› 7ycd

X-ray diffraction
2.01Å resolution

HYDROXYNITRILE LYASE FROM THE MILLIPEDE, Oxidus gracilis bound with (R)-(+)-ALPHA-HYDROXYBENZENE-ACETONITRILE

Released:
DOI: 10.2210/pdb7ycd/pdb
PDB entry 7ycd coloured by chain, front view.
PDB entry 7ycd coloured by chain, side view.
PDB entry 7ycd coloured by chain, top view.
Source organism: Oxidus gracilis
Primary publication:
Structure-Based Site-Directed Mutagenesis of Hydroxynitrile Lyase from Cyanogenic Millipede, Oxidus gracilis for Hydrocyanation and Henry Reactions.
Chaikaew S, Watanabe Y, Zheng D, Motojima F, Yamaguchi T, Asano Y
Chembiochem 25 e202400118 (2024)
PMID: 38526556

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-238832 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Hydroxynitrile lyase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 184 amino acids
Theoretical weight: 20.38 KDa
Source organism: Oxidus gracilis
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A2Z5XCT7 (Residues: 1-184; Coverage: 100%)
Gene name: OgraHNL

Ligands and Environments

2 bound ligands:
Ligand MXN 8 x MXN
Ligand SO4 6 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P63
Unit cell:
a: 123.43Å b: 123.43Å c: 129.87Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.203 0.202 0.233
Expression system: Escherichia coli

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