-13.32

223
11q12

224
11q13.3

225
11q13.3

226
12

227
17q24-q25

228
20

229
9

230
11

231
15q24-q25

233
19q13.4

234
22q11.2

235
12p13

236
9

237
3p25-p24

238
14q24.3

240
19q13.3

241
20

242
6

243
16q21-q23

244
22q11.1-q11.2

[0452]

8

TABLE 8

SEQ ID NO: in USSN

09/654,935

(Numbers to the right of

SEQ ID NO:
SEQ ID NO:
the under score correlate to

of nucleotide
of polypeptide
sequence identifiers in

sequence
sequence
USSN 09/654,935)

1
246
793_3

2
247
793_4

3
248
793_5

4
249
793_6

5
250
793_7

6
251
793_9

7
252
793_15

8
253
793_16

9
254
793_17

10
255
793_18

11
256
793_19

12
257
793_20

13
258
793_21

14
259
793_22

15
260
793_25

16
261
793_28

17
262
793_29

18
263
793_30

19
264
793_31

20
265
793_32

21
266
793_33

22
267
793_34

23
268
793_35

24
269
793_36

25
270
793_37

26
271
793_38

27
272
793_39

28
273
793_40

29
274
793_41

30
275
793_42

31
276
793_43

32
277
793_44

33
278
793_47

34
279
793_48

35
280
793_49

36
281
793_50

37
282
793_51

38
283
793_52

39
284
793_55

40
285
793_56

41
286
793_57

42
287
793_58

43
288
793_60

44
289
793_61

45
290
793_62

46
291
793_63

47
292
793_64

48
293
793_65

49
294
793_66

50
295
793_67

51
296
793_68

52
297
793_69

53
298
793_70

54
299
793_71

55
300
793_72

56
301
793_74

57
302
793_75

58
303
793_76

59
304
793_77

60
305
793_78

61
306
793_79

62
307
793_80

63
308
793_81

64
309
793_82

65
310
793_83

66
311
793_85

67
312
793_86

68
313
793_87

69
314
793_88

70
315
793_89

71
316
793_90

72
317
793_91

73
318
793_92

74
319
793_93

75
320
793_94

76
321
793_95

77
322
793_96

78
323
793_97

79
324
793_98

80
325
793_99

81
326
793_101

82
327
793_102

83
328
793_103

84
329
793_104

85
330
793_106

86
331
793_107

87
332
793_108

88
333
793_109

89
334
793_110

90
335
793_111

91
336
793_112

92
337
793_113

93
338
793_114

94
339
793_115

95
340
793_116

96
341
793_117

97
342
793_118

98
343
793_119

99
344
793_120

100
345
793_121

101
346
793_122

102
347
793_123

103
348
793_124

104
349
793_125

105
350
793_126

106
351
793_127

107
352
793_128

108
353
793_129

109
354
793_130

110
355
793_131

111
356
793_132

112
357
793_133

113
358
793_134

114
359
793_135

115
360
793_136

116
361
793_137

117
362
793_138

118
363
793_139

119
364
793_140

120
365
793_141

121
366
793_142

122
367
793_143

123
368
793_144

124
369
793_145

125
370
793_146

126
371
793_147

127
372
793_148

128
373
793_149

129
374
793_150

130
375
793_151

131
376
793_152

132
377
793_153

133
378
793_154

134
379
793_155

135
380
793_156

136
381
793_157

137
382
793_158

138
383
793_159

139
384
793_160

140
385
793_161

141
386
793_162

142
387
793_163

143
388
793_164

144
389
793_165

145
390
793_166

146
391
793_167

147
392
793_168

148
393
793_169

149
394
793_170

150
395
793_171

151
396
793_172

152
397
793_173

153
398
793_174

154
399
793_175

155
400
793_176

156
401
793_177

157
402
793_178

158
403
793_179

159
404
793_180

160
405
793_181

161
406
793_182

162
407
793_183

163
408
793_184

164
409
793_185

165
410
793_186

166
411
793_187

167
412
793_188

168
413
793_189

169
414
793_190

170
415
793_191

171
416
793_192

172
417
793_193

173
418
793_194

174
419
793_195

175
420
793_196

176
421
793_197

177
422
793_198

178
423
793_200

179
424
793_201

180
425
793_202

181
426
793_203

182
427
793_204

183
428
793_205

184
429
793_206

185
430
793_207

186
431
793_209

187
432
793_210

188
433
793_211

189
434
793_212

190
435
793_213

191
436
793_214

192
437
793_215

193
438
793_216

194
439
793_217

195
440
793_218

196
441
793_219

197
442
793_220

198
443
793_221

199
444
793_222

200
445
793_223

201
446
793_224

202
447
793_225

203
448
793_226

204
449
793_227

205
450
793_229

206
451
793_230

207
452
793_231

208
453
793_232

209
454
793_233

210
455
793_234

211
456
793_235

212
457
793_236

213
458
793_237

214
459
793_238

215
460
793_239

216
461
793_240

217
462
793_241

218
463
793_242

219
464
793_244

220
465
793_245

221
466
793_247

222
467
793_248

223
468
793_249

224
469
793_250

225
470
793_251

226
471
793_252

227
472
793_253

228
473
793_254

229
474
793_255

230
475
793_256

231
476
793_257

232
477
793_258

233
478
793_259

234
479
793_260

235
480
793_261

236
481
793_262

237
482
793_263

238
483
793_264

239
484
793_265

240
485
793_266

241
486
793_267

242
487
793_268

243
488
793_269

244
489
793_270

245
490
793_271

[0453]

Novel nucleic acids and polypeptides

Information

Publication Number

Date Filed

Date Published

Inventors

CPC

US Classifications

International Classifications

Abstract

Description

Claims

PCT Information