SMTL ID : 2f89.1

Crystal structure of human FPPS in complex with pamidronate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 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 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.54, A:Q.93 Water bridges: A:K.54, A:K.54, A:Y.55, A:R.57 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 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.54, B:Q.93 Water bridges: B:K.54, B:K.54, B:Y.55, B:R.57 Salt bridges: B:K.54, B:R.57, B:R.110

6 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 4 residues within 4Å: Chain A: D.100, D.104 Ligands: MN.4, 210.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.100, A:D.104, H2O.1, H2O.2 MN.3: 2 residues within 4Å: Chain A: D.240 Ligands: 210.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.240, H2O.1, H2O.1, H2O.2 MN.4: 4 residues within 4Å: Chain A: D.100, D.104 Ligands: MN.2, 210.5 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.2 MN.7: 4 residues within 4Å: Chain B: D.100, D.104 Ligands: MN.9, 210.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.100, B:D.104, H2O.3, H2O.4 MN.8: 2 residues within 4Å: Chain B: D.240 Ligands: 210.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.240, H2O.3, H2O.3, H2O.4 MN.9: 4 residues within 4Å: Chain B: D.100, D.104 Ligands: MN.7, 210.10 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.100, B:D.104, H2O.3, H2O.3, H2O.4

2 x 210: PAMIDRONATE(Non-covalent)

210.5: 12 residues within 4Å: Chain A: D.100, D.104, R.109, K.197, T.198, Y.201, Q.237, D.240, K.254 Ligands: MN.2, MN.3, MN.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.109, A:R.109, A:T.198, A:Q.237, A:D.240, A:K.254 Water bridges: A:D.100, A:D.101, A:S.106, A:Q.168, A:Q.168, A:K.197, A:K.197 210.10: 12 residues within 4Å: Chain B: D.100, D.104, R.109, K.197, T.198, Y.201, Q.237, D.240, K.254 Ligands: MN.7, MN.8, MN.9 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:R.109, B:R.109, B:T.198, B:Y.201, B:Q.237, B:D.240, B:K.254 Water bridges: B:D.100, B:S.106, B:Q.168, B:Q.168, B:K.197, B:K.197, B:D.244, B:D.244, B:D.244

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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