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An Information Portal to 105339 Biological Macromolecular Structures

Thrombin Inhibition
Biology and Chemistry Report
3F68
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE/HYDROLASE INHIBITOR
    Text Blood Clotting, Hydrolase Inhibitor, Acute phase, Blood coagulation, Gamma-carboxyglutamic acid, Glycoprotein, Hydrolase, Kringle, Protease, Secreted, Serine protease, Protease inhibitor, Serine protease inhibitor, Sulfation, HYDROLASE-HYDROLASE INHIBITOR COMPLEX

    Polymeric Molecules

    Chain L
    Description Prothrombin 
    Fragment UNP residues 328-363, Thrombin light chain 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 4096.6 
    Source Method natural source  
    Entity Name Coagulation factor II, Activation peptide fragment 1, Activation peptide fragment 2, Thrombin light chain, Thrombin heavy chain 
    Chain H
    Description Prothrombin 
    Fragment UNP residues 364-622, Thrombin heavy chain 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 29780.4 
    Source Method natural source  
    Entity Name Coagulation factor II, Activation peptide fragment 1, Activation peptide fragment 2, Thrombin light chain, Thrombin heavy chain 
    Chain I
    Description Hirudin variant-2 
    Fragment UNP residues 61-71 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polypeptide(L) 
    Formula Weight 1420.5 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    91U  N-acetyl-3-cyclohexyl-D-alanyl-N-(3-chlorobenzyl)-L-prolinamide  C23 H32 Cl N3 O3   433.97  View 
    NA  SODIUM ION  Na   22.99  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    L THRB_HUMAN P00734     

    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)
    3.4.21.5        
    3.4.21.5        
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain H
    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. 
    7596   Blood Coagulation  The Sequential Process in Which the Multiple Coagulation Factors of the Blood Interact Ultimately Resulting in the Formation of an Insoluble Fibrin Clot; It May Be Divided Into Three Stages: Stage 1 the Formation of Intrinsic and Extrinsic Prothrombin Converting Principle; Stage 2 the Formation of Thrombin; Stage 3 the Formation of Stable Fibrin Polymers. 
    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). 
    5509   Calcium Ion Binding  Interacting Selectively and Non Covalently with Calcium Ions (ca2+). 
    Chain L
    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. 
    7596   Blood Coagulation  The Sequential Process in Which the Multiple Coagulation Factors of the Blood Interact Ultimately Resulting in the Formation of an Insoluble Fibrin Clot; It May Be Divided Into Three Stages: Stage 1 the Formation of Intrinsic and Extrinsic Prothrombin Converting Principle; Stage 2 the Formation of Thrombin; Stage 3 the Formation of Stable Fibrin Polymers. 
    5576   Extracellular Region  The Space External to the Outermost Structure of a Cell. For Cells Without External Protective or External Encapsulating Structures This Refers to Space Outside of the Plasma Membrane. This Term Covers the Host Cell Environment Outside an Intracellular Parasite. 
    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). 


    Protein Analyses

    Measured Binding Affinities   

     
  •   Gene Details   Hide

    Natural Source

    Chain I
    Scientific Name Hirudo medicinalis  
    Chain H
    Common Name Human
    Scientific Name Homo sapiens  
    Chain L
    Common Name Human
    Scientific Name Homo sapiens  

    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    11 11p11 2147     coagulation factor II (thrombin) F2    

    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
    rs121918483 LS-SNP   dbSNP   L 10 E - > K 3/10 Helix 61% (Exposed) 11 46748284