Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 60.89 kDa 
• Atom Count: 3843 
• Modelled Residue Count: 473 
• Deposited Residue Count: 534 
• Unique protein chains: 3

1P0S

Crystal Structure of Blood Coagulation Factor Xa in Complex with Ecotin M84R

• DOI: 10.2210/pdb1P0S/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens, Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-04-10 Released: 2003-08-26 
• Deposition Author(s): Wang, S.X., Hur, E., Sousa, C.A., Brinen, L., Slivka, E.J., Fletterick, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.234 
• R-Value Work: 0.207 
• R-Value Observed: 0.207 

Literature

The Extended Interactions and Gla Domain of Blood Coagulation Factor Xa

Wang, S.X., Hur, E., Sousa, C.A., Brinen, L., Slivka, E.J., Fletterick, R.J.

(2003) Biochemistry 42: 7959-7966

• PubMed: 12834348 
• DOI: 10.1021/bi027320a
• Primary Citation of Related Structures:  
  1P0S


• PubMed Abstract: 
  

The serine protease factor Xa (FXa) is inhibited by ecotin with picomolar affinity. The structure of the tetrameric complex of ecotin variant M84R (M84R) with FXa has been determined to 2.8 A. Substrate directed induced fit of the binding interactions at the S2 and S4 pockets modulates the discrimination of the protease. Specifically, the Tyr at position 99 of FXa changes its conformation with respect to incoming ligand, changing the size of the S2 and S4 pockets. The role of residue 192 in substrate and inhibitor recognition is also examined. Gln 192 from FXa forms a hydrogen bond with the P2 carbonyl group of ecotin. This confirms previous biochemical and structural analyses on thrombin and activated protein C, which suggested that residue 192 may play a more general role in mediating the interactions between coagulation proteases and their inhibitors. The structure of ecotin M84R-FXa (M84R-FXa) also reveals the structure of the Gla domain in the presence of Mg(2+). The first 11 residues of the domain assume a novel conformation and likely represent an intermediate folding state of the domain.

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Organizational Affiliation: 

Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, California 94143, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor X precursor	L	138	Homo sapiens	Mutation(s): 11  Gene Names: F10 EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
NIH Common Fund Data Resources
PHAROS:  P00742 GTEx:  ENSG00000126218

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor X precursor	H	254	Homo sapiens	Mutation(s): 0  Gene Names: F10 EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
NIH Common Fund Data Resources
PHAROS:  P00742 GTEx:  ENSG00000126218

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ecotin precursor	E	142	Escherichia coli	Mutation(s): 1  Gene Names: ECO OR ETI OR B2209
Find proteins for P23827 (Escherichia coli (strain K12)) Explore P23827  Go to UniProtKB:  P23827

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	H, L	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	H	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CGU	L	L-PEPTIDE LINKING	C6 H9 N O6		GLU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.234 
• R-Value Work: 0.207 
• R-Value Observed: 0.207 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.839	α = 90
b = 108.05	β = 90
c = 186.305	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-04-10 
• Released Date: 2003-08-26 
Deposition Author(s): Wang, S.X., Hur, E., Sousa, C.A., Brinen, L., Slivka, E.J., Fletterick, R.J.

Revision History  

• Version 1.0: 2003-08-26
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance