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X-ray structure of the complex between human alpha thrombin and thrombin binding aptamer in the presence of potassium ions
Biology and Chemistry Report
4DII
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE/HYDROLASE INHIBITOR/DNA
    Text protein-DNA complex, serine protease, blood coagulation, aptamer, hydrolase-hydrolase inhibitor-DNA complex, serine protease fold, DNA aptamer, blood, G-quadruplex

    Polymeric Molecules

    Chain L
    Description Prothrombin 
    Fragment Light chain (UNP Residues 328-363) 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 4096.6 
    Source Method natural source  
    Entity Name Coagulation factor II, Thrombin light chain 
    Chain H
    Description Prothrombin 
    Fragment Heavy chain (UNP Residues 364-622) 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 29780.4 
    Source Method natural source  
    Entity Name Coagulation factor II, Thrombin heavy chain 
    Chain D
    Description Thrombin binding aptamer 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 4743.1 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    0G6  D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide  C21 H34 Cl N6 O3   453.99  View 
    CL  CHLORIDE ION  Cl   35.45  View 
    POTASSIUM ION  K   39.10  View 
    NA  SODIUM ION  Na   22.99  View 
    NAG  N-ACETYL-D-GLUCOSAMINE  C8 H15 N O6   221.21  View 
    ZN  ZINC ION  Zn   65.41  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    H THRB_HUMAN P00734     
    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      
     
  •   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
    rs121918483 LS-SNP   dbSNP   L 10 E - > K 3/10 Helix 63% (Exposed) 11 46748284