POP-OUT | CLOSE
Thrombin Inhibitor Complex
1YPG
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Blood Clotting/hydrolase Inhibitor
    Structure Weight: 34604.93
    Molecule: Thrombin light chain
    Polymer: 1 Type: protein Length: 27
    Chains: L
    EC#: 3.4.21.5   
    Organism Homo sapiens
    Gene Name 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 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

    Download full validation report    

     
  •   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
    1Y3V  Trypsin Inhibitor Complex with the same Inhibitor 
    1YP9  Trypsin Inhibitor Complex with different Inhibitor 
    1YPE  Thrombin Inhibitor Complex with different Inhibitor 
    1YPJ  Thrombin Inhibitor Complex with different Inhibitor 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    UIR
    Search 
    Download 
    UIR C27 H30 N4 O3
    (1R,3AS,4R,8AS,8BR)-4-(2-BENZO[1,3]DIOXOL- 5-YL-1-CYCLOPROPYL-3-OXO-DECAHYDRO-PYRROLO[3,4- A]PYRROLIZIN-4-YL)-BENZAMIDINE
    UIR:1YPG
     
  •   External Ligand Annotations Hide
    Identifier   Binding Affinity (Sequence Identity %)
    UIR
    Search 
    Download 
    UIR
    N/Ain BindingDB
    Ki: 10 nM - data from BindingMOAD  
    Ki: 10 nM - data from PDBbind  
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    TYS
    Search 
    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
Downloadable viewers:
 
 
 
  •   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
    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
    2011-07-13
    Polymer description
    2011-07-13
    Version format compliance
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   1.80
    R-Value: 0.184 (obs.)
    R-Free: 0.248
    Space Group: C 2
    Unit Cell:
      Length [Å] Angles [°]
    a = 70.99 α = 90.00 
    b = 71.62 β = 100.60 
    c = 72.29 γ = 90.00