SMTL ID : 2f94.1

Crystal structure of human FPPS in complex with ibandronate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.100, D.104 Ligands: ZN.3, BFQ.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.100, A:D.104, H2O.1, H2O.2 ZN.2: 3 residues within 4Å: Chain A: D.240, D.244 Ligands: BFQ.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.240, H2O.1, H2O.1, H2O.1 ZN.3: 4 residues within 4Å: Chain A: D.100, D.104 Ligands: ZN.1, BFQ.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 ZN.6: 4 residues within 4Å: Chain B: D.100, D.104 Ligands: ZN.8, BFQ.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.100, B:D.104, H2O.9, H2O.10 ZN.7: 3 residues within 4Å: Chain B: D.240, D.244 Ligands: BFQ.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.240, H2O.8, H2O.9, H2O.9 ZN.8: 4 residues within 4Å: Chain B: D.100, D.104 Ligands: ZN.6, BFQ.10 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.100, B:D.104, H2O.9, H2O.9, H2O.9

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

PO4.4: 5 residues within 4Å: Chain A: G.53, K.54, R.57, Q.93, R.110 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.54, A:Y.55, A:R.57, A:Q.93 Salt bridges: A:K.54, A:R.110 PO4.9: 5 residues within 4Å: Chain B: G.53, K.54, R.57, Q.93, R.110 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.54, B:Y.55, B:R.57, B:Q.93 Salt bridges: B:K.54, B:R.110

2 x BFQ: IBANDRONATE(Non-covalent)

BFQ.5: 16 residues within 4Å: Chain A: F.96, L.97, D.100, D.104, R.109, T.164, Q.168, K.197, T.198, Y.201, Q.237, D.240, K.254 Ligands: ZN.1, ZN.2, ZN.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.96, A:D.100 Hydrogen bonds: A:R.109, A:R.109, A:K.197, A:Q.237, A:D.240, A:K.254 Water bridges: A:D.100, A:S.106, A:S.106, A:S.106, A:Q.168 Salt bridges: A:D.100 BFQ.10: 16 residues within 4Å: Chain B: F.96, L.97, D.100, D.104, R.109, T.164, Q.168, K.197, T.198, Y.201, Q.237, D.240, K.254 Ligands: ZN.6, ZN.7, ZN.8 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:F.96, B:D.100 Hydrogen bonds: B:R.109, B:R.109, B:K.197, B:Y.201, B:Q.237, B:D.240, B:K.254 Water bridges: B:D.100, B:S.106, B:S.106, B:S.106, B:Q.168, B:T.198, B:D.244 Salt bridges: B:D.100

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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