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An Information Portal to 105097 Biological Macromolecular Structures

Does a Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases.
Biology and Chemistry Report
2W0D
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE
    Text GLYCOPROTEIN, METAL-BINDING, METALLOPROTEASE, SECRETED, HYDROLASE, HYDROXAMATE, EXTRACELLULAR MATRIX, COPD, MMP-12, ZYMOGEN

    Polymeric Molecules

    Chain A,B,C,D
    Description MACROPHAGE METALLOELASTASE 
    Fragment CATALYTIC DOMAIN, RESIDUES 106-263 
    Mutation YES 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 18280.6 
    Source Method genetically manipulated  
    Entity Name MME, MATRIX METALLOPROTEINASE-12, MACROPHAGE ELASTASE, ME, HME, MMP-12 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    ACT  ACETATE ION  C2 H3 O2   59.04  View 
    CA  CALCIUM ION  Ca   40.08  View 
    CGS  N-HYDROXY-2(R)-[[(4-METHOXYPHENYL)SULFONYL](3-PICOLYL)AMINO]-3-METHYLBUTANAMIDE HYDROCHLORIDE  C18 H23 N3 O5 S   393.46  View 
    CL  CHLORIDE ION  Cl   35.45  View 
    NA  SODIUM ION  Na   22.99  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 B2R9X8     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc Catalytic Site(s)
    A B C D  3.4.24.65        
    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  
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Pet11a
    Host Vector Type Plasmid


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    11 11q22.3 4321     matrix metallopeptidase 12 (macrophage elastase) 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 64% (Exposed) 11 102743607
    rs61730844 LS-SNP   dbSNP   A 127 R - > H Helix 48% (Exposed) 11 102742653
    rs202141359 LS-SNP   dbSNP   A 129 D - > V Helix 36% (Exposed) 11 102742647
    rs201046473 LS-SNP   dbSNP   A 130 V - > A Helix 0% (Buried) 11 102742644
    rs180918521 LS-SNP   dbSNP   A 135 R - > Q Helix 53% (Exposed) 11 102742629
    rs200079972 LS-SNP   dbSNP   A 139 Q - > P Helix 39% (Exposed) 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 2% (Buried) 11 102742548
    rs61730845 LS-SNP   dbSNP   A 165 R - > H Coil 49% (Exposed) 11 102742539 CA
    rs201575382 LS-SNP   dbSNP   A 165 R - > C Coil 49% (Exposed) 11 102742540 CA
    rs200263416 LS-SNP   dbSNP   A 168 H - > Y Coil 4% (Buried) 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 9% (Intermediate) 11 102738796
    rs202042208 LS-SNP   dbSNP   A 218 H - > Y Helix 20% (Intermediate) 11 102738774 ZN,CGS
    rs200751457 LS-SNP   dbSNP   A 219 E - > *K Helix 2% (Buried) 11 102738771
    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 CGS
    rs183458117 LS-SNP   dbSNP   A 249 R - > CS Coil 76% (Exposed) 11 102738681
    rs201987840 LS-SNP   dbSNP   A 249 R - > H Coil 76% (Exposed) 11 102738680