SMTL ID : 4p0v.1

Crystal structure of human farnesyl diphosphoate synthase in complex with zoledronate and taxodione

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x ZOL: ZOLEDRONIC ACID(Non-covalent)

ZOL.1: 14 residues within 4Å: Chain A: D.97, D.101, R.106, Q.165, K.194, T.195, Y.198, Q.234, D.237, K.251 Ligands: 1WO.2, MG.3, MG.4, MG.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.106, A:R.106, A:Q.234, A:D.237, A:K.251 pi-Cation interactions: A:K.194 ZOL.6: 14 residues within 4Å: Chain B: D.97, D.101, R.106, Q.165, K.194, T.195, Y.198, Q.234, D.237, K.251 Ligands: 1WO.7, MG.8, MG.9, MG.10 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.106, B:R.106, B:Y.198, B:Q.234, B:D.237, B:K.251 Water bridges: B:D.241 pi-Cation interactions: B:K.194

2 x 1WO: (5beta)-11-hydroxyabieta-7,9(11),13-triene-6,12-dione(Non-covalent)

1WO.2: 14 residues within 4Å: Chain A: G.50, K.51, Y.52, N.53, R.54, E.87, Q.90, R.106, R.107, F.233, D.237, K.251, K.347 Ligands: ZOL.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.52, A:F.233, A:F.233, A:K.251 Hydrogen bonds: A:N.53, A:R.54, A:R.54, A:R.106 Water bridges: A:K.51, A:K.51, A:Y.52 1WO.7: 14 residues within 4Å: Chain B: G.50, K.51, Y.52, N.53, R.54, E.87, Q.90, R.106, R.107, F.233, D.237, K.251, K.347 Ligands: ZOL.6 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.52, B:F.233, B:F.233, B:K.251 Hydrogen bonds: B:N.53, B:R.54, B:R.54, B:R.106 Water bridges: B:K.51, B:K.51, B:Y.52

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.97, D.101 Ligands: ZOL.1, MG.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.97, A:D.101, H2O.2 MG.4: 3 residues within 4Å: Chain A: D.237, D.255 Ligands: ZOL.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.237, H2O.1 MG.5: 5 residues within 4Å: Chain A: D.97, D.101, D.168 Ligands: ZOL.1, MG.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.97, A:D.101 MG.8: 4 residues within 4Å: Chain B: D.97, D.101 Ligands: ZOL.6, MG.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.97, B:D.101, H2O.3 MG.9: 3 residues within 4Å: Chain B: D.237, D.255 Ligands: ZOL.6 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.237, H2O.2 MG.10: 5 residues within 4Å: Chain B: D.97, D.101, D.168 Ligands: ZOL.6, MG.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.97, B:D.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Y.L. et al., Taxodione and arenarone inhibit farnesyl diphosphate synthase by binding to the isopentenyl diphosphate site. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-07-02

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Farnesyl pyrophosphate synthase