› 3hkj

X-ray diffraction
2.6Å resolution

Crystal structure of human thrombin mutant W215A/E217A in complex with the extracellular fragment of human PAR1

Released:
DOI: 10.2210/pdb3hkj/pdb
PDB entry 3hkj coloured by chain, front view.
PDB entry 3hkj coloured by chain, side view.
PDB entry 3hkj coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Mechanism of the anticoagulant activity of thrombin mutant W215A/E217A.
Gandhi PS, Page MJ, Chen Z, Bush-Pelc L, Di Cera E
J Biol Chem 284 24098-105 (2009)
PMID: 19586901

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 analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133084 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Thrombin light chain Chains: A, D
Molecule details ›
Chains: A, D
Length: 31 amino acids
Theoretical weight: 3.65 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P00734 (Residues: 333-363; Coverage: 5%)
Gene name: F2
Sequence domains: Thrombin light chain
Thrombin heavy chain Chains: B, E
Molecule details ›
Chains: B, E
Length: 259 amino acids
Theoretical weight: 29.61 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
Proteinase-activated receptor 1 Chains: C, F
Molecule details ›
Chains: C, F
Length: 21 amino acids
Theoretical weight: 2.67 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P25116 (Residues: 42-62; Coverage: 5%)
Gene names: CF2R, F2R, PAR1, TR

Ligands and Environments

1 bound ligand:
Ligand NAG 2 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 14-BM-C
Spacegroup: P1
Unit cell:
a: 53.14Å b: 61.783Å c: 67.834Å
α: 98.78° β: 110.28° γ: 92.95°
R-values:
R R work R free
0.196 0.196 0.234
Expression system: Cricetulus griseus

Quick links

Citations

4 review citations

Commercial proteases: present and future.
Li et al. (2013)
3 more

1 mention without citation

Mechanism of the anticoagulant activity of thrombin mutant W215A/E217A.
Gandhi et al. (2009)