SMTL ID : 1zw5.1

X-ray structure of Farnesyl diphosphate synthase protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.105, D.109 Ligands: MG.3, ZOL.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.105, A:D.109, H2O.1, H2O.1 MG.2: 2 residues within 4Å: Chain A: D.245 Ligands: ZOL.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.245, H2O.1, H2O.1, H2O.2 MG.3: 6 residues within 4Å: Chain A: D.105, D.109, D.176, K.268 Ligands: MG.1, ZOL.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.105, A:D.109, H2O.1, H2O.1, H2O.1 MG.6: 4 residues within 4Å: Chain B: D.105, D.109 Ligands: MG.8, ZOL.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.105, B:D.109, H2O.3, H2O.3 MG.7: 2 residues within 4Å: Chain B: D.245 Ligands: ZOL.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.245, H2O.3, H2O.3, H2O.5 MG.8: 6 residues within 4Å: Chain B: D.105, D.109, D.176, K.268 Ligands: MG.6, ZOL.10 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.105, B:D.109, H2O.3, H2O.3, H2O.3

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

IPE.4: 12 residues within 4Å: Chain A: G.58, K.59, R.62, Q.98, R.115, T.203, Y.206, S.207, F.241, Q.242, D.245 Ligands: ZOL.5 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:T.203, A:F.241, A:D.245 Hydrogen bonds: A:K.59, A:R.62, A:Q.98 Water bridges: A:K.59, A:K.59, A:K.59, A:Y.60, A:Y.60, A:Y.60, A:Y.60, A:R.62 Salt bridges: A:K.59, A:K.59, A:R.62, A:R.115 IPE.9: 12 residues within 4Å: Chain B: G.58, K.59, R.62, Q.98, R.115, T.203, Y.206, S.207, F.241, Q.242, D.245 Ligands: ZOL.10 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:T.203, B:F.241, B:D.245 Hydrogen bonds: B:K.59, B:R.62, B:Q.98 Water bridges: B:K.59, B:K.59, B:K.59, B:Y.60, B:Y.60, B:Y.60, B:Y.60, B:R.62 Salt bridges: B:K.59, B:K.59, B:R.62, B:R.115

2 x ZOL: ZOLEDRONIC ACID(Non-covalent)

ZOL.5: 13 residues within 4Å: Chain A: D.105, D.109, R.114, Q.173, K.202, T.203, Q.242, D.245, K.259 Ligands: MG.1, MG.2, MG.3, IPE.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.109, A:D.109, A:R.114, A:R.114, A:Q.242, A:D.245 Water bridges: A:S.111, A:S.111, A:Q.173, A:K.202, A:K.202, A:D.249 ZOL.10: 13 residues within 4Å: Chain B: D.105, D.109, R.114, Q.173, K.202, T.203, Q.242, D.245, K.259 Ligands: MG.6, MG.7, MG.8, IPE.9 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:D.109, B:R.114, B:R.114, B:Q.242, B:D.245 Water bridges: B:S.111, B:S.111, B:Q.173, B:K.202, B:K.202, B:K.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kavanagh, K.L. et al., The molecular mechanism of nitrogen-containing bisphosphonates as antiosteoporosis drugs. Proc.Natl.Acad.Sci.USA (2006)

Release Date

2005-06-28

Peptides

farnesyl diphosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

farnesyl diphosphate synthase