SMTL ID : 4p0w.1

Human farnesyl diphosphate synthase in complex with Arenarone and zoledronate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-dimer

Ligands

2 x 1XH: 2-{[(1S,2R,4aS,8aR)-1,2,4a-trimethyl-5-methylidenedecahydronaphthalen-1-yl]methyl}cyclohexa-2,5-diene-1,4-dione(Non-covalent)

1XH.1: 13 residues within 4Å: Chain A: G.51, K.52, Y.53, N.54, R.55, G.56, E.88, Q.91, L.95, R.107, R.108, S.200, F.234 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:K.52, A:Y.53, A:R.55, A:R.55, A:E.88, A:E.88, A:L.95, A:R.108, A:F.234 Hydrogen bonds: A:N.54, A:R.55 Water bridges: A:E.88 1XH.6: 13 residues within 4Å: Chain B: G.51, K.52, Y.53, N.54, R.55, G.56, E.88, Q.91, L.95, R.107, R.108, S.200, F.234 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:K.52, B:Y.53, B:R.55, B:R.55, B:E.88, B:E.88, B:L.95, B:R.108, B:F.234 Hydrogen bonds: B:N.54, B:R.55

2 x ZOL: ZOLEDRONIC ACID(Non-covalent)

ZOL.2: 14 residues within 4Å: Chain A: L.95, D.98, D.102, R.107, Q.166, K.195, T.196, Y.199, Q.235, D.238, K.252 Ligands: MG.3, MG.4, MG.5 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:R.107, A:R.107, A:Q.235, A:D.238, A:K.252 Water bridges: A:S.104, A:S.104, A:Q.166, A:K.195, A:K.195, A:T.196, A:D.238, A:K.252, A:K.252, A:K.252, A:K.261 pi-Cation interactions: A:K.195 ZOL.7: 14 residues within 4Å: Chain B: L.95, D.98, D.102, R.107, Q.166, K.195, T.196, Y.199, Q.235, D.238, K.252 Ligands: MG.8, MG.9, MG.10 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:D.102, B:R.107, B:R.107, B:Y.199, B:Q.235, B:D.238, B:K.252 Water bridges: B:S.104, B:S.104, B:Q.166, B:K.195, B:K.195, B:D.242, B:K.252, B:K.252, B:K.261 pi-Cation interactions: B:K.195

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.98, D.102 Ligands: ZOL.2, MG.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.98, A:D.102, H2O.2, H2O.2 MG.4: 2 residues within 4Å: Chain A: D.238 Ligands: ZOL.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.238, H2O.1, H2O.1, H2O.2 MG.5: 5 residues within 4Å: Chain A: D.98, D.102, D.169 Ligands: ZOL.2, MG.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.98, A:D.102, H2O.2, H2O.2, H2O.2 MG.8: 4 residues within 4Å: Chain B: D.98, D.102 Ligands: ZOL.7, MG.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.98, B:D.102, H2O.4, H2O.4 MG.9: 2 residues within 4Å: Chain B: D.238 Ligands: ZOL.7 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.238, H2O.3, H2O.3, H2O.4 MG.10: 5 residues within 4Å: Chain B: D.98, D.102, D.169 Ligands: ZOL.7, MG.8 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.98, B:D.102, H2O.4, H2O.4, H2O.4

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

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