SMTL ID : 2z4w.1

S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with magnesium and BPH-749

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 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, E.236 Ligands: MG.2, 749.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.80, A:D.84, A:D.84 MG.2: 4 residues within 4Å: Chain A: D.80, D.84 Ligands: MG.1, 749.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.80, A:D.84, H2O.2, H2O.6 MG.4: 4 residues within 4Å: Chain B: D.80, D.84 Ligands: MG.5, 749.6 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.80, B:D.80, B:D.84, H2O.8, H2O.12 MG.5: 6 residues within 4Å: Chain B: D.80, D.84, Q.147, D.150 Ligands: MG.4, 749.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.80, B:D.84

2 x 749: [(6E,11E)-2,6,12,16-tetramethylheptadeca-2,6,11,15-tetraene-9,9-diyl]bis(phosphonic acid)(Non-covalent)

749.3: 19 residues within 4Å: Chain A: R.44, H.73, S.76, D.80, D.84, R.89, Y.112, L.143, H.144, Q.147, K.174, F.179, Y.210, Q.211, D.214, K.238 Chain B: N.106 Ligands: MG.1, MG.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:R.44, A:L.143, A:L.143, A:Q.147, A:Q.147, A:K.174, A:F.179, A:Y.210 Hydrogen bonds: A:R.89, A:R.89, A:K.174, A:Q.211, A:K.238, A:K.238 Water bridges: A:D.214 749.6: 20 residues within 4Å: Chain A: N.106 Chain B: H.73, S.76, L.77, I.79, D.80, D.84, R.89, Y.112, L.143, H.144, Q.147, K.174, F.179, Y.210, Q.211, D.214, K.238 Ligands: MG.4, MG.5 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.77, B:I.79, B:L.143, B:L.143, B:Q.147, B:Q.147, B:F.179, B:Y.210 Hydrogen bonds: B:R.89, B:R.89, B:Q.211, B:K.238, 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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