1SR5

ANTITHROMBIN-ANHYDROTHROMBIN-HEPARIN TERNARY COMPLEX STRUCTURE

Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history. 


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

  • 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 ...

    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.

    Organizational Affiliation: 

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Antithrombin-IIIA432Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ProthrombinB36Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ProthrombinC259Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
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-glucitolD7 N/A N/A Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GU4
Query on GU4
Download Ideal Coordinates CCD File 
 H [auth C]2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose
C6 H12 O18 S4
SPIXVQOXHJQNTH-DVKNGEFBSA-N		 Ligand Interaction
NAG
Query on NAG
Download Ideal Coordinates CCD File 
 E [auth A], F [auth A], G [auth C]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900079
Query on PRD_900079		Dheparin heptasaccharideOligosaccharide /  Anticoagulant

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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 = 90.04α = 90
b = 90.7β = 90
c = 159.9γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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