Crystal Structure of Antithrombin in the Pentasaccharide-Bound Intermediate State

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.209 

Starting Model: experimental
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Crystal Structure of Antithrombin in a Heparin-Bound Intermediate State

Johnson, D.J.D.Huntington, J.A.

(2003) Biochemistry 42: 8712-8719

  • DOI: https://doi.org/10.1021/bi034524y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Antithrombin is activated as an inhibitor of the coagulation proteases through its specific interaction with a heparin pentasaccharide. The binding of heparin induces a global conformational change in antithrombin which results in the freeing of its reactive center loop for interaction with target proteases and a 1000-fold increase in heparin affinity. The allosteric mechanism by which the properties of antithrombin are altered by its interactions with the specific pentasaccharide sequence of heparin is of great interest to the medical and protein biochemistry communities. Heparin binding has previously been characterized as a two-step, three-state mechanism where, after an initial weak interaction, antithrombin undergoes a conformational change to its high-affinity state. Although the native and heparin-activated states have been determined through protein crystallography, the number and magnitude of conformational changes render problematic the task of determining which account for the improved heparin affinity and how the heparin binding region is linked to the expulsion of the reactive center loop. Here we present the structure of an intermediate pentasaccharide-bound conformation of antithrombin which has undergone all of the conformational changes associated with activation except loop expulsion and helix D elongation. We conclude that the basis of the high-affinity state is not improved interaction with the pentasaccharide but a lowering of the global free energy due to conformational changes elsewhere in antithrombin. We suggest a mechanism in which the role of helix D elongation is to lock antithrombin in the five-stranded fully activated conformation.

  • Organizational Affiliation

    Department of Haematology, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 2XY, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antithrombin-IIIA [auth I],
B [auth L]
432Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01008 (Homo sapiens)
Explore P01008 
Go to UniProtKB:  P01008
GTEx:  ENSG00000117601 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01008
Glycosylation Sites: 2Go to GlyGen: P01008-1
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth A],
D [auth B],
E [auth C]
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
3,4-di-O-methyl-2,6-di-O-sulfo-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)-3-O-methyl-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-methyl 2,3,6-tri-O-sulfo-alpha-D-glucopyranosideF [auth D],
G [auth E]
Glycosylation Resources
GlyTouCan:  G76630SM
GlyCosmos:  G76630SM
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
H [auth I],
I [auth L]
C8 H15 N O6
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.679α = 90
b = 86.76β = 109.54
c = 96.921γ = 90
Software Package:
Software NamePurpose
Adxvdata processing
SCALAdata scaling
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-30
    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: 2017-10-11
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary
  • Version 2.1: 2023-08-16
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-03-13
    Changes: Source and taxonomy, Structure summary