6yb6

X-ray diffraction
1.33Å resolution

Thrombin in complex with D-Phe-Pro-3-chloro-1,3-dihydroxybenzylamide derivative (13c)

Released:
Entry authors: Sandner A, Heine A, Klebe G, Abazi N

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:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Thrombin light chain Chain: L
Molecule details ›
Chain: L
Length: 36 amino acids
Theoretical weight: 4.1 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 328-363; Coverage: 6%)
Gene name: F2
Thrombin heavy chain Chain: H
Molecule details ›
Chain: H
Length: 259 amino acids
Theoretical weight: 29.78 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 364-622; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
Hirudin variant-2 Chain: I
Molecule details ›
Chain: I
Length: 12 amino acids
Theoretical weight: 1.55 KDa
Source organism: Hirudo medicinalis
Expression system: Not provided
UniProt:
  • Canonical: P09945 (Residues: 61-72; Coverage: 19%)
D-Phe-Pro-3-chloro-1,3-dihydroxybenzylamide derivative Chain: D
Molecule details ›
Chain: D
Length: 3 amino acids
Theoretical weight: 418 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

Experiments and Validation Details

Entry percentile scores
X-ray source: ELETTRA BEAMLINE 5.2R
Spacegroup: C2
Unit cell:
a: 70.436Å b: 71.2Å c: 72.316Å
α: 90° β: 100.2° γ: 90°
R-values:
R R work R free
0.132 0.131 0.153
Expression system: Not provided