SMTL ID : 3krp.1 (2 other biounits)

Mint heterotetrameric geranyl pyrophosphate synthase in complex with magnesium and GPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

hetero-2-2-mer

Ligands

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.1: 6 residues within 4Å: Chain A: D.83, D.89, R.94, K.180 Ligands: MG.2, MG.3 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.94, A:R.94 Salt bridges: A:R.94, A:K.180

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.83, D.84, D.89, D.91 Ligands: PPV.1, MG.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.89, A:D.91, H2O.8 MG.3: 4 residues within 4Å: Chain A: D.83, D.89 Ligands: PPV.1, MG.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.83, A:D.83, A:D.89, A:D.89, H2O.8 MG.6: 3 residues within 4Å: Chain D: D.83, D.89, D.91 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.89, D:D.91, H2O.24, H2O.30 MG.7: 4 residues within 4Å: Chain D: D.84, D.91, L.93, R.94 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.84, H2O.30

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 7 residues within 4Å: Chain C: E.9, I.12, A.41, T.42, S.45, T.46, H.70 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.9, C:T.42, C:S.45, C:T.46, C:H.70

1 x GPP: GERANYL DIPHOSPHATE(Non-covalent)

GPP.5: 13 residues within 4Å: Chain D: K.44, R.47, H.76, S.79, L.80, D.83, R.95, L.152, Q.156, K.180, F.217, Q.218, D.221 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:L.80, D:D.83, D:L.152 Hydrogen bonds: D:K.44 Water bridges: D:K.44, D:R.45 Salt bridges: D:K.44, D:K.44, D:R.47, D:H.76, D:H.76, D:R.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, T.-H. et al., Structure of a heterotetrameric geranyl pyrophosphate synthase from mint (Mentha piperita) reveals intersubunit regulation. Plant Cell (2010)

Release Date

2010-02-23

Peptides

Geranyl diphosphate synthase large subunit: AD
Geranyl diphosphate synthase small subunit: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

C
C

Geranyl diphosphate synthase large subunit

Geranyl diphosphate synthase small subunit

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