Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 85.96 kDa 
• Atom Count: 5534 
• Modelled Residue Count: 689 
• Deposited Residue Count: 727 
• Unique protein chains: 3

1SR5

ANTITHROMBIN-ANHYDROTHROMBIN-HEPARIN TERNARY COMPLEX STRUCTURE

• PDB DOI: 10.2210/pdb1SR5/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Mutation(s): No 


• 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: 3.10 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
• Primary Citation of Related Structures:  
  1SR5


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antithrombin-III	A	432	Homo sapiens	Mutation(s): 0  Gene Names: SERPINC1, AT3, PRO0309
UniProt & NIH Common Fund Data Resources
Find proteins for P01008 (Homo sapiens) Explore P01008  Go to UniProtKB:  P01008
PHAROS:  P01008

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	B	36	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	C	259	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
4-deoxy-2,3,6-tri-O-methyl-alpha-D-xylo-hexopyranose-(1-4)-2,3,6-tri-O-methyl-beta-D-glucopyranose-(1-4)-2,3-di-O-methyl-6-O-sulfo-alpha-D-glucopyranose-(1-4)-(2R,3R,4S,5S,6S)-6-(dihydroxymethyl)-3,4-dimethoxytetrahydro-2H-pyran-2,5-diol-(1-4)-2,3,6-tri-O-sulfo-alpha-D-glucopyranose-(1-4)-(2R,3R,4S,5S,6R)-6-(dihydroxymethyl)-3,4-dimethoxytetrahydro-2H-pyran-2,5-diol-(1-4)-1,5-anhydro-3-O-methyl-2,6-di-O-sulfo-D-glucitol	D	7	N/A	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GU4	H [auth C]	2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose C6 H12 O18 S4 SPIXVQOXHJQNTH-DVKNGEFBSA-N
NAG	E [auth A], F [auth A], G [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900079	D	heparin heptasaccharide	Oligosaccharide / Anticoagulant		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.278 
• R-Value Work: 0.227 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.04	α = 90
b = 90.7	β = 90
c = 159.9	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
XDS	data reduction
CNS	refinement
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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2014-09-24
  Changes: Database references
• Version 2.0: 2020-04-22
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary