SMTL ID : 2f9k.1

Crystal structure of human FPPS in complex with Zoledronate and Zn2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 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, 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 ZN.2: 3 residues within 4Å: Chain A: D.240, D.244 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 ZN.3: 5 residues within 4Å: Chain A: D.100, D.104, D.171 Ligands: ZN.1, 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 ZN.6: 4 residues within 4Å: Chain B: D.100, D.104 Ligands: ZN.8, ZOL.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.100, B:D.104, H2O.7, H2O.7 ZN.7: 3 residues within 4Å: Chain B: D.240, D.244 Ligands: ZOL.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.240, H2O.7, H2O.7, H2O.8 ZN.8: 5 residues within 4Å: Chain B: D.100, D.104, D.171 Ligands: ZN.6, ZOL.10 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.100, B:D.104, H2O.7, H2O.7, H2O.7

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 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.54, A:Q.93 Water bridges: A:Y.55, A:Y.55, A:Y.55, A:R.57, A:R.57, A:R.57, A:R.57 Salt bridges: A:K.54, A:R.57, A:R.110 PO4.9: 5 residues within 4Å: Chain B: G.53, K.54, R.57, Q.93, R.110 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:K.54, B:Q.93 Water bridges: B:Y.55, B:Y.55, B:Y.55, B:R.57, B:R.57, B:R.57, B:R.57 Salt bridges: B:K.54, B:R.57, B:R.110

2 x ZOL: ZOLEDRONIC ACID(Non-covalent)

ZOL.5: 13 residues within 4Å: Chain A: L.97, D.100, D.104, R.109, Q.168, K.197, T.198, Q.237, D.240, K.254 Ligands: ZN.1, ZN.2, ZN.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.109, A:R.109, A:K.197, A:Q.237, A:D.240 Water bridges: A:S.106, A:S.106, A:Q.168, A:T.198, A:K.254 pi-Cation interactions: A:K.197 ZOL.10: 13 residues within 4Å: Chain B: L.97, D.100, D.104, R.109, Q.168, K.197, T.198, Q.237, D.240, K.254 Ligands: ZN.6, ZN.7, ZN.8 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.109, B:R.109, B:K.197, B:Q.237, B:D.240 Water bridges: B:S.106, B:S.106, B:Q.168, 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

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