› 3vsy

X-ray diffraction
1.5Å resolution

High-resolution crystal structure of wild-type KSI in the apo form at neutral pH

Released:
DOI: 10.2210/pdb3vsy/pdb
PDB entry 3vsy coloured by chain, front view.
PDB entry 3vsy coloured by chain, side view.
PDB entry 3vsy coloured by chain, top view.
Source organism: Pseudomonas putida
Primary publication:
Incorporation of rapid thermodynamic data in fragment-based drug discovery.
Kobe A, Caaveiro JM, Tashiro S, Kajihara D, Kikkawa M, Mitani T, Tsumoto K
J Med Chem 56 2155-9 (2013)
PMID: 23419007

Function and Biology Details

Reaction catalysed: 
A 3-oxo-Delta(5)-steroid = a 3-oxo-Delta(4)-steroid
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139594 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Steroid Delta-isomerase Chains: A, B
Molecule details ›
Chains: A, B
Length: 132 amino acids
Theoretical weight: 14.5 KDa
Source organism: Pseudomonas putida
Expression system: Escherichia coli
UniProt:
  • Canonical: P07445 (Residues: 3-131; Coverage: 99%)
Gene name: ksi
Sequence domains: SnoaL-like domain
Structure domains: Nuclear Transport Factor 2; Chain: A,

Ligands and Environments

1 bound ligand:
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P212121
Unit cell:
a: 35.563Å b: 73.353Å c: 95.549Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.152 0.15 0.202
Expression system: Escherichia coli

Quick links

Citations

1 review citation

[Biophysical Analysis of the Protein-Small Molecule Interactions to Develop Small Molecule Drug Discovery].
Nagatoishi et al. (2018)
5 other articles

3 mentions without citation

Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray-derived conformational ensembles.
Yabukarski et al. (2020)
2 more