SMTL ID : 2f8z.1

Crystal structure of human FPPS in complex with zoledronate and isopentenyl diphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.100, D.104, S.106 Ligands: MG.3, ZOL.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.100, A:D.104, H2O.1, H2O.1 MG.2: 2 residues within 4Å: Chain A: D.240 Ligands: ZOL.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.240, H2O.1, H2O.1, H2O.1 MG.3: 4 residues within 4Å: Chain A: D.100, D.104 Ligands: MG.1, ZOL.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.100, A:D.100, A:D.104, H2O.1, H2O.1 MG.6: 5 residues within 4Å: Chain B: D.100, D.104, S.106 Ligands: MG.8, ZOL.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.100, B:D.104, H2O.3, H2O.4 MG.7: 2 residues within 4Å: Chain B: D.240 Ligands: ZOL.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.240, H2O.3, H2O.3, H2O.3 MG.8: 4 residues within 4Å: Chain B: D.100, D.104 Ligands: MG.6, ZOL.10 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.100, B:D.100, B:D.104, H2O.3, H2O.3

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

IPE.4: 12 residues within 4Å: Chain A: G.53, K.54, R.57, Q.93, R.109, R.110, T.198, Y.201, F.236, Q.237, D.240 Ligands: ZOL.5 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:T.198, A:F.236, A:D.240 Hydrogen bonds: A:K.54, A:Q.93 Water bridges: A:Y.55, A:R.109, A:K.254, A:R.348 Salt bridges: A:K.54, A:K.54, A:R.57, A:R.57, A:R.110, A:K.254 IPE.9: 12 residues within 4Å: Chain B: G.53, K.54, R.57, Q.93, R.109, R.110, T.198, Y.201, F.236, Q.237, D.240 Ligands: ZOL.10 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:T.198, B:F.236, B:D.240 Hydrogen bonds: B:K.54, B:Q.93 Water bridges: B:Y.55, B:R.109, B:K.254, B:R.348, B:K.350 Salt bridges: B:K.54, B:K.54, B:R.57, B:R.57, B:R.110, B:K.254

2 x ZOL: ZOLEDRONIC ACID(Non-covalent)

ZOL.5: 15 residues within 4Å: Chain A: L.97, D.100, D.104, R.109, Q.168, K.197, T.198, Y.201, Q.237, D.240, K.254 Ligands: MG.1, MG.2, MG.3, IPE.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.109, A:R.109, A:Q.237, A:D.240 Water bridges: A:D.101, A:S.106, A:Q.168, A:K.197, A:K.197 pi-Cation interactions: A:K.197 ZOL.10: 15 residues within 4Å: Chain B: L.97, D.100, D.104, R.109, Q.168, K.197, T.198, Y.201, Q.237, D.240, K.254 Ligands: MG.6, MG.7, MG.8, IPE.9 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:D.100, B:R.109, B:R.109, B:Q.237, B:D.240 Water bridges: B:D.104, B:D.104, B:D.104, B:S.106, B:Q.168, B:K.197, B:K.197, B:D.244, B:D.244, B:D.244 pi-Cation interactions: B:K.197

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rondeau, J.M. et al., Structural basis for the exceptional in vivo efficacy of bisphosphonate drugs. Chemmedchem (2006)

Release Date

2006-02-28

Peptides

Farnesyl Diphosphate Synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

Farnesyl Diphosphate Synthase

Related Entries With Identical Sequence