PDBe 1dx5

X-ray diffraction
2.3Å resolution

Crystal structure of the thrombin-thrombomodulin complex

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Thrombin light chain Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 36 amino acids
Theoretical weight: 4.1 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 328-363; Coverage: 6%)
Gene name: F2
Thrombomodulin Chains: I, J, K, L
Molecule details ›
Chains: I, J, K, L
Length: 118 amino acids
Theoretical weight: 12.69 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P07204 (Residues: 363-480; Coverage: 21%)
Gene names: THBD, THRM
Structure domains: Laminin
Thrombin heavy chain Chains: M, N, O, P
Molecule details ›
Chains: M, N, O, P
Length: 259 amino acids
Theoretical weight: 29.79 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


No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: MPG/DESY, HAMBURG BEAMLINE BW6
Spacegroup: R3
Unit cell:
a: 214.4Å b: 214.4Å c: 131.41Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.2 0.2 0.241
Expression system: Cricetulus griseus