PDBe 4mlf

X-ray diffraction
2.2Å resolution

Crystal structure for the complex of thrombin mutant D102N and hirudin

Released:
Source organisms:
Primary publication:
Essential role of conformational selection in ligand binding.
Biophys. Chem. (2013)
PMID: 24113284

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Thrombin light chain Chain: A
Molecule details ›
Chain: A
Length: 33 amino acids
Theoretical weight: 3.79 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: P00734 (Residues: 331-363; Coverage: 6%)
Gene name: F2
Thrombin heavy chain Chain: B
Molecule details ›
Chain: B
Length: 259 amino acids
Theoretical weight: 29.78 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
Hirudin variant-1 Chain: D
Molecule details ›
Chain: D
Length: 65 amino acids
Theoretical weight: 6.97 KDa
Source organism: Hirudo medicinalis
Expression system: Escherichia coli
UniProt:
  • Canonical: P01050 (Residues: 1-65; Coverage: 100%)
Sequence domains: Hirudin
Structure domains: Thrombin Inhibitor (Hirudin), subunit I

Ligands and Environments

3 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P43212
Unit cell:
a: 89.506Å b: 89.506Å c: 133.148Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.198 0.234
Expression systems:
  • Cricetulus griseus
  • Escherichia coli