1IOD

CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE COAGULATION FACTOR X BINDING PROTEIN FROM SNAKE VENOM AND THE GLA DOMAIN OF FACTOR X


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of an anticoagulant protein in complex with the Gla domain of factor X.

Mizuno, H.Fujimoto, Z.Atoda, H.Morita, T.

(2001) Proc.Natl.Acad.Sci.Usa 98: 7230-7234

  • DOI: 10.1073/pnas.131179698

  • PubMed Abstract: 
  • The gamma-carboxyglutamic acid (Gla) domain of blood coagulation factors is responsible for Ca2+-dependent phospholipid membrane binding. Factor X-binding protein (X-bp), an anticoagulant protein from snake venom, specifically binds to the Gla domain ...

    The gamma-carboxyglutamic acid (Gla) domain of blood coagulation factors is responsible for Ca2+-dependent phospholipid membrane binding. Factor X-binding protein (X-bp), an anticoagulant protein from snake venom, specifically binds to the Gla domain of factor X. The crystal structure of X-bp in complex with the Gla domain peptide of factor X at 2.3-A resolution showed that the anticoagulation is based on the fact that two patches of the Gla domain essential for membrane binding are buried in the complex formation. The Gla domain thus is expected to be a new target of anticoagulant drugs, and X-bp provides a basis for designing them. This structure also provides a membrane-bound model of factor X.


    Organizational Affiliation

    Department of Biotechnology, National Institute of Agrobiological Resources, Tsukuba, Ibaraki 305-8602, Japan. mizuno@nias.affrc.go.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COAGULATION FACTOR X BINDING PROTEIN
A
129Deinagkistrodon acutusN/A
Find proteins for Q9IAM1 (Deinagkistrodon acutus)
Go to UniProtKB:  Q9IAM1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
COAGULATION FACTOR X BINDING PROTEIN
B
123Deinagkistrodon acutusN/A
Find proteins for Q9DEF8 (Deinagkistrodon acutus)
Go to UniProtKB:  Q9DEF8
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
COAGULATION FACTOR X GLA DOMAIN
G
44Bos taurusGene Names: F10
EC: 3.4.21.6
Find proteins for P00743 (Bos taurus)
Go to Gene View: F10
Go to UniProtKB:  P00743
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, G
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CGU
Query on CGU
G
L-PEPTIDE LINKINGC6 H9 N O6GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.201 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 99.760α = 90.00
b = 99.760β = 90.00
c = 90.420γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-06-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance