Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 110.65 kDa 
• Atom Count: 7271 
• Residue Count: 869 
• Unique protein chains: 2

1SDD

Crystal Structure of Bovine Factor Vai

• DOI: 10.2210/pdb1SDD/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2004-02-13 Released: 2004-06-29 
• Deposition Author(s): Adams, T.E., Hockin, M.F., Mann, K.G., Everse, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.296 
• R-Value Work: 0.252 
• R-Value Observed: 0.262 

Literature

The crystal structure of activated protein C-inactivated bovine factor Va: Implications for cofactor function.

Adams, T.E., Hockin, M.F., Mann, K.G., Everse, S.J.

(2004) Proc Natl Acad Sci U S A 101: 8918-8923

• PubMed: 15184653 
• DOI: 10.1073/pnas.0403072101
• Primary Citation of Related Structures:  
  1SDD


• PubMed Abstract: 
  

In vertebrate hemostasis, factor Va serves as the cofactor in the prothrombinase complex that results in a 300,000-fold increase in the rate of thrombin generation compared with factor Xa alone. Structurally, little is known about the mechanism by which factor Va alters catalysis within this complex. Here, we report a crystal structure of protein C inactivated factor Va (A1.A3-C1-C2) that depicts a previously uncharacterized domain arrangement. This orientation has implications for binding to membranes essential for function. A high-affinity calcium-binding site and a copper-binding site have both been identified. Surprisingly, neither shows a direct involvement in chain association. This structure represents the largest physiologically relevant fragment of factor Va solved to date and provides a new scaffold for the future generation of models of coagulation cofactors.

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Organizational Affiliation: 

Department of Biochemistry, College of Medicine, University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor V	A	306	Bos taurus	Mutation(s): 0  Gene Names: F5
Find proteins for Q28107 (Bos taurus) Explore Q28107  Go to UniProtKB:  Q28107

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor V	B	647	Bos taurus	Mutation(s): 0  Gene Names: F5
Find proteins for Q28107 (Bos taurus) Explore Q28107  Go to UniProtKB:  Q28107

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CU	B	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.296 
• R-Value Work: 0.252 
• R-Value Observed: 0.262 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.37	α = 90
b = 86.56	β = 90
c = 229.2	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-02-13 
• Released Date: 2004-06-29 
Deposition Author(s): Adams, T.E., Hockin, M.F., Mann, K.G., Everse, S.J.

Revision History 

• Version 1.0: 2004-06-29
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary