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Thrombin Inhibitor Complex
1YPJ
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Blood Clotting/hydrolase Inhibitor
    Structure Weight: 34594.93
    Molecule: Thrombin light chain
    Polymer: 1 Type: protein Length: 27
    Chains: L
    EC#: 3.4.21.5   
    Organism: Homo sapiens
    Gene Name: Gene View for F2
    UniProtKB: Protein Feature View | Search PDB | P00734  
    Molecule: Thrombin heavy chain
    Polymer: 2 Type: protein Length: 257
    Chains: H
    EC#: 3.4.21.5   
    Organism: Homo sapiens
    Gene Name: Gene View for F2
    UniProtKB: Protein Feature View | Search PDB | P00734  
    Molecule: Hirudin
    Polymer: 3 Type: protein Length: 10
    Chains: I
    Fragment: residues 1-10
    Organism: Hirudo medicinalis
    UniProtKB: Protein Feature View | Search PDB | P28504  
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Homo sapiens   Taxonomy   Common Name: Human  
    Polymer: 2
    Scientific Name: Homo sapiens   Taxonomy   Common Name: Human  
    Polymer: 3
    Scientific Name: Synthetic construct (Hirudo medicinalis)   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    1Y3X  Trypsin Inhibitor Complex with the same Inhibitor 
    1YP9  Trypsin Inhibitor Complex with different Inhibitor 
    1YPE  Thrombin Inhibitor Complex with different Inhibitor 
    1YPG  Thrombin Inhibitor Complex with different Inhibitor 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    UIB
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    UIB C26 H32 N4 O3
    (1R,3AS,4R,8AS,8BR)-4-{5-(PHENYL[1,3]DIOXOL- 5-YLMETHYL)-4-ETHYL-2,3,3-TRIMETHYL-6-OXO- OCTAHYDRO-PYRROLO[3,4-C]PYRROL-1-YL}-BENZAMIDINE
    UIB:1YPJ
     
  •   External Ligand Annotations Hide
    Identifier   Binding Affinity (Sequence Identity %)
    UIB
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    UIB
    N/Ain BindingDB
    Ki: 95 nM - data from BindingMOAD  
    Ki: 95 nM - data from PDBbind  
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    TYS
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    TYS C9 H11 N O6 S TYR lPeptideLinking
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Biological assembly 1 assigned by authors and generated by PISA (software)
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  •   MyPDB Personal Annotations Hide
     
  •   Deposition Summary Hide
    Authors:   Fokkens, J.,  Obst-Sander, U.,  Heine, A.,  Diederich, F.,  Klebe, G.

    Deposition:   2005-01-31
    Release:   2006-01-17
    Last Modified (REVDAT):   2013-11-13
     
  •   Revision History    Hide
    Mouse over text for details
    2013-11-13
    Other
    2013-03-13
    Other
    2012-12-12
    Other
    2011-07-13
    Polymer description
    2011-07-13
    Version format compliance
    2011-07-13
    Atom nomenclature
    2011-07-13
    Binding sites and description
    2011-07-13
    Non-polymer description
    2011-07-13
    Function and keywords
    2011-07-13
    Linkage
    2011-07-13
    Sequence database correspondence
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   1.78
    R-Value: 0.195 (obs.)
    R-Free: 0.239
    Space Group: C 2
    Unit Cell:
      Length [Å] Angles [°]
    a = 70.52 α = 90.00 
    b = 71.81 β = 99.87 
    c = 71.31 γ = 90.00