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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF MMP-13 COMPLEXED WITH N-(3-METHOXYBENZYL)-4-OXO-3,4-DIHYDROTHIENO[2,3-D]PYRIMIDINE-2-CARBOXAMIDE
 
Authors :  H. Oki, Y. Tanaka
Date :  12 May 14  (Deposition) - 24 Sep 14  (Release) - 24 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Mmp-13, Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Nara, K. Sato, T. Naito, H. Mototani, H. Oki, Y. Yamamoto, H. Kuno, T. Santou, N. Kanzaki, J. Terauchi, O. Uchikawa, M. Kori
Thieno[2, 3-D]Pyrimidine-2-Carboxamides Bearing A Carboxybenzene Group At 5-Position: Highly Potent, Selective, And Orally Available Mmp-13 Inhibitors Interacting With The S1 Binding Site
Bioorg. Med. Chem. 2014
PubMed-ID: 25192810  |  Reference-DOI: 10.1016/J.BMC.2014.07.025

(-) Compounds

Molecule 1 - COLLAGENASE 3
    ChainsA, B
    EC Number3.4.24.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN, RESIDUES 104-274
    GeneMMP13
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMATRIX METALLOPROTEINASE-13, MMP-13

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (1x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 16)

Asymmetric Unit (6, 16)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3FMT2Ligand/IonFORMIC ACID
4NA2Ligand/IonSODIUM ION
5WLL2Ligand/IonN-(3-METHOXYBENZYL)-4-OXO-3,4-DIHYDROTHIENO[2,3-D]PYRIMIDINE-2-CARBOXAMIDE
6ZN4Ligand/IonZINC ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3FMT1Ligand/IonFORMIC ACID
4NA-1Ligand/IonSODIUM ION
5WLL1Ligand/IonN-(3-METHOXYBENZYL)-4-OXO-3,4-DIHYDROTHIENO[2,3-D]PYRIMIDINE-2-CARBOXAMIDE
6ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3FMT1Ligand/IonFORMIC ACID
4NA-1Ligand/IonSODIUM ION
5WLL1Ligand/IonN-(3-METHOXYBENZYL)-4-OXO-3,4-DIHYDROTHIENO[2,3-D]PYRIMIDINE-2-CARBOXAMIDE
6ZN-1Ligand/IonZINC ION
Biological Unit 3 (3, 6)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3FMT2Ligand/IonFORMIC ACID
4NA-1Ligand/IonSODIUM ION
5WLL2Ligand/IonN-(3-METHOXYBENZYL)-4-OXO-3,4-DIHYDROTHIENO[2,3-D]PYRIMIDINE-2-CARBOXAMIDE
6ZN-1Ligand/IonZINC ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:222 , HIS A:226 , HIS A:232 , FMT A:306BINDING SITE FOR RESIDUE ZN A 301
02AC2SOFTWAREHIS A:172 , ASP A:174 , HIS A:187 , HIS A:200BINDING SITE FOR RESIDUE ZN A 302
03AC3SOFTWAREASP A:179 , GLY A:180 , SER A:182 , LEU A:184 , ASP A:202 , GLU A:205BINDING SITE FOR RESIDUE CA A 303
04AC4SOFTWAREASP A:162 , ASN A:194 , GLY A:196 , ASP A:198 , HOH A:409 , HOH A:416BINDING SITE FOR RESIDUE CA A 304
05AC5SOFTWAREASP A:128 , ASP A:203 , GLU A:205 , HOH A:501BINDING SITE FOR RESIDUE NA A 305
06AC6SOFTWAREHIS A:222 , GLU A:223 , HIS A:226 , HIS A:232 , ZN A:301 , HOH A:433 , HOH A:600BINDING SITE FOR RESIDUE FMT A 306
07AC7SOFTWARETYR A:176 , HIS A:187 , ALA A:188 , PHE A:189 , PRO A:190 , HOH A:611 , HOH A:613BINDING SITE FOR RESIDUE EDO A 307
08AC8SOFTWARELEU A:218 , HIS A:222 , ALA A:238 , LEU A:239 , PHE A:241 , ILE A:243 , TYR A:244 , THR A:245 , TYR A:246 , PHE A:252 , MET A:253 , PRO A:255 , HOH A:476 , HOH A:636BINDING SITE FOR RESIDUE WLL A 308
09AC9SOFTWAREHIS B:222 , HIS B:226 , HIS B:232 , FMT B:306BINDING SITE FOR RESIDUE ZN B 301
10BC1SOFTWAREHIS B:172 , ASP B:174 , HIS B:187 , HIS B:200BINDING SITE FOR RESIDUE ZN B 302
11BC2SOFTWAREASP B:179 , GLY B:180 , SER B:182 , LEU B:184 , ASP B:202 , GLU B:205BINDING SITE FOR RESIDUE CA B 303
12BC3SOFTWAREASP B:162 , ASN B:194 , GLY B:196 , ASP B:198 , HOH B:423 , HOH B:449BINDING SITE FOR RESIDUE CA B 304
13BC4SOFTWAREASP B:128 , ASP B:203 , GLU B:205 , HOH B:533BINDING SITE FOR RESIDUE NA B 305
14BC5SOFTWAREHIS B:222 , GLU B:223 , HIS B:226 , HIS B:232 , ZN B:301 , HOH B:464BINDING SITE FOR RESIDUE FMT B 306
15BC6SOFTWARETYR B:176 , ALA B:188 , PHE B:189 , HOH B:566BINDING SITE FOR RESIDUE EDO B 307
16BC7SOFTWARELEU B:218 , HIS B:222 , GLU B:223 , ALA B:238 , LEU B:239 , PHE B:241 , ILE B:243 , TYR B:244 , THR B:245 , THR B:247 , PHE B:252 , MET B:253 , PRO B:255 , HOH B:587BINDING SITE FOR RESIDUE WLL B 308

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WV3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3WV3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_073418W207GMMP13_HUMANDisease (MDST)140059558A/BW207G
2UniProtVAR_063434H232NMMP13_HUMANDisease (MANDP1)121909500A/BH232N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_073418W207GMMP13_HUMANDisease (MDST)140059558AW207G
2UniProtVAR_063434H232NMMP13_HUMANDisease (MANDP1)121909500AH232N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_073418W207GMMP13_HUMANDisease (MDST)140059558BW207G
2UniProtVAR_063434H232NMMP13_HUMANDisease (MANDP1)121909500BH232N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_073418W207GMMP13_HUMANDisease (MDST)140059558A/BW207G
2UniProtVAR_063434H232NMMP13_HUMANDisease (MANDP1)121909500A/BH232N

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.MMP13_HUMAN219-228
 
  2A:219-228
B:219-228
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.MMP13_HUMAN219-228
 
  1A:219-228
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.MMP13_HUMAN219-228
 
  1-
B:219-228
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.MMP13_HUMAN219-228
 
  2A:219-228
B:219-228

(-) Exons   (5, 10)

Asymmetric Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002603021aENSE00001105391chr11:102826463-102826315149MMP13_HUMAN1-40400--
1.2ENST000002603022ENSE00001105386chr11:102826222-102825981242MMP13_HUMAN41-121812A:104-121
B:104-121
18
18
1.3ENST000002603023ENSE00001105401chr11:102825335-102825187149MMP13_HUMAN121-171512A:121-171
B:121-171
51
51
1.4ENST000002603024ENSE00001105398chr11:102825010-102824885126MMP13_HUMAN171-213432A:171-213
B:171-213
43
43
1.5ENST000002603025ENSE00001139473chr11:102822902-102822741162MMP13_HUMAN213-267552A:213-267 (gaps)
B:213-267
55
55
1.6ENST000002603026ENSE00000930343chr11:102820956-102820839118MMP13_HUMAN267-306402A:267-273
B:267-269
7
3
1.7ENST000002603027ENSE00000930342chr11:102819887-102819754134MMP13_HUMAN306-351460--
1.8ENST000002603028ENSE00000930341chr11:102818779-102818620160MMP13_HUMAN351-404540--
1.9ENST000002603029ENSE00000930340chr11:102816478-102816375104MMP13_HUMAN404-439360--
1.11bENST0000026030211bENSE00002188786chr11:102815095-1028137241372MMP13_HUMAN439-471330--

(-) Sequences/Alignments

Asymmetric 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:168
 aligned with MMP13_HUMAN | P45452 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:170
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273
          MMP13_HUMAN   104 YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPGDEDP 273
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee.......hhhhhhhhhhhhhhhhhh....eeeee......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh..................--......hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------G------------------------N----------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------ZINC_PROTE--------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2          -------------------------------------------------Exon 1.4  PDB: A:171-213 UniProt: 171-213  -----------------------------------------------------1.6     Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.3  PDB: A:121-171 UniProt: 121-171          -----------------------------------------Exon 1.5  PDB: A:213-267 (gaps) UniProt: 213-267       ------ Transcript 1 (2)
                 3wv3 A 104 YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTY--KSHFMLPDDDVQGIQSLYGPGDEDP 273
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243  |  | 253       263       273
                                                                                                                                                                        246  |                        
                                                                                                                                                                           249                        

Chain B from PDB  Type:PROTEIN  Length:166
 aligned with MMP13_HUMAN | P45452 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:166
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263      
          MMP13_HUMAN   104 YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPG 269
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhhh.........................hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------G------------------------N------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------ZINC_PROTE----------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2          -------------------------------------------------Exon 1.4  PDB: B:171-213 UniProt: 171-213  -----------------------------------------------------1.6 Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.3  PDB: B:121-171 UniProt: 121-171          -----------------------------------------Exon 1.5  PDB: B:213-267 UniProt: 213-267              -- Transcript 1 (2)
                 3wv3 B 104 YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPG 269
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263      

   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  (0, 0)

(no "SCOP Domain" information available for 3WV3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WV3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WV3)

(-) Gene Ontology  (42, 42)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MMP13_HUMAN | P45452)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0048306    calcium-dependent 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), in the presence of calcium.
    GO:0005518    collagen binding    Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
    GO:0001968    fibronectin binding    Interacting selectively and non-covalently with a fibronectin, a group of related adhesive glycoproteins of high molecular weight found on the surface of animal cells, connective tissue matrices, and in extracellular fluids.
    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:0050750    low-density lipoprotein particle receptor binding    Interacting selectively and non-covalently with a low-density lipoprotein receptor.
    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: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:0030282    bone mineralization    The deposition of hydroxyapatite, a form of calcium phosphate with the formula Ca10(PO4)6(OH)2, in bone tissue.
    GO:0060349    bone morphogenesis    The process in which bones are generated and organized.
    GO:0051216    cartilage development    The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
    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:0071498    cellular response to fluid shear stress    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 a fluid shear stress stimulus. Fluid shear stress is the force acting on an object in a system where the fluid is moving across a solid surface.
    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:0035116    embryonic hindlimb morphogenesis    The process, occurring in the embryo, by which the anatomical structures of the hindlimbs are generated and organized. The hindlimbs are the posterior limbs of an animal.
    GO:0001958    endochondral ossification    Replacement ossification wherein bone tissue replaces cartilage.
    GO:0044849    estrous cycle    A type of ovulation cycle, which occurs in most mammalian therian females, where the endometrium is resorbed if pregnancy does not occur.
    GO:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    GO:0003417    growth plate cartilage development    The process whose specific outcome is the progression of the cartilage that will provide a scaffold for mineralization of endochondral bones as they elongate or grow.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0001554    luteolysis    The lysis or structural demise of the corpus luteum. During normal luteolysis, two closely related events occur. First, there is loss of the capacity to synthesize and secrete progesterone (functional luteolysis) followed by loss of the cells that comprise the corpus luteum (structural luteolysis). Preventing luteolysis is crucial to maintain pregnancy.
    GO:0001503    ossification    The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
    GO:0001649    osteoblast differentiation    The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.
    GO:0007567    parturition    The reproductive process in which the parent is separated from its offspring either by giving birth to live young or by laying eggs.
    GO:0043171    peptide catabolic process    The chemical reactions and pathways resulting in the breakdown of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.
    GO:1904244    positive regulation of pancreatic trypsinogen secretion    Any process that activates or increases the frequency, rate or extent of pancreatic trypsinogen secretion.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0042493    response to drug    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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0043627    response to estrogen    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 stimulus by an estrogen, C18 steroid hormones that can stimulate the development of female sexual characteristics.
    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:0009612    response to mechanical stimulus    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 mechanical stimulus.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    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:0046581    intercellular canaliculus    An extremely narrow tubular channel located between adjacent cells. An instance of this is the secretory canaliculi occurring between adjacent parietal cells in the gastric mucosa of vertebrates.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    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.

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

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        MMP13_HUMAN | P454521eub 1fls 1fm1 1pex 1uc1 1xuc 1xud 1xur 1you 1ztq 2d1n 2e2d 2ow9 2ozr 2pjt 2yig 3elm 3i7g 3i7i 3kec 3kej 3kek 3kry 3ljz 3o2x 3tvc 3wv1 3wv2 3zxh 456c 4a7b 4fu4 4fvl 4g0d 4jp4 4jpa 4l19 5b5o 5b5p 5bot 5boy 5bpa 5uwk 5uwl 5uwm 5uwn 830c

(-) Related Entries Specified in the PDB File

3wv1 3wv2