SMTL ID : 5gp0.1 (2 other biounits)

Crystal structure of geraniol-NUDX1 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: R.30, S.36, E.114 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.30, A:R.30, A:S.36, A:E.114 Water bridges: A:N.35, A:N.35, A:N.35, A:N.35, A:S.36 GOL.4: 3 residues within 4Å: Chain C: R.30, S.36, E.114 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.30, C:N.35, C:E.114

4 x GPP: GERANYL DIPHOSPHATE(Non-covalent)

GPP.2: 12 residues within 4Å: Chain A: A.13, V.15, R.29, S.31, H.44, T.76, N.78, F.80, Y.89, S.91, F.129, P.131 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.13, A:V.15, A:F.80, A:P.131 Hydrogen bonds: A:S.31, A:Y.89 Water bridges: A:Y.89 Salt bridges: A:R.29, A:R.29, A:H.44 GPP.3: 12 residues within 4Å: Chain B: V.15, R.29, S.31, I.33, A.39, L.40, H.44, N.78, F.80, Y.89, S.91, F.129 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:V.15, B:A.39, B:L.40, B:N.78, B:F.80, B:Y.89, B:F.129, B:F.129 Hydrogen bonds: B:S.31 Water bridges: B:R.29, B:R.29, B:S.87, B:S.87, B:Y.89, B:Y.89 Salt bridges: B:R.29, B:R.29, B:H.44 GPP.5: 13 residues within 4Å: Chain C: V.15, R.29, S.31, I.33, L.40, H.44, T.76, F.80, Y.89, S.91, F.129, P.131, L.132 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:V.15, C:L.40, C:F.80, C:Y.89, C:F.129, C:P.131, C:P.131, C:L.132 Hydrogen bonds: C:S.31, C:Y.89 Salt bridges: C:R.29, C:R.29, C:H.44 GPP.6: 13 residues within 4Å: Chain D: A.13, V.15, R.29, S.31, A.39, L.40, H.44, N.78, F.80, Y.89, S.91, F.129, P.131 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:A.13, D:V.15, D:A.39, D:F.80, D:F.129, D:F.129, D:P.131 Hydrogen bonds: D:R.29, D:S.31, D:Y.89 Salt bridges: D:R.29, D:H.44, D:H.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, J. et al., Structural Insights into the Substrate Recognition Mechanism of Arabidopsis GPP-Bound NUDX1 for Noncanonical Monoterpene Biosynthesis. Mol Plant (2018)

Release Date

2017-10-04

Peptides

Nudix hydrolase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
I

D
A

Nudix hydrolase 1

Related Entries With Identical Sequence