SMTL ID : 5wwd.1

Crystal structure of AtNUDX1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

homo-dimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: P.105, K.106, N.107, G.115, W.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.116 Water bridges: A:P.105 GOL.7: 3 residues within 4Å: Chain B: W.121, E.122 Ligands: GOL.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.122, B:N.141 GOL.8: 3 residues within 4Å: Chain B: R.30, S.36, E.114 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.30, B:R.30, B:S.36, B:S.36 Water bridges: B:R.30, B:N.35, B:N.35 GOL.9: 6 residues within 4Å: Chain B: N.22, W.121, E.122, N.141, F.143 Ligands: GOL.7 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.22, B:E.122, B:E.122, B:N.141, B:N.141

1 x 2ME: METHOXYETHANE(Non-covalent)

2ME.2: 5 residues within 4Å: Chain A: N.77, N.78, V.79, W.130, K.134 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.130 Hydrogen bonds: A:V.79

1 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.3: 6 residues within 4Å: Chain A: N.78, F.80, Y.89, S.91, F.129, P.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.91, A:S.91

6 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: G.43, H.44 Ligands: MG.5 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.44, H2O.2 MG.5: 3 residues within 4Å: Chain A: E.58 Ligands: MG.4, MG.6 No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain A: E.58, E.61, E.62, E.109 Ligands: MG.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.58, A:E.61, A:E.109, H2O.2 MG.10: 3 residues within 4Å: Chain B: E.58 Ligands: MG.11, MG.12 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain B: G.43, H.44 Ligands: MG.10 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.44 MG.12: 6 residues within 4Å: Chain B: E.58, E.61, E.62, E.109, K.112 Ligands: MG.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.61, B:E.109

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

2017-11-15

Peptides

Nudix hydrolase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nudix hydrolase 1

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