POP-OUT | CLOSE
 
Crystal Structure of Human Alpha Thrombin in Complex with a 27-mer Aptamer Bound to Exosite II
Biology and Chemistry Report
4I7Y
  •   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, duplex-quadruplex junction

    Polymeric Molecules

    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, Activation peptide fragment 1, Activation peptide fragment 2, Thrombin heavy chain 
    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, Activation peptide fragment 1, Activation peptide fragment 2, Thrombin light chain 
    Chain D
    Description DNA (27-MER) 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 8485.5 
    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 
    NA  SODIUM ION  Na   22.99  View 
    NAG  N-ACETYL-D-GLUCOSAMINE  C8 H15 N O6   221.21  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 L
    Common Name Human
    Scientific Name Homo sapiens  
    Chain H
    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
    rs121918481 LS-SNP   dbSNP   H 32 M - > T Beta Ladder 0% (Buried) 11 46749554
    rs147456134 LS-SNP   dbSNP   H 35 R - > W Beta Ladder 35% (Intermediate) 11 46749562
    rs147456134 LS-SNP   dbSNP   H 35 R - > W Beta Ladder 35% (Intermediate) 11 46749562
    rs5897 LS-SNP   dbSNP   H 38 P - > T Turn 71% (Exposed) 11 46749571
    rs5897 LS-SNP   dbSNP   H 38 P - > T Turn 71% (Exposed) 11 46749571
    rs121918485 LS-SNP   dbSNP   H 77 R - > H Coil 14% (Intermediate) 11 46749689
    rs121918479 LS-SNP   dbSNP   H 77 R - > C Coil 14% (Intermediate) 11 46749688
    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 89% (Exposed) 11 46749692
    rs150569436 LS-SNP   dbSNP   H 78 I - > T Turn 89% (Exposed) 11 46749692
    rs121918482 LS-SNP   dbSNP   H 83 R - > H Beta Ladder 8% (Buried) 11 46749707
    rs121918482 LS-SNP   dbSNP   H 83 R - > H Beta Ladder 8% (Buried) 11 46749707
    rs143498218 LS-SNP   dbSNP   H 108 R - > Q Beta Ladder 0% (Buried) 11 46750282
    rs143498218 LS-SNP   dbSNP   H 108 R - > Q Beta Ladder 0% (Buried) 11 46750282
    rs139552841 LS-SNP   dbSNP   H 108 R - > W Beta Ladder 0% (Buried) 11 46750281
    rs139552841 LS-SNP   dbSNP   H 108 R - > W Beta Ladder 0% (Buried) 11 46750281
    rs121918478 LS-SNP   dbSNP   H 113 R - > W Coil 80% (Exposed) 11 46750296
    rs121918478 LS-SNP   dbSNP   H 113 R - > W Coil 80% (Exposed) 11 46750296
    rs202076180 LS-SNP   dbSNP   H 140 T - > M Beta Ladder 1% (Buried) 11 46750378
    rs202076180 LS-SNP   dbSNP   H 140 T - > M Beta Ladder 1% (Buried) 11 46750378
    rs202003146 LS-SNP   dbSNP   H 152 R - > Q Coil 5% (Buried) 11 46750956
    rs202003146 LS-SNP   dbSNP   H 152 R - > Q Coil 5% (Buried) 11 46750956
    rs140404878 LS-SNP   dbSNP   H 162 T - > M Beta 7% (Buried) 11 46750986
    rs140404878 LS-SNP   dbSNP   H 162 T - > M Beta 7% (Buried) 11 46750986
    rs144011338 LS-SNP   dbSNP   H 166 N - > S Helix 63% (Exposed) 11 46750998
    rs199772906 LS-SNP   dbSNP   H 166 N - > K Helix 63% (Exposed) 11 46750999
    rs144011338 LS-SNP   dbSNP   H 166 N - > S Helix 63% (Exposed) 11 46750998
    rs199772906 LS-SNP   dbSNP   H 166 N - > K Helix 63% (Exposed) 11 46750999
    rs144885724 LS-SNP   dbSNP   H 168 G - > V Helix 2% (Buried) 11 46751004
    rs144885724 LS-SNP   dbSNP   H 168 G - > V Helix 2% (Buried) 11 46751004
    rs201541084 LS-SNP   dbSNP   H 186 P - > L Turn 47% (Exposed) 11 46751058
    rs201541084 LS-SNP   dbSNP   H 186 P - > L Turn 47% (Exposed) 11 46751058
    rs143064939 LS-SNP   dbSNP   H 195 R - > L Turn 0% (Buried) 11 46751085 NULL
    rs143064939 LS-SNP   dbSNP   H 195 R - > L Turn 0% (Buried) 11 46751085 NULL
    rs121918486 LS-SNP   dbSNP   H 247 D - > E Coil 0% (Buried) 11 46760874
    rs121918486 LS-SNP   dbSNP   H 247 D - > E Coil 0% (Buried) 11 46760874
    rs121918480 LS-SNP   dbSNP   H 253 G - > V Coil 0% (Buried) 11 46760891
    rs121918480 LS-SNP   dbSNP   H 253 G - > V Coil 0% (Buried) 11 46760891
    rs142495261 LS-SNP   dbSNP   H 260 R - > C Coil 0% (Buried) 11 46760911
    rs142495261 LS-SNP   dbSNP   H 260 R - > C Coil 0% (Buried) 11 46760911
    rs74616944 LS-SNP   dbSNP   H 266 Q - > K Coil 0% (Buried) 11 46760929
    rs74616944 LS-SNP   dbSNP   H 266 Q - > K Coil 0% (Buried) 11 46760929