4BXW

Crystal Structure of the Prothrombinase Complex from the Venom of Pseudonaja Textilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of the Prothrombinase Complex from the Venom of Pseudonaja Textilis.

Lechtenberg, B.C.Murray-Rust, T.A.Johnson, D.J.Adams, T.E.Krishnaswamy, S.Camire, R.M.Huntington, J.A.

(2013) Blood 122: 2777

  • DOI: 10.1182/blood-2013-06-511733
  • Primary Citation of Related Structures:  
    4BXS, 4BXW

  • PubMed Abstract: 
  • The prothrombinase complex, composed of the protease factor (f)Xa and cofactor fVa, efficiently converts prothrombin to thrombin by specific sequential cleavage at 2 sites. How the complex assembles and its mechanism of prothrombin processing are of central importance to human health and disease, because insufficient thrombin generation is the root cause of hemophilia, and excessive thrombin production results in thrombosis ...

    The prothrombinase complex, composed of the protease factor (f)Xa and cofactor fVa, efficiently converts prothrombin to thrombin by specific sequential cleavage at 2 sites. How the complex assembles and its mechanism of prothrombin processing are of central importance to human health and disease, because insufficient thrombin generation is the root cause of hemophilia, and excessive thrombin production results in thrombosis. Efforts to determine the crystal structure of the prothrombinase complex have been thwarted by the dependence of complex formation on phospholipid membrane association. Pseutarin C is an intrinsically stable prothrombinase complex preassembled in the venom gland of the Australian Eastern Brown Snake (Pseudonaja textilis). Here we report the crystal structures of the fX-fV complex and of activated fXa from P textilis venom and the derived model of active pseutarin C. Structural analysis supports a single substrate binding channel on fVa, to which prothrombin and the intermediate meizothrombin bind in 2 different orientations, providing insight into the architecture and mechanism of the prothrombinase complex-the molecular engine of blood coagulation.


    Organizational Affiliation

    Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; and.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FACTOR XAA, B423Pseudonaja textilisMutation(s): 0 
EC: 3.4.21.6
UniProt
Find proteins for Q56VR3 (Pseudonaja textilis)
Explore Q56VR3 
Go to UniProtKB:  Q56VR3
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
COAGULATION FACTOR VC [auth F]18Escherichia coliMutation(s): 0 
UniProt
Find proteins for Q593B6 (Pseudonaja textilis)
Explore Q593B6 
Go to UniProtKB:  Q593B6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0GJ (Subject of Investigation/LOI)
Query on 0GJ

Download Ideal Coordinates CCD File 
D [auth A], G [auth B]L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide
C14 H28 Cl N6 O5
XELWNHKFCNMWQO-LPEHRKFASA-O
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A], H [auth B], I [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000288 (0GJ)
Query on PRD_000288
D [auth A], G [auth B]GLU-GLY-ARG-CHLOROMETHYL KETONEPeptide-like /  Inhibitor  Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.159 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 179.31α = 90
b = 179.31β = 90
c = 179.31γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2013-10-30
    Changes: Database references