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(-) Description

Title :  THE 1.2 ANGSTROM STRUCTURE OF KUNITZ TYPE DOMAIN C5
 
Authors :  K. Merigeau, B. Arnoux, A. Ducruix
Date :  15 Jan 97  (Deposition) - 15 May 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Kunitz Inhibitor, Extracellular Matrix, Connective Tissue (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Merigeau, B. Arnoux, D. Perahia, K. Norris, F. Norris, A. Ducruix
1. 2 A Refinement Of The Kunitz-Type Domain From The Alpha3 Chain Of Human Type Vi Collagen.
Acta Crystallogr. , Sect. D V. 54 306 1998
PubMed-ID: 9761897  |  Reference-DOI: 10.1107/S0907444997010846
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COLLAGEN
    ChainsA
    EngineeredYES
    Expression SystemSACCHAROMYCES CEREVISIAE
    Expression System CommonBAKER'S YEAST
    Expression System StrainMT-663
    Expression System Taxid4932
    FragmentDOMAIN C5, C-TERMINUS OF TYPE VI COLLAGEN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsKUNITZ-TYPE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:21 , LYS A:28 , GLY A:46 , SER A:47 , GLN A:48 , HOH A:215 , HOH A:240 , HOH A:242BINDING SITE FOR RESIDUE PO4 A 59

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:5 -A:55
2A:14 -A:38
3A:30 -A:51

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2KNT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2KNT)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BPTI_KUNITZ_2PS50279 Pancreatic trypsin inhibitor (Kunitz) family profile.CO6A3_HUMAN3112-3162  1A:5-55
2BPTI_KUNITZ_1PS00280 Pancreatic trypsin inhibitor (Kunitz) family signature.CO6A3_HUMAN3140-3158  1A:33-51

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002955501aENSE00001910299chr2:238323018-238322596423CO6A3_HUMAN-00--
1.2aENST000002955502aENSE00001339012chr2:238305490-238305370121CO6A3_HUMAN1-31310--
1.3ENST000002955503ENSE00001073784chr2:238303847-238303230618CO6A3_HUMAN31-2372070--
1.4aENST000002955504aENSE00001073778chr2:238296827-238296225603CO6A3_HUMAN237-4382020--
1.6ENST000002955506ENSE00001073762chr2:238290142-238289558585CO6A3_HUMAN438-6331960--
1.7ENST000002955507ENSE00001073761chr2:238287878-238287279600CO6A3_HUMAN633-8332010--
1.8bENST000002955508bENSE00001073779chr2:238285987-238285415573CO6A3_HUMAN833-10241920--
1.9ENST000002955509ENSE00001073741chr2:238283663-238283055609CO6A3_HUMAN1024-12272040--
1.10aENST0000029555010aENSE00001073780chr2:238280980-238280375606CO6A3_HUMAN1227-14292030--
1.11aENST0000029555011aENSE00001266203chr2:238277820-238277206615CO6A3_HUMAN1429-16342060--
1.12ENST0000029555012ENSE00002150712chr2:238275929-238275330600CO6A3_HUMAN1634-18342010--
1.13ENST0000029555013ENSE00001618417chr2:238274678-238274341338CO6A3_HUMAN1834-19461130--
1.14ENST0000029555014ENSE00001769937chr2:238273071-23827299379CO6A3_HUMAN1947-1973270--
1.15ENST0000029555015ENSE00001761108chr2:238272041-238271896146CO6A3_HUMAN1973-2021490--
1.16ENST0000029555016ENSE00001605098chr2:238270474-23827038293CO6A3_HUMAN2022-2052310--
1.17ENST0000029555017ENSE00001720752chr2:238269817-23826976454CO6A3_HUMAN2053-2070180--
1.18ENST0000029555018ENSE00001792444chr2:238268802-23826873172CO6A3_HUMAN2071-2094240--
1.19ENST0000029555019ENSE00001695168chr2:238268031-23826800527CO6A3_HUMAN2095-210390--
1.20ENST0000029555020ENSE00001780362chr2:238267893-23826784945CO6A3_HUMAN2104-2118150--
1.21ENST0000029555021ENSE00001690516chr2:238267731-23826767854CO6A3_HUMAN2119-2136180--
1.22ENST0000029555022ENSE00001722049chr2:238267226-23826716463CO6A3_HUMAN2137-2157210--
1.23bENST0000029555023bENSE00001799827chr2:238266525-23826646066CO6A3_HUMAN2158-2179220--
1.24aENST0000029555024aENSE00001629352chr2:238266034-23826598154CO6A3_HUMAN2180-2197180--
1.25bENST0000029555025bENSE00001757174chr2:238263577-23826354236CO6A3_HUMAN2198-2209120--
1.26ENST0000029555026ENSE00001689707chr2:238262046-23826198463CO6A3_HUMAN2210-2230210--
1.27ENST0000029555027ENSE00001739702chr2:238261227-23826116563CO6A3_HUMAN2231-2251210--
1.28ENST0000029555028ENSE00001696821chr2:238259835-23825977363CO6A3_HUMAN2252-2272210--
1.29ENST0000029555029ENSE00001675495chr2:238258852-23825879063CO6A3_HUMAN2273-2293210--
1.30ENST0000029555030ENSE00001799552chr2:238257306-23825725651CO6A3_HUMAN2294-2310170--
1.31ENST0000029555031ENSE00001696073chr2:238257027-23825699236CO6A3_HUMAN2311-2322120--
1.32ENST0000029555032ENSE00001598419chr2:238256512-23825645063CO6A3_HUMAN2323-2343210--
1.33ENST0000029555033ENSE00001727243chr2:238255208-23825514663CO6A3_HUMAN2344-2364210--
1.34ENST0000029555034ENSE00001801832chr2:238253856-23825382433CO6A3_HUMAN2365-2375110--
1.35ENST0000029555035ENSE00001766604chr2:238253737-23825370137CO6A3_HUMAN2376-2388130--
1.36ENST0000029555036ENSE00001795418chr2:238253595-23825358412CO6A3_HUMAN2388-239250--
1.37bENST0000029555037bENSE00001073728chr2:238253486-238252993494CO6A3_HUMAN2392-25561650--
1.37dENST0000029555037dENSE00001706361chr2:238250804-23825070897CO6A3_HUMAN2557-2589330--
1.38aENST0000029555038aENSE00001715298chr2:238249793-238249095699CO6A3_HUMAN2589-28222340--
1.39aENST0000029555039aENSE00001642272chr2:238247760-238247658103CO6A3_HUMAN2822-2856350--
1.40ENST0000029555040ENSE00001738522chr2:238245175-238244778398CO6A3_HUMAN2856-29891340--
1.41aENST0000029555041aENSE00001673740chr2:238243532-238243269264CO6A3_HUMAN2989-3077890--
1.42aENST0000029555042aENSE00001779644chr2:238242191-23824209399CO6A3_HUMAN3077-3110341A:1-33
1.43bENST0000029555043bENSE00001648162chr2:238234367-238234203165CO6A3_HUMAN3110-3165561A:3-5856
1.44dENST0000029555044dENSE00001713829chr2:238233457-238232655803CO6A3_HUMAN3165-3177131A:58-581

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:58
 aligned with CO6A3_HUMAN | P12111 from UniProtKB/Swiss-Prot  Length:3177

    Alignment length:58
                                  3117      3127      3137      3147      3157        
         CO6A3_HUMAN   3108 ETDICKLPKDEGTCRDFILKWYYDPNTKSCARFWYGGCGGNENKFGSQKECEKVCAPV 3165
               SCOP domains d2knta_ A: Collagen type VI (domain C5 from alpha 3 chain) SCOP domains
               CATH domains 2kntA00 A:1-58 Factor Xa Inhibitor                         CATH domains
               Pfam domains ---Kunitz_BPTI-2kntA01 A:4-56                           -- Pfam domains
         Sec.struct. author ..hhhh...........eeeeeee....eeeeeee............hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----BPTI_KUNITZ_2  PDB: A:5-55 UniProt: 3112-3162      --- PROSITE (1)
                PROSITE (2) --------------------------------BPTI_KUNITZ_1      ------- PROSITE (2)
           Transcript 1 (1) 1.4------------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) --Exon 1.43b  PDB: A:3-58 UniProt: 3110-3165               Transcript 1 (2)
                2knt A    1 ETDICKLPKDEGTCRDFILKWYYDPNTKSCARFWYGGCGGNENKFGSQKECEKVCAPV   58
                                    10        20        30        40        50        

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CO6A3_HUMAN | P12111)
molecular function
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    GO:0004867    serine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0030574    collagen catabolic process    The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells.
    GO:0030198    extracellular matrix organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
    GO:0007517    muscle organ development    The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
cellular component
    GO:0005581    collagen trimer    A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures.
    GO:0005589    collagen type VI trimer    A collagen heterotrimer containing type VI alpha chains in alpha1(VI)alpha2(VI)alpha3(VI) trimers; type VI collagen triple helices associate to form beaded fibrils.
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:1903561    extracellular vesicle    Any vesicle that is part of the extracellular region.
    GO:0005578    proteinaceous extracellular matrix    A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.
    GO:0042383    sarcolemma    The outer membrane of a muscle cell, consisting of the plasma membrane, a covering basement membrane (about 100 nm thick and sometimes common to more than one fiber), and the associated loose network of collagen fibers.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CO6A3_HUMAN | P121111knt 1kth 1kun

(-) Related Entries Specified in the PDB File

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