Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - ABC 

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

Macromolecule Content

• Total Structure Weight: 85957.52 
• Atom Count: 5459 
• Residue Count: 727 
• Unique protein chains: 3

1SR5

ANTITHROMBIN-ANHYDROTHROMBIN-HEPARIN TERNARY COMPLEX STRUCTURE

• DOI: 10.2210/pdb1SR5/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens


• Deposited: 2004-03-22 Released: 2004-08-17 
• Deposition Author(s): Dementiev, A., Petitou, M., Gettins, P.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.1 Å
• R-Value Free: 0.278 
• R-Value Work: 0.227 

Literature

The ternary complex of antithrombin-anhydrothrombin-heparin reveals the basis of inhibitor specificity.

Dementiev, A., Petitou, M., Herbert, J.M., Gettins, P.G.

(2004) Nat.Struct.Mol.Biol. 11: 863-867

• PubMed: 15311268 
• DOI: 10.1038/nsmb810


• PubMed Abstract: 
  

Antithrombin, the principal physiological inhibitor of the blood coagulation proteinase thrombin, requires heparin as a cofactor. We report the crystal structure of the rate-determining encounter complex formed between antithrombin, anhydrothrombin and an optimal synthetic 16-mer oligosaccharide. The antithrombin reactive center loop projects from the serpin body and adopts a canonical conformation that makes extensive backbone and side chain contacts from P5 to P6' with thrombin's restrictive specificity pockets, including residues in the 60-loop. These contacts rationalize many earlier mutagenesis studies on thrombin specificity. The 16-mer oligosaccharide is just long enough to form the predicted bridge between the high-affinity pentasaccharide-binding site on antithrombin and the highly basic exosite 2 on thrombin, validating the design strategy for this synthetic heparin. The protein-protein and protein-oligosaccharide interactions together explain the basis for heparin activation of antithrombin as a thrombin inhibitor.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, 900 S. Ashland, Chicago, Illinois 60607, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Antithrombin-III	A	432	Homo sapiens	Mutation(s): 0  Gene Names: SERPINC1 (AT3)
Find proteins for P01008 (Homo sapiens) Go to Gene View: SERPINC1 Go to UniProtKB:  P01008

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Prothrombin	B	36	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Go to Gene View: F2 Go to UniProtKB:  P00734

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Prothrombin	C	259	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Go to Gene View: F2 Go to UniProtKB:  P00734

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NAG	A, C	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NT2	C	2,3,4,6-TETRA-O-SULFOHEXOPYRANOSE C6 H12 O18 S4 SPIXVQOXHJQNTH-DVKNGEFBSA-N
NT1	A	HEPARIN HEPTASACCHARIDE C55 H98 O54 S6 QNKPWFIPDVKGET-ARQCQYMKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.1 Å
• R-Value Free: 0.278 
• R-Value Work: 0.227 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 90.040	α = 90.00
b = 90.700	β = 90.00
c = 159.900	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data scaling
XDS	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-03-22 
• Released Date: 2004-08-17 
• Deposition Author(s): Dementiev, A., Petitou, M., Gettins, P.G.

Revision History 

• Version 1.0: 2004-08-17
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance
• Version 1.3: 2014-09-24
  Type: Database references