› 1bhx

X-ray diffraction
2.3Å resolution

X-RAY STRUCTURE OF THE COMPLEX OF HUMAN ALPHA THROMBIN WITH THE INHIBITOR SDZ 229-357

Released:
DOI: 10.2210/pdb1bhx/pdb
PDB entry 1bhx coloured by chain, front view.
PDB entry 1bhx coloured by chain, side view.
PDB entry 1bhx coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Rational design, synthesis, and X-ray structure of selective noncovalent thrombin inhibitors.
Wagner J, Kallen J, Ehrhardt C, Evenou JP, Wagner D
J Med Chem 41 3664-74 (1998)
PMID: 9733491

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 domain:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133059 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Thrombin light chain Chain: A
Molecule details ›
Chain: A
Length: 30 amino acids
Theoretical weight: 3.46 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 331-360; Coverage: 5%)
Gene name: F2
Sequence domains: Thrombin light chain
Thrombin heavy chain Chain: B
Molecule details ›
Chain: B
Length: 147 amino acids
Theoretical weight: 17.07 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 364-510; Coverage: 25%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Thrombin heavy chain Chain: F
Molecule details ›
Chain: F
Length: 105 amino acids
Theoretical weight: 11.97 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 518-622; Coverage: 18%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
ALPHA THROMBIN Chain: E
Molecule details ›
Chain: E
Length: 5 amino acids
Theoretical weight: 652 Da
Source organism: Homo sapiens

Ligands and Environments

1 bound ligand:
Ligand R56 1 x R56
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ENRAF-NONIUS FR571
Spacegroup: C2
Unit cell:
a: 71Å b: 72.2Å c: 73.1Å
α: 90° β: 100.7° γ: 90°
R-values:
R R work R free
0.187 0.187 0.232

Quick links

Citations

4 review citations

Design, synthesis, and application of azabicyclo[X.Y.0]alkanone amino acids as constrained dipeptide surrogates and peptide mimics.
Cluzeau et al. (2005)
3 more

2 mentions without citation

Using parallelized incremental meta-docking can solve the conformational sampling issue when docking large ligands to proteins.
Devaurs et al. (2019)
1 more