SMTL ID : 2z4v.1

S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with magnesium and GGPP (inhibitory site)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.80, D.84, D.150 Ligands: MG.2, GRG.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.80, A:D.84, H2O.1, H2O.1, H2O.2 MG.2: 4 residues within 4Å: Chain A: D.80, D.84 Ligands: MG.1, GRG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.80, A:D.84, H2O.1, H2O.11 MG.4: 5 residues within 4Å: Chain B: D.80, D.84, R.89 Ligands: MG.5, GRG.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.80, B:D.84, H2O.18, H2O.21 MG.5: 4 residues within 4Å: Chain B: D.80, D.84 Ligands: MG.4, GRG.6 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.80, B:D.84, H2O.17, H2O.18, H2O.21

2 x GRG: GERANYLGERANYL DIPHOSPHATE(Non-covalent)

GRG.3: 22 residues within 4Å: Chain A: R.44, L.47, I.48, V.69, H.73, L.77, D.80, D.84, R.89, L.143, Q.147, K.174, L.178, F.179, T.182, I.203, Y.210, Q.211, D.214, K.238 Ligands: MG.1, MG.2 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:L.47, A:L.47, A:I.48, A:H.73, A:L.77, A:L.143, A:L.178, A:F.179, A:F.179, A:T.182, A:I.203, A:Y.210 Hydrogen bonds: A:Q.211 Water bridges: A:R.89, A:R.89, A:D.150, A:K.238, A:K.238, A:K.238 Salt bridges: A:R.89, A:K.174, A:K.238, A:K.238 GRG.6: 23 residues within 4Å: Chain B: L.47, I.48, I.51, V.69, H.73, S.76, L.77, D.80, D.84, R.89, L.143, Q.147, K.174, L.178, F.179, T.182, I.203, Y.210, Q.211, D.214, K.238 Ligands: MG.4, MG.5 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:L.47, B:L.47, B:I.48, B:I.51, B:V.69, B:H.73, B:L.77, B:L.143, B:L.178, B:F.179, B:F.179, B:T.182, B:I.203, B:Y.210 Hydrogen bonds: B:Q.147, B:Q.211 Water bridges: B:D.84, B:D.84, B:D.84, B:D.150, B:Y.210, B:Y.210, B:Y.210, B:K.238, B:K.238, B:K.238 Salt bridges: B:R.89, B:K.174, B:K.238, B:K.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, C.K.-M. et al., Inhibition of geranylgeranyl diphosphate synthase by bisphosphonates: a crystallographic and computational investigation. J.Med.Chem. (2008)

Release Date

2008-07-01

Peptides

Geranylgeranyl pyrophosphate synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Geranylgeranyl pyrophosphate synthetase

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