› 3gdn

X-ray diffraction
1.67Å resolution

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188191 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (5 distinct):
(R)-mandelonitrile lyase 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 521 amino acids
Theoretical weight: 56.54 KDa
Source organism: Prunus dulcis
UniProt:
  • Canonical: Q945K2 (Residues: 28-548; Coverage: 97%)
Gene names: HNL1, MDL2
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand FAD 2 x FAD
Carbohydrate polymer : NEW Components: NAG, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, MAN, FUC, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, MAN, BMA
Carbohydrate polymer
3 bound ligands:
Ligand NAG 2 x NAG
Ligand HBX 2 x HBX
Ligand MXN 4 x MXN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE BW7B
Spacegroup: P21
Unit cell:
a: 68.98Å b: 93.79Å c: 86.9Å
α: 90° β: 106.47° γ: 90°
R-values:
R R work R free
0.174 0.174 0.197

Quick links

Citations

4 review citations

Convergent evolution in plant specialized metabolism.
Pichersky et al. (2011)
3 more

2 mentions without citation

Substrate binding in the FAD-dependent hydroxynitrile lyase from almond provides insight into the mechanism of cyanohydrin formation and explains the absence of dehydrogenation activity.
Dreveny et al. (2009)
1 more