SMTL ID : 1rqi.1

Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.224, D.228 Ligands: DST.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.224, H2O.1, H2O.1, H2O.1 MG.2: 5 residues within 4Å: Chain A: D.85, D.91, K.248 Ligands: MG.3, DST.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.85, A:D.91, H2O.1, H2O.1, H2O.1 MG.3: 5 residues within 4Å: Chain A: D.85, D.91, D.93 Ligands: MG.2, DST.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.85, A:D.91, H2O.1, H2O.1 MG.7: 3 residues within 4Å: Chain B: D.224, D.228 Ligands: DST.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.224, H2O.5, H2O.5, H2O.5 MG.8: 4 residues within 4Å: Chain B: D.85, D.91 Ligands: MG.9, DST.10 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.85, B:D.91, H2O.5, H2O.5, H2O.7 MG.9: 6 residues within 4Å: Chain B: D.85, D.91, D.93, R.96 Ligands: MG.8, DST.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.85, B:D.91, H2O.5, H2O.5

2 x DST: DIMETHYLALLYL S-THIOLODIPHOSPHATE(Non-covalent)

DST.4: 16 residues within 4Å: Chain A: S.81, L.82, D.85, D.91, R.96, M.155, Q.159, K.182, T.183, Q.221, D.224, K.238 Ligands: MG.1, MG.2, MG.3, IPR.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.82, A:D.85, A:Q.159 Hydrogen bonds: A:K.182, A:Q.221 Water bridges: A:R.96, A:R.96, A:Q.159, A:D.224, A:D.228, A:K.248 Salt bridges: A:R.96, A:K.238 DST.10: 15 residues within 4Å: Chain B: S.81, L.82, D.85, D.91, R.96, M.155, Q.159, K.182, Q.221, D.224, K.238 Ligands: MG.7, MG.8, MG.9, IPR.11 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.82, B:D.85, B:Q.159 Hydrogen bonds: B:D.91, B:K.182, B:Q.221 Water bridges: B:D.91, B:D.91, B:D.91, B:Q.159, B:Q.159, B:K.238, B:K.238 Salt bridges: B:R.96, B:K.238

2 x IPR: ISOPENTYL PYROPHOSPHATE(Non-covalent)

IPR.5: 11 residues within 4Å: Chain A: G.45, K.46, R.49, H.78, L.82, R.97, T.183, F.220, Q.221, D.224 Ligands: DST.4 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:L.82, A:T.183, A:F.220, A:D.224 Hydrogen bonds: A:K.46, A:R.298 Water bridges: A:K.46, A:R.47, A:R.47, A:R.49, A:H.78, A:R.96, A:K.300 Salt bridges: A:K.46, A:K.46, A:R.49, A:H.78, A:H.78, A:R.97, A:K.238 IPR.11: 11 residues within 4Å: Chain B: G.45, K.46, R.49, H.78, L.82, R.97, T.183, F.220, Q.221, D.224 Ligands: DST.10 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:L.82, B:F.220, B:D.224 Hydrogen bonds: B:K.46 Water bridges: B:K.46, B:K.46, B:R.47, B:R.49, B:R.49, B:H.78, B:K.238, B:R.298 Salt bridges: B:K.46, B:K.46, B:R.49, B:H.78, B:H.78, B:R.97

1 x DPO: DIPHOSPHATE(Non-covalent)

DPO.6: 8 residues within 4Å: Chain A: Q.7, A.10, C.11, Q.14, F.51, Y.54, A.55, H.58 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.7, A:A.10 Water bridges: A:H.58, A:T.64 Salt bridges: A:H.58, A:H.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hosfield, D.J. et al., Structural basis for bisphosphonate-mediated inhibition of isoprenoid biosynthesis. J.Biol.Chem. (2004)

Release Date

2004-03-02

Peptides

Geranyltranstransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Geranyltranstransferase