1SR5

ANTITHROMBIN-ANHYDROTHROMBIN-HEPARIN TERNARY COMPLEX STRUCTURE

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.3 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

  • 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 a ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antithrombin-III
A
432Homo sapiensMutation(s): 0 
Gene Names: SERPINC1 (AT3)
Find proteins for P01008 (Homo sapiens)
Go to Gene View: SERPINC1
Go to UniProtKB:  P01008
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Prothrombin
B
36Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
Prothrombin
C
259Homo sapiensMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download SDF File 
Download CCD File 
A, C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
NT2
Query on NT2
Download SDF File 
Download CCD File 
C
2,3,4,6-TETRA-O-SULFOHEXOPYRANOSE
C6 H12 O18 S4
SPIXVQOXHJQNTH-DVKNGEFBSA-N
 Ligand Interaction
NT1
Query on NT1
Download SDF File 
Download CCD File 
A
HEPARIN HEPTASACCHARIDE
C55 H98 O54 S6
QNKPWFIPDVKGET-ARQCQYMKSA-N
 Ligand Interaction
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 = 90.040α = 90.00
b = 90.700β = 90.00
c = 159.900γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
XDSdata scaling
XDSdata reduction
CNSphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

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