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

Mint deletion mutant of heterotetrameric geranyl pyrophosphate synthase in complex with ligands

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-2-2-mer

Ligands

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.1: 3 residues within 4Å: Chain A: K.44, R.47, H.76 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.44 Water bridges: A:R.47, A:R.47, A:R.95, A:R.95 Salt bridges: A:R.47, A:H.76, A:H.76

2 x DST: DIMETHYLALLYL S-THIOLODIPHOSPHATE(Non-covalent)

DST.2: 10 residues within 4Å: Chain A: S.79, L.80, D.83, D.89, R.94, L.152, Q.156, K.180 Ligands: MG.3, MG.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.152, A:K.180 Hydrogen bonds: A:K.180 Water bridges: A:D.89, A:D.159 Salt bridges: A:R.94 DST.7: 16 residues within 4Å: Chain D: S.79, L.80, D.83, D.89, R.94, L.152, Q.156, K.180, T.181, Q.218, D.221, K.235, K.245 Ligands: IPE.6, MG.8, MG.9 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:L.80, D:L.152, D:K.180 Hydrogen bonds: D:K.180, D:Q.218 Water bridges: D:D.89, D:D.89, D:D.89, D:D.89, D:K.245, D:K.245 Salt bridges: D:R.94, D:K.235

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.83, D.89 Ligands: DST.2, MG.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.83, A:D.83, A:D.89, H2O.4, H2O.4 MG.4: 7 residues within 4Å: Chain A: D.83, D.84, D.89, D.91, R.94 Ligands: DST.2, MG.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.83, A:D.89, H2O.5 MG.8: 4 residues within 4Å: Chain D: D.221, D.225, D.240 Ligands: DST.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.221 MG.9: 4 residues within 4Å: Chain D: D.83, D.89, D.91 Ligands: DST.7 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.83, D:D.89, H2O.18, H2O.22

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

EDO.5: 6 residues within 4Å: Chain C: I.12, A.41, T.42, S.45, T.46, H.70 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.42, C:H.70 Water bridges: C:E.9, C:T.42

1 x IPE: 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

IPE.6: 11 residues within 4Å: Chain D: G.43, K.44, R.47, H.76, L.80, R.95, T.181, F.217, Q.218, D.221 Ligands: DST.7 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:L.80, D:F.217, D:D.221 Hydrogen bonds: D:K.44, D:R.293 Water bridges: D:R.45, D:R.47, D:R.47, D:K.235 Salt bridges: D:K.44, D:K.44, D:R.47, D:H.76, D:H.76, D:R.95, D:K.235

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hsieh, F.-L. et al., Enhanced specificity of mint geranyl pyrophosphate synthase by modifying the R-loop interactions. J.Mol.Biol. (2010)

Release Date

2010-11-03

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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