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An Information Portal to 105212 Biological Macromolecular Structures

Human MMP13 in complex with L-glutamate motif inhibitor
Biology and Chemistry Report
3TVC
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE/HYDROLASE INHIBITOR
    Text pseudo dipeptides, potent inhibitors, metzincin, Zinc metalloprotease, HYDROLASE-HYDROLASE INHIBITOR complex

    Polymeric Molecules

    Chain A
    Description Collagenase 3 
    Fragment MMP-13 catalytic subunit (UNP residues 104-272) 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 19024.3 
    Source Method genetically manipulated  
    Entity Name Matrix metalloproteinase-13, MMP-13 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    CA  CALCIUM ION  Ca   40.08  View 
    E3P  N~2~-[3-(1,1':4',1''-terphenyl-4-yl)propanoyl]-L-alpha-glutamine  C26 H26 N2 O4   430.50  View 
    PEG  DI(HYDROXYETHYL)ETHER  C4 H10 O3   106.12  View 
    ZN  ZINC ION  Zn   65.41  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A MMP13_HUMAN A8K846     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    3.4.24      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    6508   Proteolysis  The Hydrolysis of Proteins Into Smaller Polypeptides And/or Amino Acids by Cleavage of Their Peptide Bonds. 
    30574   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. 
    5576   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. 
    31012   Extracellular Matrix  A Structure Lying External to One or More Cells Which Provides Structural Support For Cells or Tissues; May Be Completely External to the Cell (as in Animals and Bacteria) or Be Part of the Cell (as in Plants). 
    4222   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. 
    8237   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. 
    8270   Zinc Ion Binding  Interacting Selectively and Non Covalently with Zinc (zn) Ions. 


    Protein Analyses

    Measured Binding Affinities   

     
  •   Gene Details   Hide

    Genetic Source

    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Details Expressed As Pro Mmp13
    Gene mmp13
    Host Scientific Name Escherichia coli  
    Host Strain Bl21
    Host Vector Type Pet24a


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    11 11q22.3 4322     matrix metallopeptidase 13 (collagenase 3) MMP13    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs189974040 LS-SNP   dbSNP   A 109 R - > L 3/10 Helix 92% (Exposed) 11 102826017
    rs143292324 LS-SNP   dbSNP   A 155 R - > S Beta Ladder 55% (Exposed) 11 102825233
    rs181426884 LS-SNP   dbSNP   A 158 D - > N Bend 62% (Exposed) 11 102825226
    rs148746302 LS-SNP   dbSNP   A 165 I - > M Beta Ladder 0% (Buried) 11 102825203
    rs145243532 LS-SNP   dbSNP   A 170 K - > T Bend 51% (Exposed) 11 102825189
    rs202231908 LS-SNP   dbSNP   A 171 E - > G Bend 69% (Exposed) 11 102825010
    rs150048151 LS-SNP   dbSNP   A 198 D - > V Coil 2% (Buried) 11 102824929 CA
    rs140059558 LS-SNP   dbSNP   A 207 W - > G Beta Ladder 1% (Buried) 11 102824903 CA
    rs147544761 LS-SNP   dbSNP   A 221 A - > V Helix 0% (Buried) 11 102822878
    rs121909500 LS-SNP   dbSNP   A 232 H - > N Coil 37% (Exposed) 11 102822846 ZN,E3P
    rs140993310 LS-SNP   dbSNP   A 257 D - > V Helix 13% (Intermediate) 11 102822770
    rs202123339 LS-SNP   dbSNP   A 262 I - > F Helix 0% (Buried) 11 102822756