1NQ9

Crystal Structure of Antithrombin in the Pentasaccharide-Bound Intermediate State

• PDB DOI: https://doi.org/10.2210/pdb1NQ9/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2003-01-21 Released: 2003-09-30 
• Deposition Author(s): Huntington, J.A., Johnson, D.J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.250 
• R-Value Work: 0.209 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 103.24 kDa 
• Atom Count: 6,779 
• Modelled Residue Count: 819 
• Deposited Residue Count: 864 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antithrombin-III	A [auth I], B [auth L]	432	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01008 (Homo sapiens) Explore P01008  Go to UniProtKB:  P01008
PHAROS:  P01008 GTEx:  ENSG00000117601

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth A], D [auth B], E [auth C]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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-glucopyranoside	F [auth D], G [auth E]	5		N/A
Glycosylation Resources
GlyTouCan:  G76630SM GlyCosmos:  G76630SM

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	H [auth I], I [auth L]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900031	F [auth D], G [auth E]	heparin pentasaccharide	Oligosaccharide / Anticoagulant

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 69.679	α = 90
b = 86.76	β = 109.54
c = 96.921	γ = 90

Software Package:

Software Name	Purpose
Adxv	data processing
SCALA	data scaling
MOLREP	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-09-30 
Deposition Author(s): Huntington, J.A., Johnson, D.J.D.

Revision History  

• 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