SMTL ID : 2zev.1

S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Magnesium, IPP and BPH-715

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.23 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, B71.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.80, A:D.84 MG.2: 4 residues within 4Å: Chain A: D.80, D.84 Ligands: MG.1, B71.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.80, A:D.84 MG.4: 5 residues within 4Å: Chain B: D.80, D.84, R.89 Ligands: MG.5, B71.7 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, B71.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.80, B:D.84, H2O.16

2 x B71: 3-(DECYLOXY)-1-(2,2-DIPHOSPHONOETHYL)PYRIDINIUM(Non-covalent)

B71.3: 20 residues within 4Å: Chain A: R.44, L.47, V.69, H.73, L.77, D.80, D.84, R.89, L.143, Q.147, K.174, T.175, F.179, T.182, Y.210, Q.211, D.214, K.238 Ligands: MG.1, MG.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:R.44, A:L.47, A:V.69, A:L.143, A:K.174, A:T.175, A:F.179, A:F.179, A:T.182, A:Y.210 Hydrogen bonds: A:R.89, A:R.89, A:Q.211, A:Q.211, A:K.238, A:K.238 Water bridges: A:D.214, A:D.233 B71.7: 20 residues within 4Å: Chain B: R.44, L.47, V.69, H.73, L.77, D.80, D.84, R.89, L.143, Q.147, K.174, L.178, F.179, T.182, Q.211, D.214, K.238 Ligands: MG.4, MG.5, IPE.6 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:R.44, B:R.44, B:L.47, B:V.69, B:L.143, B:K.174, B:L.178, B:F.179, B:F.179 Hydrogen bonds: B:R.89, B:R.89, B:K.174, B:Q.211, B:D.214, B:K.238, B:K.238 Water bridges: B:S.76

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

IPE.6: 7 residues within 4Å: Chain B: K.38, R.44, H.73, L.77, Y.210, Q.211 Ligands: B71.7 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.77, B:Y.210 Hydrogen bonds: B:R.89, B:Y.210 Water bridges: B:R.90 Salt bridges: B:K.38, B:R.44, B:H.73, B:H.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., Lipophilic bisphosphonates as dual farnesyl/geranylgeranyl diphosphate synthase inhibitors: an X-ray and NMR investigation. J.Am.Chem.Soc. (2009)

Release Date

2008-12-23

Peptides

Geranylgeranyl pyrophosphate synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Geranylgeranyl pyrophosphate synthetase

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