› 1sr5

X-ray diffraction
3.1Å resolution

ANTITHROMBIN-ANHYDROTHROMBIN-HEPARIN TERNARY COMPLEX STRUCTURE

Released:
DOI: 10.2210/pdb1sr5/pdb
PDB entry 1sr5 coloured by chain, front view.
PDB entry 1sr5 coloured by chain, side view.
PDB entry 1sr5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The ternary complex of antithrombin-anhydrothrombin-heparin reveals the basis of inhibitor specificity.
Dementiev A, Petitou M, Herbert JM, Gettins PG
Nat Struct Mol Biol 11 863-7 (2004)
PMID: 15311268

Function and Biology Details

Reaction catalysed: 
Selective cleavage of Arg-|-Gly bonds in fibrinogen to form fibrin and release fibrinopeptides A and B.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133063 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (4 distinct):
Antithrombin-III Chain: A
Molecule details ›
Chain: A
Length: 432 amino acids
Theoretical weight: 49.1 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P01008 (Residues: 33-464; Coverage: 100%)
Gene names: AT3, PRO0309, SERPINC1
Sequence domains: Serpin (serine protease inhibitor)
Structure domains:
Thrombin light chain Chain: B
Molecule details ›
Chain: B
Length: 36 amino acids
Theoretical weight: 4.1 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 328-363; Coverage: 6%)
Gene name: F2
Sequence domains: Thrombin light chain
Thrombin heavy chain Chain: C
Molecule details ›
Chain: C
Length: 259 amino acids
Theoretical weight: 29.78 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 364-622; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases

Ligands and Environments

Carbohydrate polymer : NEW Components: YYB, U9J, GU6, U9M, U9G, GU8, U9D
Ligand YYB 1 x YYB
Ligand U9J 1 x U9J
Ligand GU6 1 x GU6
Ligand U9M 1 x U9M
Ligand U9G 1 x U9G
Ligand GU8 1 x GU8
Ligand U9D 1 x U9D
2 bound ligands:
Ligand NAG 3 x NAG
Ligand GU4 1 x GU4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 90.04Å b: 90.7Å c: 159.9Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.227 0.227 0.278

Quick links

Citations

23 review citations

Demystifying heparan sulfate-protein interactions.
Xu et al. (2014)
22 more

7 mentions without citation

Molecular simulations of carbohydrates and protein-carbohydrate interactions: motivation, issues and prospects.
Fadda et al. (2010)
6 more