› 1tb6

X-ray diffraction
2.5Å resolution

2.5A Crystal Structure of the Antithrombin-Thrombin-Heparin Ternary Complex

Released:
DOI: 10.2210/pdb1tb6/pdb
PDB entry 1tb6 coloured by chain, front view.
PDB entry 1tb6 coloured by chain, side view.
PDB entry 1tb6 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of the antithrombin-thrombin-heparin ternary complex reveals the antithrombotic mechanism of heparin.
Li W, Johnson DJ, Esmon CT, Huntington JA
Nat Struct Mol Biol 11 857-62 (2004)
PMID: 15311269

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 (7 distinct):
Thrombin light chain Chain: L
Molecule details ›
Chain: L
Length: 49 amino acids
Theoretical weight: 5.64 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P00734 (Residues: 315-363; Coverage: 8%)
Gene name: F2
Sequence domains: Thrombin light chain
Structure domains: Thrombin light chain domain
Thrombin heavy chain Chain: H
Molecule details ›
Chain: H
Length: 259 amino acids
Theoretical weight: 29.76 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P00734 (Residues: 364-622; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Antithrombin-III Chain: I
Molecule details ›
Chain: I
Length: 432 amino acids
Theoretical weight: 49.09 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P01008 (Residues: 33-464; Coverage: 100%)
Gene names: AT3, PRO0309, SERPINC1
Sequence domains: Serpin (serine protease inhibitor)
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: GU3, GU2, GU6, GU1, GU5, GU8, GU9, GU0, GU4
Carbohydrate polymer
2 bound ligands:
Ligand MPD 8 x MPD
Ligand NAG 1 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SRS BEAMLINE PX14.1
Spacegroup: P212121
Unit cell:
a: 88.409Å b: 88.404Å c: 117.218Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.208 0.245
Expression system: Cricetulus griseus

Quick links

Citations

48 review citations

The structure of glycosaminoglycans and their interactions with proteins.
Gandhi et al. (2008)
47 more

35 mentions without citation

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