Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 100.16 kDa 
• Atom Count: 6377 
• Residue Count: 816 
• Unique protein chains: 2

2BEH

Crystal structure of antithrombin variant S137A/V317C/T401C with plasma latent antithrombin

• DOI: 10.2210/pdb2BEH/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Mesocricetus auratus
• Mutation(s): Yes 


• Deposited: 2005-10-24 Released: 2005-11-01 
• Deposition Author(s): Johnson, D.J., Luis, S.A., Huntington, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.265 
• R-Value Work: 0.219 
• R-Value Observed: 0.219 

Literature

Crystal structure of monomeric native antithrombin reveals a novel reactive center loop conformation.

Johnson, D.J., Langdown, J., Li, W., Luis, S.A., Baglin, T.P., Huntington, J.A.

(2006) J Biol Chem 281: 35478-35486

• PubMed: 16973611 
• DOI: 10.1074/jbc.M607204200
• Primary Citation of Related Structures:  
  2B5T, 2BEH, 1T1F


• PubMed Abstract: 
  

The poor inhibitory activity of circulating antithrombin (AT) is critical to the formation of blood clots at sites of vascular damage. AT becomes an efficient inhibitor of the coagulation proteases only after binding to a specific heparin pentasaccharide, which alters the conformation of the reactive center loop (RCL). The molecular basis of this activation event lies at the heart of the regulation of hemostasis and accounts for the anticoagulant properties of the low molecular weight heparins. Although several structures of AT have been solved, the conformation of the RCL in native AT remains unknown because of the obligate crystal contact between the RCL of native AT and its latent counterpart. Here we report the crystallographic structure of a variant of AT in its monomeric native state. The RCL shifted approximately 20 A, and a salt bridge was observed between the P1 residue (Arg-393) and Glu-237. This contact explains the effect of mutations at the P1 position on the affinity of AT for heparin and also the properties of AT-Truro (E237K). The relevance of the observed conformation was verified through mutagenesis studies and by solving structures of the same variant in different crystal forms. We conclude that the poor inhibitory activity of the circulating form of AT is partially conferred by intramolecular contacts that restrain the RCL, orient the P1 residue away from attacking proteases, and additionally block the exosite utilized in protease recognition.

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Organizational Affiliation: 

Department of Haematology, Division of Structural Medicine, Thrombosis Research Unit, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 2XY, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antithrombin-III	I	432	Homo sapiens	Mutation(s): 3  Gene Names: SERPINC1, AT3, PRO0309
Find proteins for P01008 (Homo sapiens) Explore P01008  Go to UniProtKB:  P01008
NIH Common Fund Data Resources
PHAROS  P01008 GTEx  ENSG00000117601

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antithrombin-III	L	432	Homo sapiens	Mutation(s): 0  Gene Names: SERPINC1, AT3, PRO0309
Find proteins for P01008 (Homo sapiens) Explore P01008  Go to UniProtKB:  P01008
NIH Common Fund Data Resources
PHAROS  P01008 GTEx  ENSG00000117601

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	A, C	2		N-Glycosylation

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	I, L	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	I	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.265 
• R-Value Work: 0.219 
• R-Value Observed: 0.219 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.073	α = 90
b = 97.274	β = 105.03
c = 87.388	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-10-24 
• Released Date: 2005-11-01 
Deposition Author(s): Johnson, D.J., Luis, S.A., Huntington, J.A.

Revision History 

• Version 1.0: 2005-11-01
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, 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