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An Information Portal to 105097 Biological Macromolecular Structures

Human Thrombin in complex with MI354
Biology and Chemistry Report
3RM0
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE/HYDROLASE INHIBITOR
    Text Serine Protease, Kringle, Hydrolase, Blood Coagulation, Blood Clotting, Convertion of Fibrinogen to Fibrin, Hirudin, Glycosylation, Blood, HYDROLASE-HYDROLASE INHIBITOR complex

    Polymeric Molecules

    Chain L
    Description Thrombin Light Chain 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 4096.6 
    Source Method natural source  
    Chain H
    Description Thrombin Heavy Chain 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 29780.4 
    Source Method natural source  
    Chain I
    Description Hirudin variant-2 
    Fragment residues in UNP 60-72 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polypeptide(L) 
    Formula Weight 1662.7 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    GOL  GLYCEROL  C3 H8 O3   92.09  View 
    NA  SODIUM ION  Na   22.99  View 
    NAG  N-ACETYL-D-GLUCOSAMINE  C8 H15 N O6   221.21  View 
    PO4  PHOSPHATE ION  O4 P   94.97  View 
    S54  N-(benzylsulfonyl)-D-valyl-N-(4-carbamimidoylbenzyl)-L-prolinamide  C25 H33 N5 O4 S   499.63  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    H THRB_HUMAN P00734     
    I HIRV2_HIRME P09945     
    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
    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 I
    GO ID   Ontology GO Term Definition
    4867   Serine Type Endopeptidase Inhibitor Activity  Stops Prevents or Reduces the Activity of Serine Type Endopeptidases Enzymes That Catalyze the Hydrolysis of Nonterminal Peptide Bonds in a Polypeptide Chain; a Serine Residue (and a Histidine Residue) Are At the Active Center of the Enzyme. 
    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 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
    rs121918481 LS-SNP   dbSNP   H 32 M - > T Beta Ladder 0% (Buried) 11 46749554
    rs147456134 LS-SNP   dbSNP   H 35 R - > W Beta Ladder 29% (Intermediate) 11 46749562
    rs5897 LS-SNP   dbSNP   H 38 P - > T Beta Ladder 34% (Intermediate) 11 46749571
    rs121918479 LS-SNP   dbSNP   H 77 R - > C Coil 14% (Intermediate) 11 46749688
    rs121918485 LS-SNP   dbSNP   H 77 R - > H Coil 14% (Intermediate) 11 46749689
    rs150569436 LS-SNP   dbSNP   H 78 I - > T Turn 84% (Exposed) 11 46749692
    rs121918482 LS-SNP   dbSNP   H 83 R - > H Beta Ladder 11% (Intermediate) 11 46749707
    rs143498218 LS-SNP   dbSNP   H 108 R - > Q Beta Ladder 2% (Buried) 11 46750282
    rs139552841 LS-SNP   dbSNP   H 108 R - > W Beta Ladder 2% (Buried) 11 46750281
    rs121918478 LS-SNP   dbSNP   H 113 R - > W Coil 68% (Exposed) 11 46750296
    rs202076180 LS-SNP   dbSNP   H 140 T - > M Beta Ladder 0% (Buried) 11 46750378
    rs202003146 LS-SNP   dbSNP   H 152 R - > Q Coil 4% (Buried) 11 46750956
    rs140404878 LS-SNP   dbSNP   H 162 T - > M Beta 7% (Buried) 11 46750986
    rs199772906 LS-SNP   dbSNP   H 166 N - > K Helix 62% (Exposed) 11 46750999
    rs144011338 LS-SNP   dbSNP   H 166 N - > S Helix 62% (Exposed) 11 46750998
    rs144885724 LS-SNP   dbSNP   H 168 G - > V Helix 3% (Buried) 11 46751004
    rs201541084 LS-SNP   dbSNP   H 186 P - > L 3/10 Helix 56% (Exposed) 11 46751058
    rs143064939 LS-SNP   dbSNP   H 195 R - > L Turn 17% (Intermediate) 11 46751085 S54