› 6jby

X-ray diffraction
1.6Å resolution

Crystal structure of endo-deglycosylated hydroxynitrile lyase isozyme 5 of Prunus communis

Released:
DOI: 10.2210/pdb6jby/pdb
PDB entry 6jby coloured by chain, front view.
PDB entry 6jby coloured by chain, side view.
PDB entry 6jby coloured by chain, top view.
Source organism: Prunus dulcis
Primary publication:
Structure-Guided Tuning of a Hydroxynitrile Lyase to Accept Rigid Pharmaco Aldehydes.
Zheng YC, Li FL, Lin ZM, Lin GQ, Hong R, Yu HL, Xu JH
ACS Catalysis (2020)

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127668 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
(R)-mandelonitrile lyase 1 Chain: A
Molecule details ›
Chain: A
Length: 542 amino acids
Theoretical weight: 59.19 KDa
Source organism: Prunus dulcis
Expression system: Komagataella pastoris
UniProt:
  • Canonical: O24243 (Residues: 26-559; Coverage: 100%)
Gene name: MDL1
Sequence domains:

Ligands and Environments


Cofactor: Ligand FAD 1 x FAD
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
1 bound ligand:
Ligand NAG 5 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P212121
Unit cell:
a: 49.525Å b: 91.307Å c: 132.018Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.159 0.158 0.183
Expression system: Komagataella pastoris

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