An Information Portal to 111558 Biological Macromolecular Structures

Crystal structure of the catalytic domain of MMP-12 in complex with a twin inhibitor.
Biology and Chemistry Report
  •   Structure Details   Hide

    Structure Keywords

    Keywords hydrolase/hydrolase inhibitor
    Text divalent inhibitor, carboxylic twin inhibitor, Dimerisation, METZINCIN, Zinc protease, hydrolase-hydrolase inhibitor complex

    Polymeric Molecules

    Chain A,B,C,D
    Description Macrophage metalloelastase 
    Fragment Human MMP12 catalytic domain 
    Mutation F171D 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 17615.8 
    Source Method genetically manipulated  
    Entity Name MME, Macrophage elastase, ME, hME, Matrix metalloproteinase-12, MMP-12 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    CA  CALCIUM ION  Ca   40.08  View 
    DMS  DIMETHYL SULFOXIDE  C2 H6 O S   78.13  View 
    GOL  GLYCEROL  C3 H8 O3   92.09  View 
    L29  N,N'-bis(2-{(biphenyl-4-ylsulfonyl)[(2R)-1-(hydroxyamino)-3-methyl-1-oxobutan-2-yl]amino}ethyl)benzene-1,3-dicarboxamide (non-preferred name)  C46 H52 N6 O10 S2   913.07  View 
    PEG  DI(HYDROXYETHYL)ETHER  C4 H10 O3   106.12  View 
    PGO  S-1,2-PROPANEDIOL  C3 H8 O2   76.09  View 
    ZN  ZINC ION  Zn   65.41  View 
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B,C,D MMP12_HUMAN P39900     

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B C D      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B,C,D
    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. 
    42060   Wound Healing  The Series of Events That Restore Integrity to a Damaged Tissue Following an Injury. 
    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. 

  •   Gene Details   Hide

    Genetic Source

    Chain A,B,C,D
    Common Name Human
    Scientific Name Homo sapiens  
    Gene hme, mmp12
    Host Scientific Name Escherichia coli  
    Host Strain Bl21
    Host Vector Type Plasmid
    Host Plasmid Name PET24A

    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    11 11q22.3 4321     matrix metallopeptidase 12 MMP12    

    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
    rs201868025 LS-SNP   dbSNP   A 113 Y - > C Beta Ladder 82% (Exposed) 11 102743607
    rs61730844 LS-SNP   dbSNP   A 127 R - > H Helix 60% (Exposed) 11 102742653 NULL
    rs202141359 LS-SNP   dbSNP   A 129 D - > V Helix 35% (Intermediate) 11 102742647
    rs201046473 LS-SNP   dbSNP   A 130 V - > A Helix 0% (Buried) 11 102742644
    rs180918521 LS-SNP   dbSNP   A 135 R - > Q Helix 49% (Exposed) 11 102742629
    rs200079972 LS-SNP   dbSNP   A 139 Q - > P Helix 35% (Intermediate) 11 102742617
    rs188003361 LS-SNP   dbSNP   A 147 L - > F Coil 0% (Buried) 11 102742592
    rs199891377 LS-SNP   dbSNP   A 162 V - > G Beta Ladder 14% (Intermediate) 11 102742548
    rs201575382 LS-SNP   dbSNP   A 165 R - > C Coil 58% (Exposed) 11 102742540 NULL
    rs61730845 LS-SNP   dbSNP   A 165 R - > H Coil 58% (Exposed) 11 102742539 NULL
    rs200263416 LS-SNP   dbSNP   A 168 H - > Y Coil 24% (Intermediate) 11 102742447 NULL
    rs201174015 LS-SNP   dbSNP   A 198 D - > N Beta Ladder 0% (Buried) 11 102742357 NULL
    rs200787919 LS-SNP   dbSNP   A 210 T - > N Beta Ladder 10% (Intermediate) 11 102738796
    rs202042208 LS-SNP   dbSNP   A 218 H - > Y Helix 14% (Intermediate) 11 102738774 NULL
    rs200751457 LS-SNP   dbSNP   A 219 E - > *K Helix 6% (Buried) 11 102738771 NULL
    rs199654990 LS-SNP   dbSNP   A 220 I - > L Helix 2% (Buried) 11 102738768
    rs201408320 LS-SNP   dbSNP   A 221 G - > A Helix 0% (Buried) 11 102738764
    rs200176944 LS-SNP   dbSNP   A 233 K - > T Turn 78% (Exposed) 11 102738728
    rs199783271 LS-SNP   dbSNP   A 235 V - > I Turn 16% (Intermediate) 11 102738723
    rs201987840 LS-SNP   dbSNP   A 249 R - > H Coil 70% (Exposed) 11 102738680
    rs183458117 LS-SNP   dbSNP   A 249 R - > CS Coil 70% (Exposed) 11 102738681