› 3gis

X-ray diffraction
2.4Å resolution

Crystal Structure of Na-free Thrombin in Complex with Thrombomodulin

Released:
DOI: 10.2210/pdb3gis/pdb
PDB entry 3gis coloured by chain, front view.
PDB entry 3gis coloured by chain, side view.
PDB entry 3gis coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular basis of thrombomodulin activation of slow thrombin.
Adams TE, Li W, Huntington JA
J Thromb Haemost 7 1688-95 (2009)
PMID: 19656282

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-133072 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Thrombin light chain Chains: A, C, E
Molecule details ›
Chains: A, C, E
Length: 49 amino acids
Theoretical weight: 5.64 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
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 Chains: B, D, F
Molecule details ›
Chains: B, D, F
Length: 259 amino acids
Theoretical weight: 29.76 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P00734 (Residues: 364-622; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Thrombomodulin Chains: X, Y, Z
Molecule details ›
Chains: X, Y, Z
Length: 121 amino acids
Theoretical weight: 12.93 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P07204 (Residues: 363-483; Coverage: 22%)
Gene names: THBD, THRM
Sequence domains: Complement Clr-like EGF-like
Structure domains: Laminin

Ligands and Environments

2 bound ligands:
Ligand SO4 15 x SO4
Ligand CA 3 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SRS BEAMLINE PX14.2
Spacegroup: P212121
Unit cell:
a: 66.25Å b: 100.34Å c: 229.28Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.247 0.211 0.259
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Thrombin as a multi-functional enzyme. Focus on in vitro and in vivo effects.
Siller-Matula et al. (2011)
1 more

3 mentions without citation

Molecular basis of thrombomodulin activation of slow thrombin.
Adams et al. (2009)
2 more