› 8jm8

X-ray diffraction
1.7Å resolution

Endo-deglycosylated hydroxynitrile lyase isozyme 5 mutant L331A from Prunus communis complexed with (R)-2-(2,2-dimethyl-4H-benzo[d][1,3]dioxin-6-yl)-2-hydroxyacetonitrile

Released:
DOI: 10.2210/pdb8jm8/pdb
PDB entry 8jm8 coloured by chain, front view.
PDB entry 8jm8 coloured by chain, side view.
PDB entry 8jm8 coloured by chain, top view.
Source organism: Prunus dulcis
Entry authors: Zheng Y-C, Li F-L, Yu H-L, Xu J-H

Function and Biology Details

Reaction catalysed: 
(R)-mandelonitrile = cyanide + benzaldehyde
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-275009 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
(R)-mandelonitrile lyase Chain: A
Molecule details ›
Chain: A
Length: 540 amino acids
Theoretical weight: 59 KDa
Source organism: Prunus dulcis
Expression system: Komagataella pastoris
UniProt:
  • Canonical: Q7XJE8 (Residues: 26-559; Coverage: 100%)
Gene name: hnl5
Sequence domains:

Ligands and Environments


Cofactor: Ligand FAD 1 x FAD
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
4 bound ligands:
Ligand E2Y 1 x E2Y
Ligand NAG 5 x NAG
Ligand PEG 1 x PEG
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P212121
Unit cell:
a: 49.339Å b: 90.442Å c: 125.498Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.179 0.177 0.214
Expression system: Komagataella pastoris

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