High affinity inhibitor of human thrombin
3UTU
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Hydrolase/hydrolase Inhibitor
    Structure Weight: 36023.59
    Molecule: Thrombin light chain
    Polymer: 1 Type: protein Length: 36
    Chains: L
    EC#: 3.4.21.5   
    Organism: Homo sapiens
    Gene Name: Gene View for F2
    UniProtKB: Search PDB | P00734   Protein Feature View
    Molecule: Thrombin heavy chain
    Polymer: 2 Type: protein Length: 259
    Chains: H
    EC#: 3.4.21.5   
    Organism: Homo sapiens
    Gene Name: Gene View for F2
    UniProtKB: Search PDB | P00734   Protein Feature View
    Molecule: Hirudin variant-1
    Polymer: 3 Type: protein Length: 11
    Chains: I
    Fragment: UNP RESIDUES 54-64
    Organism: Hirudo medicinalis
    UniProtKB: Search PDB | P01050   Protein Feature View
     
  •   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
    2zfo    
    2ziq    
    3dt0    
    3dux    
    3eqo    
    3f68    
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    1TS
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    1TS C32 H34 Cl N7 O6 S
    (2S)-N-[(4-carbamimidoylphenyl)methyl]-1- [(2S)-2-[(3-chloro-4-methoxybenzene)sulfonamido]- 3-{[(4-cyanophenyl)methyl]carbamoyl}propanoyl]pyrrolidine- 2-carboxamide
    NA
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    NA Na
    SODIUM ION
     
  •   External Ligand Annotations Hide
    Identifier   Binding Affinity (Sequence Identity %)
    1TS
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    1TS
    N/Ain BindingDB
    Ki: 0.012 nM - data from BindingMOAD  
    Ki: 0.012 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:   Baum, B.,  Steinmetzer, T.,  Heine, A.,  Klebe, G.

    Deposition:   2011-11-26
    Release:   2012-08-29
    Last Modified (REVDAT):   2014-03-12
     
  •   Revision History    Hide
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    2014-03-12
    Citation
    2013-03-13
    Other
    2012-12-12
    Other
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   1.55
    R-Value: 0.244 (obs.)
    R-Free: 0.271
    Space Group: C 1 2 1
    Unit Cell:
      Length [Å] Angles [°]
    a = 70.77 α = 90.00 
    b = 71.35 β = 100.65 
    c = 72.39 γ = 90.00