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Crystal structure of MMP-12 complexed to 2-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)ethyl-4-(4-ethoxy[1,1-biphenyl]-4-yl)-4-oxobutanoic acid
Biology and Chemistry Report
1ROS
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE
    Text Macrophage metalloelastase, non-zinc chelator, MMP-12, MMP12 inhibitor, HYDROLASE

    Polymeric Molecules

    Chain A,B
    Description Macrophage metalloelastase 
    Fragment residues 106-268 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 18101.3 
    Source Method genetically manipulated  
    Entity Name HME, Matrix metalloproteinase-12, MMP-12, Macrophage elastase, ME 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    CA  CALCIUM ION  Ca   40.08  View 
    DEO  2-[2-(1,3-DIOXO-1,3-DIHYDRO-2H-ISOINDOL-2-YL)ETHYL]-4-(4'-ETHOXY-1,1'-BIPHENYL-4-YL)-4-OXOBUTANOIC ACID  C28 H25 N O6   471.50  View 
    ZN  ZINC ION  Zn   65.41  View 
     
  •   Protein Details   Hide

    UniProtKB Information

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

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc Catalytic Site(s)
    A B  3.4.24.65        
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    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
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Gene mmp12, hme
    Host Scientific Name Escherichia coli bl21(de3)  
    Host Genus Escherichia
    Host Species Escherichia Coli
    Host Strain Bl21 (de3)
    Host Vector Type Plasmid
    Host Plasmid Name pGEMEX1


    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 76% (Exposed) 11 102743607
    rs61730844 LS-SNP   dbSNP   A 127 R - > H Helix 63% (Exposed) 11 102742653
    rs202141359 LS-SNP   dbSNP   A 129 D - > V Helix 31% (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 59% (Exposed) 11 102742629
    rs200079972 LS-SNP   dbSNP   A 139 Q - > P Helix 43% (Exposed) 11 102742617
    rs188003361 LS-SNP   dbSNP   A 147 L - > F Coil 1% (Buried) 11 102742592
    rs199891377 LS-SNP   dbSNP   A 162 V - > G Beta Ladder 20% (Intermediate) 11 102742548
    rs61730845 LS-SNP   dbSNP   A 165 R - > H Coil 56% (Exposed) 11 102742539
    rs201575382 LS-SNP   dbSNP   A 165 R - > C Coil 56% (Exposed) 11 102742540
    rs200263416 LS-SNP   dbSNP   A 168 H - > Y Coil 27% (Intermediate) 11 102742447 ZN
    rs201174015 LS-SNP   dbSNP   A 198 D - > N Beta Ladder 0% (Buried) 11 102742357 CA
    rs200787919 LS-SNP   dbSNP   A 210 T - > N Beta Ladder 13% (Intermediate) 11 102738796
    rs202042208 LS-SNP   dbSNP   A 218 H - > Y Helix 15% (Intermediate) 11 102738774 ZN,DEO
    rs200751457 LS-SNP   dbSNP   A 219 E - > *K Helix 7% (Buried) 11 102738771 ZN,DEO
    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 76% (Exposed) 11 102738728
    rs199783271 LS-SNP   dbSNP   A 235 V - > I Turn 15% (Intermediate) 11 102738723 DEO
    rs183458117 LS-SNP   dbSNP   A 249 R - > CS Coil 88% (Exposed) 11 102738681
    rs201987840 LS-SNP   dbSNP   A 249 R - > H Coil 88% (Exposed) 11 102738680