Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 98.64 kDa 
• Atom Count: 6636 
• Residue Count: 817 
• Unique protein chains: 1

2ANT

THE 2.6 A STRUCTURE OF ANTITHROMBIN INDICATES A CONFORMATIONAL CHANGE AT THE HEPARIN BINDING SITE

• DOI: 10.2210/pdb2ANT/pdb

• Classification: SERPIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1997-01-28 Released: 1997-06-16 
• Deposition Author(s): Skinner, R., Abrahams, J.-P., Whisstock, J.C., Lesk, A.M., Carrell, R.W., Wardell, M.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.290 
• R-Value Work: 0.217 

Literature

The 2.6 A structure of antithrombin indicates a conformational change at the heparin binding site.

Skinner, R., Abrahams, J.P., Whisstock, J.C., Lesk, A.M., Carrell, R.W., Wardell, M.R.

(1997) J Mol Biol 266: 601-609

• PubMed: 9067613 
• DOI: 10.1006/jmbi.1996.0798
• Primary Citation of Related Structures:  
  2ANT


• PubMed Abstract: 
  

The crystal structure of a dimeric form of intact antithrombin has been solved to 2.6 A, representing the highest-resolution structure of an active, inhibitory serpin to date. The crystals were grown under microgravity conditions on Space Shuttle mission STS-67. The overall confidence in the structure, determined earlier from lower resolution data, is increased and new insights into the structure-function relationship are gained. Clear and continuous electron density is present for the reactive centre loop region P12 to P14 inserting into the top of the A-beta-sheet. Areas of the extended amino terminus, unique to antithrombin and important in the binding of the glycosaminoglycan heparin, can now be traced further than in the earlier structures. As in the earlier studies, the crystals contain one active and one latent molecule per asymmetric unit. Better definition of the electron density surrounding the D-helix and of the residues implicated in the binding of the heparin pentasaccharide (Arg47, Lys114, Lys125, Arg129) provides an insight into the change of affinity of binding that accompanies the change in conformation. In particular, the observed hydrogen bonding of these residues to the body of the molecule in the latent form explains the mechanism for the release of newly formed antithrombin-protease complexes into the circulation for catabolic removal.

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Related Citations: 

• Improved Diffraction of Antithrombin Crystals Grown in Microgravity
  Wardell, M.R., Skinner, R., Carter, D.C., Twigg, P.D., Abrahams, J.-P.
  () To be published --: --

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Organizational Affiliation: 

Department of Haematology, University of Cambridge, MRC Centre, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTITHROMBIN	I, L	432	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAA	I, L	2-acetamido-2-deoxy-beta-D-allopyranose C8 H15 N O6 OVRNDRQMDRJTHS-UIAUGNHASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.290 
• R-Value Work: 0.217 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.41	α = 90
b = 98.31	β = 103.32
c = 90.41	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
TNT	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-01-28 
• Released Date: 1997-06-16 
Deposition Author(s): Skinner, R., Abrahams, J.-P., Whisstock, J.C., Lesk, A.M., Carrell, R.W., Wardell, M.R.

Revision History 

• Version 1.0: 1997-06-16
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary