SMTL ID : 1yv5.1

Human farnesyl diphosphate synthase complexed with Mg and risedronate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.124, D.128 Ligands: MG.3, RIS.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.124, A:D.128, H2O.1, H2O.1 MG.2: 3 residues within 4Å: Chain A: D.264, D.268 Ligands: RIS.6 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.264, H2O.2, H2O.2, H2O.3 MG.3: 4 residues within 4Å: Chain A: D.124, D.128 Ligands: MG.1, RIS.6 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.124, A:D.128, H2O.1, H2O.2, H2O.2 MG.7: 4 residues within 4Å: Chain B: D.124, D.128 Ligands: MG.9, RIS.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.124, B:D.128, H2O.4, H2O.4 MG.8: 3 residues within 4Å: Chain B: D.264, D.268 Ligands: RIS.12 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.264, H2O.5, H2O.5, H2O.7 MG.9: 4 residues within 4Å: Chain B: D.124, D.128 Ligands: MG.7, RIS.12 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.124, B:D.128, H2O.4, H2O.5, H2O.5

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

PO4.4: 6 residues within 4Å: Chain A: G.77, K.78, R.81, Q.117, R.134 Ligands: PO4.5 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.78, A:Q.117 Water bridges: A:Y.79, A:Y.79, A:Y.79, A:N.80, A:R.81, A:E.114, A:R.134 Salt bridges: A:R.81, A:R.134 PO4.5: 9 residues within 4Å: Chain A: R.81, Q.117, L.121, R.133, F.260, D.264, K.278 Ligands: PO4.4, RIS.6 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.117, A:Q.117 Water bridges: A:R.81, A:R.133, A:R.133 Salt bridges: A:R.81, A:R.133, A:K.278 PO4.10: 6 residues within 4Å: Chain B: G.77, K.78, R.81, Q.117, R.134 Ligands: PO4.11 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.78, B:Q.117 Water bridges: B:Y.79, B:Y.79, B:Y.79, B:N.80, B:R.81, B:E.114, B:R.134 Salt bridges: B:R.81, B:R.134 PO4.11: 9 residues within 4Å: Chain B: R.81, Q.117, L.121, R.133, F.260, D.264, K.278 Ligands: PO4.10, RIS.12 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.117, B:Q.117 Water bridges: B:R.81, B:R.133, B:R.133 Salt bridges: B:R.81, B:R.133, B:K.278

2 x RIS: 1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID(Non-covalent)

RIS.6: 15 residues within 4Å: Chain A: L.121, D.124, D.128, R.133, Q.192, K.221, T.222, Y.225, Q.261, D.264, K.278 Ligands: MG.1, MG.2, MG.3, PO4.5 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:D.124 Hydrogen bonds: A:R.133, A:R.133, A:K.221, A:Y.225, A:Q.261, A:D.264 Water bridges: A:D.128, A:D.128, A:D.128, A:S.130, A:Q.192, A:Q.192, A:D.268 RIS.12: 15 residues within 4Å: Chain B: L.121, D.124, D.128, R.133, Q.192, K.221, T.222, Y.225, Q.261, D.264, K.278 Ligands: MG.7, MG.8, MG.9, PO4.11 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:D.124 Hydrogen bonds: B:R.133, B:R.133, B:K.221, B:Q.261, B:D.264 Water bridges: B:D.128, B:S.130, B:S.130, B:Q.192, B:Q.192, B:T.222, B:D.264, B:K.278

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kavanagh, K.L. et al., The molecular mechanism of nitrogen-containing bisphosphonates as antiosteoporosis drugs. Proc.Natl.Acad.Sci.USA (2006)

Release Date

2005-03-01

Peptides

Farnesyl pyrophosphate synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Farnesyl pyrophosphate synthetase

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