Biological Assembly 1  

 3D View: Structure | Electron Density | 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: 92.16 kDa 
• Atom Count: 6324 
• Residue Count: 714 
• Unique protein chains: 3

1TB6

2.5A Crystal Structure of the Antithrombin-Thrombin-Heparin Ternary Complex

• DOI: 10.2210/pdb1TB6/pdb

• Classification: HYDROLASE/BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2004-05-19 Released: 2004-08-17 
• Deposition Author(s): Li, W., Johnson, D.J., Esmon, C.T., Huntington, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.245 
• R-Value Work: 0.208 

Literature

Structure of the antithrombin-thrombin-heparin ternary complex reveals the antithrombotic mechanism of heparin.

Li, W., Johnson, D.J., Esmon, C.T., Huntington, J.A.

(2004) Nat Struct Mol Biol 11: 857-862

• PubMed: 15311269 
• DOI: 10.1038/nsmb811
• Primary Citation of Related Structures:  
  1TB6


• PubMed Abstract: 
  

The maintenance of normal blood flow depends completely on the inhibition of thrombin by antithrombin, a member of the serpin family. Antithrombin circulates at a high concentration, but only becomes capable of efficient thrombin inhibition on interaction with heparin or related glycosaminoglycans. The anticoagulant properties of therapeutic heparin are mediated by its interaction with antithrombin, although the structural basis for this interaction is unclear. Here we present the crystal structure at a resolution of 2.5 A of the ternary complex between antithrombin, thrombin and a heparin mimetic (SR123781). The structure reveals a template mechanism with antithrombin and thrombin bound to the same heparin chain. A notably close contact interface, comprised of extensive active site and exosite interactions, explains, in molecular detail, the basis of the antithrombotic properties of therapeutic heparin.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
thrombin	L	49	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
thrombin	H	259	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

Entity ID: 3
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

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	A	3		N-Glycosylation

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose-(1-4)-2,3,6-tri-O-sulfo-alpha-D-glucopyranose-(1-4)-2,3,6-tri-O-sulfonato-beta-D-glucopyranose-(1-4)-2,3-di-O-methyl-6-O-sulfonato-alpha-D-glucopyranose-(1-4)-2,3,6-tri-O-methyl-beta-D-glucopyranose-(1-4)-2,3,6-tri-O-methyl-alpha-D-glucopyranose-(1-4)-2,3,6-tri-O-methyl-beta-D-glucopyranose-(1-4)-2,3,6-tri-O-methyl-alpha-D-glucopyranose-(1-4)-2,3,6-tri-O-methyl-beta-D-glucopyranose-(1-4)-2,3,6-tri-O-methyl-alpha-D-glucopyranose-(1-4)-2,3,6-tri-O-methyl-beta-D-glucopyranose-(1-4)-2,3-di-O-methyl-6-O-sulfonato-alpha-D-glucopyranose-(1-4)-2,3-di-O-methyl-beta-D-glucopyranuronic acid-(1-4)-2,3,6-tri-O-sulfo-alpha-D-glucopyranose-(1-4)-2,3-di-O-methyl-alpha-L-idopyranuronic acid-(1-4)-methyl 3-O-methyl-2,6-di-O-sulfo-alpha-D-glucopyranoside	B	16		N/A

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	5		N-Glycosylation

Entity ID: 7
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	3		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	I	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MPD	H, I	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.245 
• R-Value Work: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.409	α = 90
b = 88.404	β = 90
c = 117.218	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-05-19 
• Released Date: 2004-08-17 
Deposition Author(s): Li, W., Johnson, D.J., Esmon, C.T., Huntington, J.A.

Revision History 

• Version 1.0: 2004-08-17
  Type: Initial release
  
• Version 1.1: 2008-04-30
  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