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.

Macromolecule Content

• Total Structure Weight: 48.19 kDa 
• Atom Count: 3172 
• Modelled Residue Count: 354 
• Deposited Residue Count: 424 
• Unique protein chains: 2

3K65

Crystal Structure of Prethombin-2/Fragment-2 Complex

• DOI: 10.2210/pdb3K65/pdb

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


• Deposited: 2009-10-08 Released: 2010-09-29 
• Deposition Author(s): Adams, T.E., Huntington, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.229 
• R-Value Work: 0.213 
• R-Value Observed: 0.219 

Literature

Structural transitions during prothrombin activation: On the importance of fragment 2.

Adams, T.E., Huntington, J.A.

(2016) Biochimie 122: 235-242

• PubMed: 26365066 
• DOI: 10.1016/j.biochi.2015.09.013
• Primary Citation of Related Structures:  
  3K65


• PubMed Abstract: 
  

Prothrombin is activated to thrombin by the prothrombinase complex through sequential cleavage at two distinct sites. This occurs at sites of vascular injury in a highly regulated cascade of serine protease and cofactor activation, where activated platelets provide a suitable surface for protease/cofactor/substrate assembly. The precise structural and conformational changes undergone during the transition from prothrombin to thrombin have been studied for decades, and several structures of prothrombin fragments along the activation pathway have been solved. Here we present a new structure analyzed in context of other recent structures and biochemical studies. What emerges is an unexpected mechanism that involves a change in the mode of binding of the F2 domain (fragment 2) on the catalytic domain after cleavage at Arg320, and a subsequent reorientation of the linker between the F2 and catalytic domain to present the Arg271 site for cleavage.

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Organizational Affiliation: 

Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, United Kingdom. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	A	116	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	B	308	Homo sapiens	Mutation(s): 1  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734 GTEx:  ENSG00000180210

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BU1	A	1,4-BUTANEDIOL C4 H10 O2 WERYXYBDKMZEQL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.229 
• R-Value Work: 0.213 
• R-Value Observed: 0.219 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.53	α = 90
b = 73.53	β = 90
c = 205.88	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction
DNA	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-10-08 
• Released Date: 2010-09-29 
Deposition Author(s): Adams, T.E., Huntington, J.A.

Revision History  

• Version 1.0: 2010-09-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-09-25
  Changes: Derived calculations
• Version 1.3: 2017-07-05
  Changes: Database references