PDBe 4dt7

X-ray diffraction
1.9Å resolution

Crystal structure of thrombin bound to the activation domain QEDQVDPRLIDGKMTRRGDS of protein C

Released:

Function and Biology Details

Reactions catalysed:
Selective cleavage of Arg-|-Gly bonds in fibrinogen to form fibrin and release fibrinopeptides A and B.
Degradation of blood coagulation factors Va and VIIIa.
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Thrombin light chain Chains: A, C
Molecule details ›
Chains: A, C
Length: 32 amino acids
Theoretical weight: 3.7 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P00734 (Residues: 332-363; Coverage: 5%)
Gene name: F2
Thrombin heavy chain Chains: B, D
Molecule details ›
Chains: B, D
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
Activation peptide Chains: E, F
Molecule details ›
Chains: E, F
Length: 20 amino acids
Theoretical weight: 2.32 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P04070 (Residues: 204-223; Coverage: 5%)
Gene name: PROC

Ligands and Environments

3 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P21
Unit cell:
a: 46.395Å b: 84.272Å c: 66.363Å
α: 90° β: 94.59° γ: 90°
R-values:
R R work R free
0.178 0.176 0.218
Expression systems:
  • Escherichia coli
  • Not provided