SMTL ID : 2e8t.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.80, D.84 Ligands: MG.2, FPS.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.80, A:D.84, H2O.1, H2O.3 MG.2: 4 residues within 4Å: Chain A: D.80, D.84 Ligands: MG.1, FPS.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.80, A:D.84, H2O.9, H2O.9 MG.5: 5 residues within 4Å: Chain B: D.80, D.84, R.89 Ligands: MG.6, FPS.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.80, B:D.84, H2O.19 MG.6: 5 residues within 4Å: Chain B: D.80, D.84, Q.147 Ligands: MG.5, FPS.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.80, B:D.84, H2O.12

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

IPE.3: 8 residues within 4Å: Chain A: R.44, H.73, L.77, R.90, Y.210, Q.211, D.214 Ligands: FPS.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.210 Hydrogen bonds: A:Y.210 Water bridges: A:R.44, A:R.44 Salt bridges: A:R.44, A:H.73, A:H.73, A:R.90 IPE.7: 9 residues within 4Å: Chain B: K.38, R.44, H.73, L.77, R.90, Y.210, Q.211, D.214 Ligands: FPS.8 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.77, B:Y.210 Hydrogen bonds: B:R.44, B:Y.210 Water bridges: B:R.90, B:R.90, B:D.214 Salt bridges: B:K.38, B:H.73, B:H.73, B:R.90, B:R.90

2 x FPS: S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE(Non-covalent)

FPS.4: 21 residues within 4Å: Chain A: L.72, S.76, L.77, I.79, D.80, D.84, R.89, Y.112, L.140, L.143, H.144, Q.147, D.150, K.174, L.178, Q.211, D.214, K.238 Ligands: MG.1, MG.2, IPE.3 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:L.77, A:I.79, A:Y.112, A:L.140, A:L.143, A:L.143, A:Q.147, A:Q.147, A:L.178 Hydrogen bonds: A:K.174, A:Q.211, A:D.214, A:D.214, A:K.238 Water bridges: A:D.80, A:D.84, A:D.84, A:D.150, A:K.174, A:D.233 Salt bridges: A:R.89, A:K.238 FPS.8: 21 residues within 4Å: Chain B: L.72, S.76, L.77, I.79, D.80, D.84, R.89, Y.112, L.140, L.143, H.144, Q.147, D.150, K.174, L.178, Q.211, D.214, K.238 Ligands: MG.5, MG.6, IPE.7 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.72, B:L.77, B:I.79, B:Y.112, B:L.140, B:L.143, B:L.143, B:L.143, B:Q.147, B:K.174, B:L.178 Hydrogen bonds: B:K.174, B:Q.211, B:D.214, B:K.238 Salt bridges: B:R.89, B:K.238

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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