› 6yb6

X-ray diffraction
1.33Å resolution

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

Released:
DOI: 10.2210/pdb6yb6/pdb
PDB entry 6yb6 coloured by chain, front view.
PDB entry 6yb6 coloured by chain, side view.
PDB entry 6yb6 coloured by chain, top view.
Source organisms:
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:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133082 (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
Sequence domains: Thrombin light chain
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

6 bound ligands:
Ligand NA 2 x NA
Ligand DMS 2 x DMS
Ligand NAG 1 x NAG
Ligand PO4 1 x PO4
Ligand PRO 1 x PRO
Ligand OJK 1 x OJK
2 modified residues:
Ligand TYS 1 x TYS
Ligand DPN 1 x DPN

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

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