SMTL ID : 5z0c.1

Nerol dehydrogenase from Persicaria minor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.104, H.105, C.107, C.110, C.118 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.104, A:C.107, A:C.110, A:C.118 ZN.2: 4 residues within 4Å: Chain A: C.51, S.53, H.73, C.167 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.51, A:H.73, A:C.167, H2O.6 ZN.6: 5 residues within 4Å: Chain B: C.104, H.105, C.107, C.110, C.118 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.104, B:C.107, B:C.110, B:C.118 ZN.7: 4 residues within 4Å: Chain B: C.51, S.53, H.73, C.167 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.51, B:H.73, B:C.167, H2O.21

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: E.327, I.329, P.330, Y.333 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.327, A:E.327 GOL.4: 7 residues within 4Å: Chain A: Y.178, Y.179, G.180, K.274 Chain B: K.274, M.298 Ligands: GOL.9 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.274, A:K.274, B:K.274, B:K.274 Water bridges: A:Y.178 GOL.8: 4 residues within 4Å: Chain B: E.327, I.329, P.330, Y.333 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.327, B:E.327 GOL.9: 7 residues within 4Å: Chain A: K.274, M.298 Chain B: Y.178, Y.179, G.180, K.274 Ligands: GOL.4 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.274, A:K.274, B:K.274, B:K.274 Water bridges: B:Y.178

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.5: 5 residues within 4Å: Chain A: C.51, H.52, G.195, L.196, R.349 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.52, A:R.349, A:R.349 BME.10: 5 residues within 4Å: Chain B: C.51, H.52, G.195, L.196, R.349 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.52, B:R.349, B:R.349

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, C.S. et al., Structural and kinetic studies of a novel nerol dehydrogenase from Persicaria minor, a nerol-specific enzyme for citral biosynthesis. Plant Physiol. Biochem. (2017)

Release Date

2018-01-17

Peptides

Nerol dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Nerol dehydrogenase