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(-) Description

Authors :  A. M. Libson, A. G. Gittis, I. E. Collier, B. L. Marmer, G. G. Goldberg, E. E. Lattman
Date :  19 Jul 95  (Deposition) - 17 Aug 96  (Release) - 24 Feb 09  (Revision)
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Hemopexin Domain, Metalloprotease, Hydrolase (Metalloprotease) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  A. M. Libson, A. G. Gittis, I. E. Collier, B. L. Marmer, G. I. Goldberg, E. E. Lattman
Crystal Structure Of The Haemopexin-Like C-Terminal Domain Of Gelatinase A.
Nat. Struct. Biol. V. 2 938 1995
PubMed-ID: 7583664  |  Reference-DOI: 10.1038/NSB1195-938
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GELATINASE A
    EC Number3.4.24.24
    Expression SystemESCHERICHIA COLI
    Expression System GeneHUMAN GELATINASE A
    Expression System PlasmidPFLAG1
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
4ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
2AC2SOFTWAREHOH A:316 , HOH A:329 , HOH A:335 , ASP A:476 , ASP A:521 , ASP A:569 , ASP A:618BINDING SITE FOR RESIDUE CA A 302
3AC3SOFTWARENA A:304 , ILE A:478 , ALA A:522 , VAL A:523 , ALA A:570 , ALA A:571 , ALA A:619 , VAL A:620BINDING SITE FOR RESIDUE CL A 303

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
1A:469 -A:660

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
1Gly A:505 -Pro A:506
2Tyr A:552 -Pro A:553
3Phe A:602 -Pro A:603

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

Asymmetric/Biological Unit (5, 5)
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
2CancerSNPVAR_MMP2_HUMAN_CCDS10752_1_02 *T498MMMP2_HUMANDisease (Colorectal cancer)  ---AT498M
4UniProtVAR_036138S644IMMP2_HUMANUnclassified  ---AS644I
5CancerSNPVAR_MMP2_HUMAN_CCDS10752_1_03 *S644IMMP2_HUMANDisease (Colorectal cancer)  ---AS644I
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 5)

Asymmetric/Biological Unit (2, 5)
1HEMOPEXIN_2PS51642 Hemopexin repeat profile.MMP2_HUMAN472-516
2HEMOPEXINPS00024 Hemopexin domain signature.MMP2_HUMAN606-621  1A:606-621

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength

(-) 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:200
 aligned with MMP2_HUMAN | P08253 from UniProtKB/Swiss-Prot  Length:660

    Alignment length:200
                                   470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660
               SCOP domains d1gena_ A: Gelatinase A (MMP-2), C-terminal domain                                                                                                                                                       SCOP domains
               CATH domains 1genA00 A:461-660 Hemopexin                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeee..eeeeee..eeeee............hhh..........eeeee....eeeeee..eeeee............hhhh..........eeeee....eeeeee..eeeee..............hhhh.........eeee.....eeeeee..eeeeee..eeeeeeeeehhhh.... Sec.struct. author
             SAPs(SNPs) (1) -------------------------------------M--------------------------------------------------------------------------------------------------------------------------L----------------------I---------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------M-------------------------------------------------------------------------------------------------------------------------------------------------I---------------- SAPs(SNPs) (2)
                PROSITE (1) -----------HEMOPEXIN_2  PDB: A:472-516 UniProt: 472-516 HEMOPEXIN_2  PDB: A:517-563 UniProt: 517-563   -HEMOPEXIN_2  PDB: A:565-613 UniProt: 565-613     HEMOPEXIN_2  PDB: A:614-660 UniProt: 614-660    PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------HEMOPEXIN       --------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.10  PDB: A:461-491      ---------------------------------------------Exon 1.12  PDB: A:537-590 UniProt: 537-590            ------------------------------------Exon 1.14b  PDB: A:627-660         Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.11  PDB: A:491-537 UniProt: 491-537     ----------------------------------------------------Exon 1.13  PDB: A:590-627             --------------------------------- Transcript 1 (2)
                                   470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660

   Legend:   → Mismatch (orange background)
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  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
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GEN)

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MMP2_HUMAN | P08253)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0001955    blood vessel maturation    A developmental process, independent of morphogenetic (shape) change, that is required for a blood vessel to attain its fully functional state.
    GO:0060346    bone trabecula formation    The process of creating a trabecula in the bone. A trabecula is a tissue element in the form of a small beam, strut or rod.
    GO:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0071230    cellular response to amino acid stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups.
    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:0007566    embryo implantation    Attachment of the blastocyst to the uterine lining.
    GO:0035987    endodermal cell differentiation    The process in which a relatively unspecialized cell acquires the specialized features of an endoderm cell, a cell of the inner of the three germ layers of the embryo.
    GO:0048013    ephrin receptor signaling pathway    The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
    GO:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    GO:0060325    face morphogenesis    The process in which the anatomical structures of the face are generated and organized. The face is the ventral division of the head.
    GO:0001957    intramembranous ossification    Direct ossification that occurs within mesenchyme or an accumulation of relatively unspecialized cells.
    GO:0045089    positive regulation of innate immune response    Any process that activates or increases the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0001666    response to hypoxia    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0048705    skeletal system morphogenesis    The process in which the anatomical structures of the skeleton are generated and organized.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    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:0030017    sarcomere    The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs.


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 Related Entries

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

        MMP2_HUMAN | P082531ck7 1cxw 1eak 1gxd 1hov 1j7m 1ks0 1qib 1rtg 3ayu

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1GEN)