3EVJ

Intermediate structure of antithrombin bound to the natural pentasaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The critical role of hinge-region expulsion in the induced-fit heparin binding mechanism of antithrombin.

Langdown, J.Belzar, K.J.Savory, W.J.Baglin, T.P.Huntington, J.A.

(2009) J. Mol. Biol. 386: 1278-1289


  • PubMed Abstract: 
  • Antithrombin (AT) is the most important inhibitor of coagulation proteases. Its activity is stimulated by glycosaminoglycans, such as heparin, through allosteric and template mechanisms. AT utilises an induced-fit mechanism to bind with high affinity ...

    Antithrombin (AT) is the most important inhibitor of coagulation proteases. Its activity is stimulated by glycosaminoglycans, such as heparin, through allosteric and template mechanisms. AT utilises an induced-fit mechanism to bind with high affinity to a pentasaccharide sequence found in about one-third of heparin chains. The conformational changes behind this mechanism have been characterised by several crystal structures of AT in the absence and in the presence of pentasaccharide. Pentasaccharide binding ultimately results in a conformational change that improves affinity by about 1000-fold. Crystal structures show several differences, including the expulsion of the hinge region of the reactive centre loop from beta-sheet A, which is known to be critical for the allosteric activation of AT. Here, we present data that reveal an energetically distinct intermediate on the path to full activation where the majority of conformational changes have already occurred. A crystal structure of this intermediate shows that the hinge region is in a native-like state in spite of having the pentasaccharide bound in the normal fashion. We engineered a disulfide bond to lock the hinge in its native position to determine the energetic contributions of the initial and final conformational events. Approximately 60% of the free-energy contribution of conformational change is provided by the final step of hinge-region expulsion and subsequent closure of the main beta-sheet A. A new analysis of the individual structural changes provides a plausible mechanism for propagation of conformational change from the heparin binding site to the remote hinge region in beta-sheet A.


    Organizational Affiliation

    Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antithrombin-III
I, L
432Homo sapiensGene Names: SERPINC1 (AT3)
Find proteins for P01008 (Homo sapiens)
Go to Gene View: SERPINC1
Go to UniProtKB:  P01008
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
I, L
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
I, L
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
NTO
Query on NTO

Download SDF File 
Download CCD File 
I, L
TRISULFOAMINO HEPARIN PENTASACCHARIDE
Fondaparinux
C31 H53 N3 O49 S8
KANJSNBRCNMZMV-ABRZTLGGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.231 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 65.846α = 90.00
b = 87.055β = 106.18
c = 92.383γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-06-21
    Type: Database references
  • Version 1.3: 2017-07-12
    Type: Advisory, Structure summary