SMTL ID : 2e8w.1

S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with magnesium and IPP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 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, Q.147 Ligands: MG.2, IPE.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.80, A:D.84, A:D.84, H2O.3, H2O.3 MG.2: 4 residues within 4Å: Chain A: D.80, D.84 Ligands: MG.1, IPE.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.80, A:D.84, H2O.3, H2O.6 MG.4: 5 residues within 4Å: Chain B: D.80, D.84, R.89 Ligands: MG.5, IPE.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.80, B:D.84 MG.5: 5 residues within 4Å: Chain B: D.80, D.84, Q.147 Ligands: MG.4, IPE.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.80, B:D.84, H2O.10

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

IPE.3: 12 residues within 4Å: Chain A: S.76, D.80, D.84, R.89, L.143, Q.147, K.174, Q.211, D.214, K.238 Ligands: MG.1, MG.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.143 Hydrogen bonds: A:Q.211, A:D.214 Water bridges: A:D.80, A:D.80, A:D.84, A:D.84, A:R.89, A:Q.147, A:K.174, A:N.218, A:K.238 Salt bridges: A:R.89, A:K.174, A:K.238, A:K.238 IPE.6: 13 residues within 4Å: Chain B: S.76, D.80, D.84, R.89, L.143, Q.147, K.174, Q.211, D.214, K.238 Ligands: MG.4, MG.5, IPE.7 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:K.174 Hydrogen bonds: B:Q.211, B:Q.211, B:D.214 Water bridges: B:N.218, B:K.238, B:K.238 Salt bridges: B:R.89, B:K.174, B:K.238, B:K.238 IPE.7: 11 residues within 4Å: Chain B: K.38, P.39, G.40, R.44, H.73, L.77, R.90, Y.210, Q.211, D.214 Ligands: IPE.6 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.210 Hydrogen bonds: B:R.44, B:Y.210 Water bridges: B:G.40 Salt bridges: B:K.38, B:H.73, B:H.73, B:R.90, B:R.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, R.T. et al., Bisphosphonates target multiple sites in both cis- and trans-prenyltransferases. Proc.Natl.Acad.Sci.Usa (2007)

Release Date

2007-06-12

Peptides

Geranylgeranyl pyrophosphate synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Geranylgeranyl pyrophosphate synthetase

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