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Crystal structure of an MMP twin inhibitor complexing two MMP-9 catalytic domains
Biology and Chemistry Report
4H2E
  •   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 human MMP-9 catalytic domain wild-type 
    Fragment unp residues 110-214 and 391-444 
    Mutation E402Q 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 18338.5 
    Source Method genetically manipulated  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    0Y3  N,N'-bis(4-{[(3R)-3-[(biphenyl-4-ylsulfonyl)(propan-2-yloxy)amino]-4-(hydroxyamino)-4-oxobutyl]amino}-4-oxobutyl)benzene-1,3-dicarboxamide  C54 H66 N8 O14 S2   1115.28  View 
    ACT  ACETATE ION  C2 H3 O2   59.04  View 
    BCN  BICINE  C6 H13 N O4   163.17  View 
    CA  CALCIUM ION  Ca   40.08  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,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  
    Gene mmp9, clg4b
    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
    rs200316960 LS-SNP   dbSNP   A 109 T - > I Beta 23% (Intermediate) 20 44638692
    rs202158739 LS-SNP   dbSNP   A 115 K - > R Coil 34% (Intermediate) 20 44638710
    rs200144358 LS-SNP   dbSNP   A 125 I - > N Beta Ladder 6% (Buried) 20 44639124
    rs3918252 LS-SNP   dbSNP   A 127 N - > K Coil 34% (Intermediate) 20 44639131
    rs193209205 LS-SNP   dbSNP   A 133 P - > S Coil 60% (Exposed) 20 44639147
    rs200637345 LS-SNP   dbSNP   A 134 R - > W Helix 57% (Exposed) 20 44639150
    rs146456046 LS-SNP   dbSNP   A 138 D - > G Helix 15% (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 50% (Exposed) 20 44639187
    rs143024943 LS-SNP   dbSNP   A 155 T - > I Beta Ladder 42% (Exposed) 20 44639214
    rs8125581 LS-SNP   dbSNP   A 165 D - > N Bend 25% (Intermediate) 20 44639243 NULL
    rs202214757 LS-SNP   dbSNP   A 173 A - > E Bend 34% (Intermediate) 20 44639268
    rs141088574 LS-SNP   dbSNP   A 179 Y - > H Coil 63% (Exposed) 20 44639575 NULL
    rs199676062 LS-SNP   dbSNP   A 180 P - > L Coil 65% (Exposed) 20 44639579 NULL
    rs201932479 LS-SNP   dbSNP   A 183 G - > E Bend 20% (Intermediate) 20 44639588 NULL
    rs55789927 LS-SNP   dbSNP   A 187 L - > FV Coil 21% (Intermediate) 20 44639599 NULL
    rs139218878 LS-SNP   dbSNP   A 208 E - > Q Bend 1% (Buried) 20 44639662 NULL
    rs199602749 LS-SNP   dbSNP   A 213 G - > D Coil 5% (Buried) 20 44639678
    rs200848405 LS-SNP   dbSNP   A 219 P - > L Beta Ladder 5% (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 10% (Intermediate) 20 44639835
    rs28763886 LS-SNP   dbSNP   A 239 R - > H Coil 25% (Intermediate) 20 44639848
    rs200507335 LS-SNP   dbSNP   A 239 R - > S Coil 25% (Intermediate) 20 44639847
    rs199564350 LS-SNP   dbSNP   A 240 S - > C Turn 51% (Exposed) 20 44639851
    rs200792951 LS-SNP   dbSNP   A 247 D - > E Coil 37% (Exposed) 20 44639873
    rs41529445 LS-SNP   dbSNP   A 258 T - > I Helix 78% (Exposed) 20 44639905
    rs200516594 LS-SNP   dbSNP   A 259 T - > M Helix 9% (Intermediate) 20 44639908
    rs144229833 LS-SNP   dbSNP   A 261 N - > S Helix 12% (Intermediate) 20 44639914
    rs148726595 LS-SNP   dbSNP   A 262 Y - > C Helix 54% (Exposed) 20 44639917
    rs141318648 LS-SNP   dbSNP   A 274 E - > D Coil 0% (Buried) 20 44639954
    rs17576 LS-SNP   dbSNP   A 279 Q - > R Coil 0% (Buried) 20 44640225
    rs201069467 LS-SNP   dbSNP   A 280 D - > G Coil 0% (Buried) 20 44640228
    rs201975453 LS-SNP   dbSNP   A 293 I - > N Coil 0% (Buried) 20 44640267
    rs144098289 LS-SNP   dbSNP   A 296 G - > S Coil 0% (Buried) 20 44640275
    rs201130620 LS-SNP   dbSNP   A 298 S - > C Coil 0% (Buried) 20 44640282
    rs201344509 LS-SNP   dbSNP   A 306 G - > C Coil 0% (Buried) 20 44640305
    rs202151407 LS-SNP   dbSNP   A 320 Y - > N Coil 0% (Buried) 20 44640347
    rs200418910 LS-SNP   dbSNP   A 322 R - > W Coil 0% (Buried) 20 44640353
    rs199569524 LS-SNP   dbSNP   A 327 G - > R Coil 0% (Buried) 20 44640368
    rs200814121 LS-SNP   dbSNP   A 329 C - > S Coil 0% (Buried) 20 44640374
    rs201503729 LS-SNP   dbSNP   A 330 P - > L Coil 0% (Buried) 20 44640378
    rs200477815 LS-SNP   dbSNP   A 332 R - > G Coil 0% (Buried) 20 44640383
    rs199860204 LS-SNP   dbSNP   A 335 S - > L Coil 0% (Buried) 20 44640782
    rs199741040 LS-SNP   dbSNP   A 337 V - > A Coil 0% (Buried) 20 44640788
    rs149701392 LS-SNP   dbSNP   A 337 V - > M Coil 0% (Buried) 20 44640787
    rs201161911 LS-SNP   dbSNP   A 338 M - > T Coil 0% (Buried) 20 44640791
    rs145450508 LS-SNP   dbSNP   A 347 C - > Y Coil 0% (Buried) 20 44640818
    rs200855672 LS-SNP   dbSNP   A 356 K - > E Coil 0% (Buried) 20 44640844
    rs201995611 LS-SNP   dbSNP   A 360 T - > N Coil 0% (Buried) 20 44640857
    rs201492378 LS-SNP   dbSNP   A 362 T - > I Coil 0% (Buried) 20 44640863
    rs202242171 LS-SNP   dbSNP   A 377 S - > L Coil 0% (Buried) 20 44640908
    rs201524123 LS-SNP   dbSNP   A 390 D - > Y Coil 0% (Buried) 20 44640946
    rs200590350 LS-SNP   dbSNP   A 399 A - > V Coil 0% (Buried) 20 44641087
    rs201417784 LS-SNP   dbSNP   A 403 F - > Y Coil 0% (Buried) 20 44641099
    rs201131366 LS-SNP   dbSNP   A 422 M - > R Coil 0% (Buried) 20 44641156
    rs146895638 LS-SNP   dbSNP   A 429 P - > H Coil 0% (Buried) 20 44641177
    rs199893610 LS-SNP   dbSNP   A 434 D - > N Coil 0% (Buried) 20 44641191
    rs201169008 LS-SNP   dbSNP   A 438 G - > A Coil 0% (Buried) 20 44641204
    rs147960167 LS-SNP   dbSNP   A 440 R - > Q Coil 0% (Buried) 20 44641210
    rs141702644 LS-SNP   dbSNP   A 441 H - > L Coil 0% (Buried) 20 44641213
    rs6017725 LS-SNP   dbSNP   A 447 P - > L Coil 0% (Buried) 20 44641903
    rs6032623 LS-SNP   dbSNP   A 449 P - > L Coil 0% (Buried) 20 44641909
    rs200271676 LS-SNP   dbSNP   A 450 E - > G Coil 0% (Buried) 20 44641912
    rs201191171 LS-SNP   dbSNP   A 452 R - > Q Coil 0% (Buried) 20 44641918
    rs147087483 LS-SNP   dbSNP   A 459 P - > S Coil 0% (Buried) 20 44641938
    rs200236055 LS-SNP   dbSNP   A 459 P - > L Coil 0% (Buried) 20 44641939