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Crystal structure of an MMP twin carboxylate based inhibitor LC20 in complex with the MMP-9 catalytic domain
Biology and Chemistry Report
4HMA
  •   Structure Details   Hide

    Structure Keywords

    Keywords Hydrolase/Hydrolase Inhibitor
    Text HYDROLASE/TWIN INHIBITOR, Zincin-like, Gelatinase, Collagenase (Catalytic Domain), Hydrolase-Hydrolase Inhibitor complex

    Polymeric Molecules

    Chain A,B
    Description Matrix metalloproteinase-9 
    Fragment MMP-9 catalytic domain 107-215,391-443 
    Mutation V391Q E402Q 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 17933.0 
    Source Method genetically manipulated  
    Entity Name MMP-9, 92 kDa gelatinase, 92 kDa type IV collagenase, Gelatinase B, GELB, 67 kDa matrix metalloproteinase-9, 82 kDa matrix metalloproteinase-9 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    0ZD  N,N'-bis(2-[(biphenyl-4ylsulfonyl)[(2R)-1-hydroxy-3-methyl-1-oxobutan-2-yl]-amino]ethyl)benzene-1,3-dicarboxamide  C46 H50 N4 O10 S2   883.04  View 
    CA  CALCIUM ION  Ca   40.08  View 
    GOL  GLYCEROL  C3 H8 O3   92.09  View 
    MLT  D-MALATE  C4 H6 O5   134.09  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 MMP9_HUMAN P14780     

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B  3.4.24.35      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    1503   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. 
    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. 
    50900   Leukocyte Migration  The Movement of a Leukocyte Within or Between Different Tissues and Organs of the Body. 
    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  
    Details Construct: 110 216 and 392 444 Mutagenesis: Glu402gln Structure: Renumbered Omitting Missing Domain.
    Gene clg4b, mmp9
    Host Scientific Name Escherichia coli  
    Host Strain Bl21 (de3 Star)
    Host Vector Type Pt7 Promoter
    Host Plasmid Name pET-14b


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    20 20q13.12 4318     matrix metallopeptidase 9 MMP9    

    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
    rs202158739 LS-SNP   dbSNP   A 115 K - > R Coil 31% (Intermediate) 20 44638710
    rs200144358 LS-SNP   dbSNP   A 125 I - > N Beta Ladder 4% (Buried) 20 44639124
    rs3918252 LS-SNP   dbSNP   A 127 N - > K Coil 39% (Exposed) 20 44639131
    rs193209205 LS-SNP   dbSNP   A 133 P - > S Coil 60% (Exposed) 20 44639147
    rs200637345 LS-SNP   dbSNP   A 134 R - > W Helix 61% (Exposed) 20 44639150
    rs146456046 LS-SNP   dbSNP   A 138 D - > G Helix 20% (Intermediate) 20 44639163
    rs199948478 LS-SNP   dbSNP   A 144 A - > S Helix 0% (Buried) 20 44639180
    rs201130037 LS-SNP   dbSNP   A 146 A - > V Helix 54% (Exposed) 20 44639187
    rs143024943 LS-SNP   dbSNP   A 155 T - > I Beta Ladder 39% (Exposed) 20 44639214
    rs8125581 LS-SNP   dbSNP   A 165 D - > N Bend 19% (Intermediate) 20 44639243 NULL
    rs202214757 LS-SNP   dbSNP   A 173 A - > E Bend 25% (Intermediate) 20 44639268
    rs141088574 LS-SNP   dbSNP   A 179 Y - > H Coil 64% (Exposed) 20 44639575 NULL
    rs199676062 LS-SNP   dbSNP   A 180 P - > L Coil 55% (Exposed) 20 44639579
    rs201932479 LS-SNP   dbSNP   A 183 G - > E Bend 29% (Intermediate) 20 44639588 NULL
    rs55789927 LS-SNP   dbSNP   A 187 L - > FV Coil 26% (Intermediate) 20 44639599 NULL
    rs139218878 LS-SNP   dbSNP   A 208 E - > Q Bend 2% (Buried) 20 44639662 NULL
    rs199602749 LS-SNP   dbSNP   A 213 G - > D Bend 45% (Exposed) 20 44639678
    rs200848405 LS-SNP   dbSNP   A 219 P - > L Beta Ladder 4% (Buried) 20 44639788
    rs143230916 LS-SNP   dbSNP   A 224 N - > Y Helix 0% (Buried) 20 44639802
    rs202205222 LS-SNP   dbSNP   A 235 I - > V Coil 60% (Exposed) 20 44639835 NULL
    rs28763886 LS-SNP   dbSNP   A 239 R - > H Coil 45% (Exposed) 20 44639848
    rs200507335 LS-SNP   dbSNP   A 239 R - > S Coil 45% (Exposed) 20 44639847
    rs199564350 LS-SNP   dbSNP   A 240 S - > C Turn 44% (Exposed) 20 44639851
    rs200792951 LS-SNP   dbSNP   A 247 D - > E Bend 32% (Intermediate) 20 44639873 NULL
    rs41529445 LS-SNP   dbSNP   A 258 T - > I Helix 87% (Exposed) 20 44639905
    rs200516594 LS-SNP   dbSNP   A 259 T - > M Helix 37% (Exposed) 20 44639908
    rs144229833 LS-SNP   dbSNP   A 261 N - > S Helix 27% (Intermediate) 20 44639914
    rs148726595 LS-SNP   dbSNP   A 262 Y - > C Helix 62% (Exposed) 20 44639917