SMTL ID : 2f8c.1

Crystal structure of FPPS in complex with Zoledronate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 5 residues within 4Å: Chain A: G.53, K.54, R.57, Q.93, R.110 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:K.54, A:Q.93 Water bridges: A:G.53, A:K.54, A:K.54, A:Y.55, A:Y.55, A:R.57, A:R.57, A:K.254 Salt bridges: A:K.54, A:R.57, A:R.110 PO4.6: 5 residues within 4Å: Chain B: G.53, K.54, R.57, Q.93, R.110 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:K.54, B:Q.93 Water bridges: B:G.53, B:K.54, B:K.54, B:Y.55, B:Y.55, B:R.57, B:R.57, B:K.254 Salt bridges: B:K.54, B:R.57, B:R.110

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.100, D.104 Ligands: MG.4, 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.3: 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.4: 4 residues within 4Å: Chain A: D.100, D.104 Ligands: MG.2, ZOL.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.100, A:D.104, H2O.1, H2O.1, H2O.1 MG.7: 4 residues within 4Å: Chain B: D.100, D.104 Ligands: MG.9, ZOL.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.100, B:D.104, H2O.6, H2O.6 MG.8: 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.6, H2O.6, H2O.6 MG.9: 4 residues within 4Å: Chain B: D.100, D.104 Ligands: MG.7, ZOL.10 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.100, B:D.104, H2O.6, H2O.6, H2O.6

2 x ZOL: ZOLEDRONIC ACID(Non-covalent)

ZOL.5: 14 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.2, MG.3, MG.4 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:R.109, A:R.109, A:Q.237, A:D.240 Water bridges: A:S.106, A:S.106, A:S.106, A:Q.168, A:K.197, A:K.197, A:T.198, A:D.240, A:K.254, A:K.254, A:K.254, A:K.254 pi-Cation interactions: A:K.197 ZOL.10: 14 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.7, MG.8, MG.9 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:R.109, B:R.109, B:Y.201, B:Q.237, B:D.240 Water bridges: B:D.104, B:D.104, B:S.106, B:S.106, B:Q.168, B:K.197, B:K.197, B:D.244, B:D.244, B:D.244, B:K.254, B:K.254 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

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