SMTL ID : 2z7i.1

S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with inhibitor BPH-742

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.80, D.84 Ligands: 742.2 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.3: 3 residues within 4Å: Chain B: D.80, D.84 Ligands: 742.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.80, B:D.84, H2O.15

2 x 742: (2,2-DIPHOSPHONOETHYL)(DODECYL)DIMETHYLPHOSPHONIUM(Non-covalent)

742.2: 19 residues within 4Å: Chain A: R.44, L.47, I.51, H.73, L.77, D.80, D.84, R.89, Q.147, K.174, T.175, F.179, T.182, I.203, Y.210, Q.211, D.214, K.238 Ligands: MG.1 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:R.44, A:L.47, A:I.51, A:F.179, A:F.179, A:T.182, A:I.203 Hydrogen bonds: A:R.89, A:R.89, A:Q.211, A:Q.211, A:D.214, A:K.238, A:K.238 Water bridges: A:Q.147, A:D.150, A:D.150 742.4: 19 residues within 4Å: Chain B: R.44, L.47, V.69, H.73, L.77, D.80, D.84, R.89, Q.147, K.174, T.175, F.179, T.182, I.203, Y.210, Q.211, D.214, K.238 Ligands: MG.3 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:R.44, B:L.47, B:V.69, B:F.179, B:F.179, B:T.182, B:I.203, B:Y.210 Hydrogen bonds: B:R.89, B:R.89, B:Q.147, B:Q.211, B:Q.211, B:K.238, B:K.238 Water bridges: B:Y.210

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

2008-07-08

Peptides

Geranylgeranyl pyrophosphate synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Geranylgeranyl pyrophosphate synthetase

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