SMTL ID : 2opn.1

Human Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-527

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 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, R.133 Ligands: SUF.6 No protein-ligand interaction detected (PLIP) MG.2: 3 residues within 4Å: Chain A: D.264, D.282 Ligands: SUF.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.264 MG.3: 4 residues within 4Å: Chain A: D.124, D.128, D.195 Ligands: SUF.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.124, A:D.128, H2O.3 MG.7: 4 residues within 4Å: Chain B: D.124, D.128, R.133 Ligands: SUF.12 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain B: D.264, D.282 Ligands: SUF.12 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.264 MG.9: 4 residues within 4Å: Chain B: D.124, D.128, D.195 Ligands: SUF.12 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.124, B:D.128, H2O.7

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

PO4.4: 5 residues within 4Å: Chain A: K.78, R.81, Q.117, R.134 Ligands: PO4.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.78, A:Q.117, A:Q.117 Water bridges: A:K.78, A:Y.79, A:N.80, A:R.134 Salt bridges: A:R.81, A:R.134 PO4.5: 6 residues within 4Å: Chain A: K.78, R.81, Q.117, F.260, D.264 Ligands: PO4.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.117 Water bridges: A:K.78 Salt bridges: A:K.78, A:R.81 PO4.10: 5 residues within 4Å: Chain B: K.78, R.81, Q.117, R.134 Ligands: PO4.11 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.78, B:Q.117, B:Q.117 Water bridges: B:K.78, B:Y.79, B:N.80, B:R.134 Salt bridges: B:R.81, B:R.134 PO4.11: 6 residues within 4Å: Chain B: K.78, R.81, Q.117, F.260, D.264 Ligands: PO4.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.117 Water bridges: B:K.78 Salt bridges: B:K.78, B:R.81

2 x SUF: [2-(DIMETHYL-LAMBDA~4~-SULFANYL)-1-HYDROXYETHANE-1,1-DIYL]BIS(PHOSPHONIC ACID)(Non-covalent)

SUF.6: 12 residues within 4Å: Chain A: D.124, D.128, R.133, D.195, K.221, T.222, Y.225, Q.261, D.264 Ligands: MG.1, MG.2, MG.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.124, A:R.133, A:K.221, A:Q.261, A:Q.261 Salt bridges: A:D.124 SUF.12: 12 residues within 4Å: Chain B: D.124, D.128, R.133, D.195, K.221, T.222, Y.225, Q.261, D.264 Ligands: MG.7, MG.8, MG.9 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.124, B:D.124, B:R.133, B:K.221, B:T.222, B:Q.261, B:Q.261 Water bridges: B:D.195, B:D.195 Salt bridges: B:D.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., Bisphosphonates: Teaching Old Drugs with New Tricks. To be Published

Release Date

2007-10-02

Peptides

Farnesyl pyrophosphate synthetase (FPP synthetase) (FPS) (Farnesyl diphosphate synthetase) [Includes: Dimethylallyltranstransferase (EC 2.5.1.1); Geranyltranstransferase (EC 2.5.1.10)]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Farnesyl pyrophosphate synthetase (FPP synthetase) (FPS) (Farnesyl diphosphate synthetase) [Includes: Dimethylallyltranstransferase (EC 2.5.1.1); Geranyltranstransferase (EC 2.5.1.10)]

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