Thrombin in complex with inhibitor
4BAQ
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Hydrolase
    Structure Weight: 36136.30
    Molecule: THROMBIN LIGHT CHAIN
    Polymer: 1 Type: protein Length: 36
    Chains: A
    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: 259
    Chains: B
    EC#: 3.4.21.5   
    Organism: Homo sapiens
    Gene Name: Gene View for F2
    UniProtKB: Protein Feature View | Search PDB | P00734  
    Molecule: HIRUDIN VARIANT-1
    Polymer: 3 Type: protein Length: 12
    Chains: D
    Fragment: RESIDUES 53-64
    Details: SYNTHETIC C-TERMINAL PEPTIDE 53-64 (WITH SULFATO-TYR63)
    Organism: Hirudo medicinalis
    UniProtKB: Protein Feature View | Search PDB | P01050  
     
  •   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
    4BAH   THROMBIN IN COMPLEX WITH INHIBITOR 
    4BAK   THROMBIN IN COMPLEX WITH INHIBITOR 
    4BAM   THROMBIN IN COMPLEX WITH INHIBITOR 
    4BAN   THROMBIN IN COMPLEX WITH INHIBITOR 
    4BAO   THROMBIN IN COMPLEX WITH INHIBITOR 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    M4Z
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    M4Z C24 H36 N6 O3
    (2S)-N-[(4-carbamimidoylphenyl)methyl]-1- [(2R)-2-cyclohexyl-2-[[2-(ethylamino)-2-oxidanylidene- ethyl]amino]ethanoyl]azetidine-2-carboxamide
    M4Z:4BAQ
    NA
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    NA Na
    SODIUM ION
    NAG
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    NAG C8 H15 N O6
    N-ACETYL-D-GLUCOSAMINE
     
  •   External Ligand Annotations Hide
    Identifier   Binding Affinity (Sequence Identity %)
    M4Z
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    M4Z
    N/Ain BindingDB
    Ki: 0.98 nM - data from BindingMOAD  
    N/Ain 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:   Xue, Y.,  Musil, D.

    Deposition:   2012-09-14
    Release:   2013-01-16
    Last Modified (REVDAT):   2013-03-13
     
  •   Revision History    Hide
    Mouse over text for details
    2013-03-13
    Binding sites and description
    2013-02-20
    Citation
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    Resolution[Å]:   1.89
    R-Value: 0.188 (obs.)
    R-Free: 0.221
    Space Group: C 1 2 1
    Unit Cell:
      Length [Å] Angles [°]
    a = 69.41 α = 90.00 
    b = 71.51 β = 100.34 
    c = 72.16 γ = 90.00