› 6t53

X-ray diffraction
1.35Å resolution

Thrombin in Complex with a D-Phe-Pro-p-benzylamine derivative

Released:
DOI: 10.2210/pdb6t53/pdb
PDB entry 6t53 coloured by chain, front view.
PDB entry 6t53 coloured by chain, side view.
PDB entry 6t53 coloured by chain, top view.
Source organisms:
Entry authors: Ngo K, Abazi N, Heine A, Klebe G

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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133076 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 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: 11 amino acids
Theoretical weight: 1.49 KDa
Source organism: Hirudo medicinalis
Expression system: Not provided
UniProt:
  • Canonical: P09945 (Residues: 62-72; Coverage: 17%)

Ligands and Environments

6 bound ligands:
Ligand NA 2 x NA
Ligand DMS 2 x DMS
Ligand K73 1 x K73
Ligand GOL 6 x GOL
Ligand PO4 1 x PO4
Ligand NAG 1 x NAG
1 modified residue:
Ligand TYS 1 x TYS

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: C2
Unit cell:
a: 70.167Å b: 71.412Å c: 72.475Å
α: 90° β: 100.567° γ: 90°
R-values:
R R work R free
0.13 0.129 0.151
Expression system: Not provided

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