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Crystal structure of human protease-activated receptor 1 (PAR1) bound with antagonist vorapaxar at 2.2 angstrom
Biology and Chemistry Report
3VW7
  •   Structure Details   Hide

    Structure Keywords

    Keywords Signaling protein/antagonist
    Text High resolution structure, protease-activated receptor 1, inactive conformation, antagonist vorapaxar, G protein-coupled receptor, signaling protein, membrane protein, thrombin receptor-antagonist complex, Signaling protein-antagonist complex

    Polymeric Molecules

    Chain A
    Description Proteinase-activated receptor 1, Lysozyme 
    Mutation N250G, N259S, D1020N, C1054T, C1097A 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 54339.5 
    Source Method genetically manipulated  
    Entity Name PAR-1, Coagulation factor II receptor, Thrombin receptor, Endolysin, Lysis protein, Muramidase 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    CL  CHLORIDE ION  Cl   35.45  View 
    NA  SODIUM ION  Na   22.99  View 
    OLC  (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate  C21 H40 O4   356.54  View 
    VPX  ethyl [(1R,3aR,4aR,6R,8aR,9S,9aS)-9-{(E)-2-[5-(3-fluorophenyl)pyridin-2-yl]ethenyl}-1-methyl-3-oxododecahydronaphtho[2,3-c]furan-6-yl]carbamate  C29 H33 F N2 O4   492.58  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A ENLYS_BPT4 P00720     
    A PAR1_HUMAN P25116     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    3.2.1.17      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    7186   G Protein Coupled Receptor Signaling Pathway  A Series of Molecular Signals That Proceeds with an Activated Receptor Promoting the Exchange of GDP For GTP On the Alpha Subunit of an Associated Heterotrimeric G Protein Complex. the GTP Bound Activated Alpha G Protein Then Dissociates From the Beta and Gamma Subunits to Further Transmit the Signal Within the Cell. the Pathway Begins with Receptor Ligand Interaction or For Basal Gpcr Signaling the Pathway Begins with the Receptor Activating Its G Protein in the Absence of an Agonist and Ends with Regulation of a Downstream Cellular Process E.g. Transcription. 
    8152   Metabolic Process  The Chemical Reactions and Pathways Including Anabolism and Catabolism by Which Living Organisms Transform Chemical Substances. Metabolic Processes Typically Transform Small Molecules But Also Include Macromolecular Processes Such As DNA Repair and Replication and Protein Synthesis and Degradation. 
    9253   Peptidoglycan Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of Peptidoglycans Any of a Class of Glycoconjugates Found in Bacterial Cell Walls. 
    16998   Cell Wall Macromolecule Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of Macromolecules That Form Part of a Cell Wall. 
    19076   Viral Release From Host Cell  The Dissemination of Mature Viral Particles From the Host Cell E.g. by Cell Lysis or the Budding of Virus Particles From the Cell Membrane. 
    19835   Cytolysis  The Rupture of Cell Membranes and the Loss of Cytoplasm. 
    42742   Defense Response to Bacterium  Reactions Triggered in Response to the Presence of a Bacterium That Act to Protect the Cell or Organism. 
    16021   Integral Component of Membrane  The Component of a Membrane Consisting of Gene Products and Protein Complexes That Have Some Part That Penetrates At Least One Leaflet of the Membrane Bilayer. This Component Includes Gene Products That Are Buried in the Bilayer with No Exposure Outside the Bilayer. 
    30430   Host Cell Cytoplasm  The Cytoplasm of a Host Cell. 
    3796   Lysozyme Activity  Catalysis of the Hydrolysis of the Beta (1 >4) Linkages Between N Acetylmuramic Acid and N Acetyl D Glucosamine Residues in a Peptidoglycan and Between N Acetyl D Glucosamine Residues in Chitodextrins. 
    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. 
    4930   G Protein Coupled Receptor Activity  Combining with an Extracellular Signal and Transmitting the Signal Across the Membrane by Activating an Associated G Protein; Promotes the Exchange of GDP For GTP On the Alpha Subunit of a Heterotrimeric G Protein Complex. 
    16787   Hydrolase Activity  Catalysis of the Hydrolysis of Various Bonds E.g. C O C N C C Phosphoric Anhydride Bonds Etc. Hydrolase Is the Systematic Name For Any Enzyme of EC Class 3. 
    16798   Hydrolase Activity Acting On Glycosyl Bonds  Catalysis of the Hydrolysis of Any Glycosyl Bond. 


    Protein Analyses

    Measured Binding Affinities   

     
  •   Gene Details   Hide

    Genetic Source

    Chain A
    Common Name Human
    Scientific Name Homo sapiens, enterobacteria phage t4, homo sapiens  
    Host Scientific Name Spodoptera frugiperda  
    Host Vector Type Baculovirus


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    5 5q13 2149     coagulation factor II (thrombin) receptor F2R    

    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
    rs142195677 LS-SNP   dbSNP   A 115 V - > A Helix 51% (Exposed) 5 76028394 OLC
    rs145788708 LS-SNP   dbSNP   A 122 M - > V Helix 55% (Exposed) 5 76028414 OLC
    rs138496271 LS-SNP   dbSNP   A 131 M - > T 3/10 Helix 24% (Intermediate) 5 76028442
    rs5893 LS-SNP   dbSNP   A 166 S - > G Bend 0% (Buried) 5 76028546
    rs2230849 LS-SNP   dbSNP   A 187 Y - > N Helix 1% (Buried) 5 76028609 VPX
    rs143981953 LS-SNP   dbSNP   A 240 K - > R Bend 39% (Exposed) 5 76028769 OLC
    rs2227832 LS-SNP   dbSNP   A 257 V - > L Bend 18% (Intermediate) 5 76028819 VPX
    rs144447562 LS-SNP   dbSNP   A 266 Y - > C Helix 88% (Exposed) 5 76028847
    rs1055103 LS-SNP   dbSNP   A 268 A - > P Helix 8% (Buried) 5 76028852
    rs139787379 LS-SNP   dbSNP   A 281 V - > LM Helix 48% (Exposed) 5 76028891 OLC
    rs142662743 LS-SNP   dbSNP   A 288 V - > A Helix 58% (Exposed) 5 76028913 OLC
    rs142652494 LS-SNP   dbSNP   A 310 R - > Q Helix 14% (Intermediate) 5 76028979
    rs17849599 LS-SNP   dbSNP   A 335 A - > V Helix 9% (Intermediate) 5 76029054
    rs111993668 LS-SNP   dbSNP   A 349 A - > V Helix 25% (Intermediate) 5 76029096 VPX,OLC
    rs140912041 LS-SNP   dbSNP   A 355 L - > F Helix 35% (Intermediate) 5 76029113 OLC
    rs150193057 LS-SNP   dbSNP   A 378 C - > G Coil 105% (Exposed) 5 76029182