› 6t54

X-ray diffraction
1.57Å resolution

Thrombin in Complex with a D-Phe-Pro-2-bromothiophene Derivative

Released:
DOI: 10.2210/pdb6t54/pdb
PDB entry 6t54 coloured by chain, front view.
PDB entry 6t54 coloured by chain, side view.
PDB entry 6t54 coloured by chain, top view.
Source organisms:
Entry authors: Ngo K, Abazi N, Heine A, Klebe G

Function and Biology Details

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

5 bound ligands:
Ligand NA 2 x NA
Ligand DMS 2 x DMS
Ligand GOL 1 x GOL
Ligand NAG 1 x NAG
Ligand MJK 1 x MJK
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: 70.291Å b: 71.383Å c: 72.751Å
α: 90° β: 100.574° γ: 90°
R-values:
R R work R free
0.139 0.138 0.17
Expression system: Not provided

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