› 1y5b

X-ray diffraction
1.65Å resolution

Dianhydrosugar-based benzamidine, factor Xa specific inhibitor in complex with bovine trypsin mutant

Released:
DOI: 10.2210/pdb1y5b/pdb
PDB entry 1y5b coloured by chain, front view.
PDB entry 1y5b coloured by chain, side view.
PDB entry 1y5b coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
Understanding binding selectivity toward trypsin and factor Xa: the role of aromatic interactions.
Di Fenza A, Heine A, Koert U, Klebe G
ChemMedChem 2 297-308 (2007)
PMID: 17191291

Function and Biology Details

Reaction catalysed: 
Preferential cleavage: Arg-|-, Lys-|-.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133319 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Serine protease 1 Chain: T
Molecule details ›
Chain: T
Length: 223 amino acids
Theoretical weight: 23.39 KDa
Source organism: Bos taurus
Expression system: Escherichia coli
UniProt:
  • Canonical: P00760 (Residues: 24-246; Coverage: 97%)
Gene names: PRSS1, TRP1, TRY1, TRYP1
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases

Ligands and Environments

4 bound ligands:
Ligand SO4 2 x SO4
Ligand CA 1 x CA
Ligand TL3 1 x TL3
Ligand IMD 1 x IMD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: P3121
Unit cell:
a: 54.366Å b: 54.366Å c: 105.14Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.162 0.16 0.221
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Aromatic rings in chemical and biological recognition: energetics and structures.
Salonen et al. (2011)
1 more