2HIJ | pdb_00002hij

Crystal Structure of P14 Alanine Variant of Antithrombin

• PDB DOI: https://doi.org/10.2210/pdb2HIJ/pdb

• Classification: BLOOD CLOTTING/ HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Drosophila melanogaster
• Mutation(s): Yes 


• Deposited: 2006-06-29 Released: 2007-06-19 
• Deposition Author(s): Luis, S.A., Bock, S.C., Huntington, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.249 (Depositor) 
• R-Value Work: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of P14 Alanine Variant of Antithrombin

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 100.22 kDa 
• Atom Count: 6,355 
• Modeled Residue Count: 820 
• Deposited Residue Count: 864 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antithrombin-III	A [auth I]	432	Homo sapiens	Mutation(s): 2  Gene Names: SERPINC1, AT3
UniProt & NIH Common Fund Data Resources
Find proteins for P01008 (Homo sapiens) Explore P01008  Go to UniProtKB:  P01008
PHAROS:  P01008 GTEx:  ENSG00000117601
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P01008-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antithrombin-III	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
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P01008-1

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth A]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G62182OO GlyCosmos:  G62182OO GlyGen:  G62182OO

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth I], G [auth L], H [auth L], I [auth L]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	F [auth I], J [auth L]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.249 (Depositor) 
• R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.743	α = 90
b = 98.627	β = 101.4
c = 87.569	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-19 
Deposition Author(s): Luis, S.A., Bock, S.C., Huntington, J.A.

Revision History  

• Version 1.0: 2007-06-19
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2021-10-20
  Changes: Database references, Structure summary
• Version 2.2: 2023-08-30
  Changes: Data collection, Refinement description
• Version 2.3: 2024-10-30
  Changes: Structure summary