› 1d3p

X-ray diffraction
2.1Å resolution

CRYSTAL STRUCTURE OF HUMAN APLHA-THROMBIN IN COMPLEX WITH BENZO[B]THIOPHENE INHIBITOR 3

Released:
DOI: 10.2210/pdb1d3p/pdb
PDB entry 1d3p coloured by chain, front view.
PDB entry 1d3p coloured by chain, side view.
PDB entry 1d3p coloured by chain, top view.
Source organisms:
Primary publication:
The crystal structures of human alpha-thrombin complexed with active site-directed diamino benzo[b]thiophene derivatives: a binding mode for a structurally novel class of inhibitors.
Chirgadze NY, Sall DJ, Briggs SL, Clawson DK, Zhang M, Smith GF, Schevitz RW
Protein Sci 9 29-36 (2000)
PMID: 10739244

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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133065 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Thrombin light chain Chain: A
Molecule details ›
Chain: A
Length: 36 amino acids
Theoretical weight: 4.1 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P00734 (Residues: 328-363; Coverage: 6%)
Gene name: F2
Sequence domains: Thrombin light chain
Thrombin heavy chain Chain: B
Molecule details ›
Chain: B
Length: 259 amino acids
Theoretical weight: 29.78 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P00734 (Residues: 364-622; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Hirudin variant-1 Chain: H
Molecule details ›
Chain: H
Length: 12 amino acids
Theoretical weight: 1.55 KDa
Source organism: Hirudo medicinalis
UniProt:
  • Canonical: P01050 (Residues: 54-65; Coverage: 19%)

Ligands and Environments

3 bound ligands:
Ligand NAG 1 x NAG
Ligand NA 2 x NA
Ligand BT3 1 x BT3
1 modified residue:
Ligand TYS 1 x TYS

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: C2
Unit cell:
a: 71.37Å b: 72.01Å c: 73.44Å
α: 90° β: 100.36° γ: 90°
R-values:
R R work R free
0.179 0.179 0.214
Expression system: Not provided

Quick links

Citations

2 review citations

Implications of protein flexibility for drug discovery.
Teague SJ. (2003)
1 more

5 mentions without citation

BP-Dock: a flexible docking scheme for exploring protein-ligand interactions based on unbound structures.
Bolia et al. (2014)
4 more