› 5eb5

X-ray diffraction
2.8Å resolution

The crystal structure of almond HNL, PaHNL5 V317A, in complex with benzyl alcohol

Released:
DOI: 10.2210/pdb5eb5/pdb
Model geometry
Fit model/data
PDB entry 5eb5 coloured by chain, front view.
PDB entry 5eb5 coloured by chain, side view.
PDB entry 5eb5 coloured by chain, top view.
Source organism: Prunus dulcis
Primary publication:
Structures of almond hydroxynitrile lyase isoenzyme 5 provide a rationale for the lack of oxidoreductase activity in flavin dependent HNLs.
Pavkov-Keller T, Bakhuis J, Steinkellner G, Jolink F, Keijmel E, Birner-Gruenberger R, Gruber K
J Biotechnol 235 24-31 (2016)
PMID: 27067080

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 Chains: A, B
Molecule details ›
Chains: A, B
Length: 532 amino acids
Theoretical weight: 57.9 KDa
Source organism: Prunus dulcis
Expression system: Aspergillus niger
UniProt:
  • Canonical: O24243 (Residues: 28-559; Coverage: 100%)
Gene name: MDL1
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand FAD 2 x FAD
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
2 bound ligands:
Ligand NAG 4 x NAG
Ligand 010 2 x 010
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ELETTRA BEAMLINE 5.2R
Spacegroup: P21
Unit cell:
a: 68.364Å b: 95.161Å c: 92.19Å
α: 90° β: 90.01° γ: 90°
R-values:
R R work R free
0.224 0.222 0.259
Expression system: Aspergillus niger

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Citations

1 citations in other articles

Structural characterization of Linum usitatissimum hydroxynitrile lyase: A new cyanohydrin decomposition mechanism involving a cyano-zinc complex.
Zheng et al. (2022)