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New Pharmacophore for Serine Protease Inhibition Revealed by Crystal Structure of Human Urokinase-type Plasminogen Activator Complexed with a Cyclic Peptidyl Inhibitor, upain-1
Biology and Chemistry Report
2NWN
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE
    Text urokinase-type plasminogen activator, peptidyl inhibitor, pharmacophore, Structural Genomics, Structural Genomics Consortium, SGC, HYDROLASE

    Polymeric Molecules

    Chain A
    Description Plasminogen activator, urokinase 
    Fragment C-terminal domain, residues 16-250 
    Mutation C122A/N145Q 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 28442.6 
    Source Method genetically manipulated  
    Entity Name uPA 
    Chain B
    Description upain-1 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 1494.7 
    Source Method synthetic  

     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A UROK_HUMAN P00749     

    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)
    3.4.21.73        
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    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. 
    3824   Catalytic Activity  Catalysis of a Biochemical Reaction At Physiological Temperatures. in Biologically Catalyzed Reactions the Reactants Are Known As Substrates and the Catalysts Are Naturally Occurring Macromolecular Substances Known As Enzymes. Enzymes Possess Specific Binding Sites For Substrates and Are Usually Composed Wholly or Largely of Protein But RNA That Has Catalytic Activity (ribozyme) Is Often Also Regarded As Enzymatic. 
    4252   Serine Type Endopeptidase Activity  Catalysis of the Hydrolysis of Internal Alpha Peptide Bonds in a Polypeptide Chain by a Catalytic Mechanism That Involves a Catalytic Triad Consisting of a Serine Nucleophile That Is Activated by a Proton Relay Involving an Acidic Residue (e.g. Aspartate or Glutamate) and a Basic Residue (usually Histidine). 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Host Scientific Name Pichia pastoris  
    Host Genus Pichia
    Host Strain X 33
    Host Vector Type Plasmid
    Host Plasmid Name pPICZALPHAA


    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
    rs140333999 LS-SNP   dbSNP   A 17 I - > F Beta 14% (Intermediate) 10 75673374
    rs145865648 LS-SNP   dbSNP   A 31 A - > V Beta Ladder 0% (Buried) 10 75673417
    rs145070893 LS-SNP   dbSNP   A 38 R - > W Coil 67% (Exposed) 10 75673437
    rs1050120 LS-SNP   dbSNP   A 51 I - > M Beta Ladder 11% (Intermediate) 10 75673478
    rs148318390 LS-SNP   dbSNP   A 58 S - > C 3/10 Helix 0% (Buried) 10 75673497
    rs201795845 LS-SNP   dbSNP   A 59 A - > T Turn 0% (Buried) 10 75673500
    rs2227567 LS-SNP   dbSNP   A 68 K - > Q Beta Ladder 0% (Buried) 10 75673748
    rs192623012 LS-SNP   dbSNP   A 69 K - > N Bend 0% (Buried) 10 75673753
    rs150389556 LS-SNP   dbSNP   A 73 I - > V Bend 5% (Buried) 10 75673763
    rs201687228 LS-SNP   dbSNP   A 106 T - > M Beta Ladder 0% (Buried) 10 75673863
    rs183371156 LS-SNP   dbSNP   A 110 H - > Y Coil 7% (Buried) 10 75673874
    rs34930250 LS-SNP   dbSNP   A 119 R - > H Coil 43% (Exposed) 10 75674549
    rs149650503 LS-SNP   dbSNP   A 138 P - > L Beta Ladder 0% (Buried) 10 75674606
    rs146899371 LS-SNP   dbSNP   A 162 D - > N Beta Ladder 3% (Buried) 10 75675011
    rs139271997 LS-SNP   dbSNP   A 166 P - > L Helix 84% (Exposed) 10 75675024
    rs72816325 LS-SNP   dbSNP   A 187 Y - > H Coil 72% (Exposed) 10 75675086
    rs147382460 LS-SNP   dbSNP   A 191 E - > D Coil 0% (Buried) 10 75675100
    rs199520267 LS-SNP   dbSNP   A 193 T - > N Turn 0% (Buried) 10 75675105
    rs150522269 LS-SNP   dbSNP   A 224 R - > C Beta Ladder 20% (Intermediate) 10 75676186
    rs3805118 LS-SNP   dbSNP   A 235 R - > L Helix 10% (Intermediate) 10 75676220