SMTL ID : 1rqj.3 (2 other biounits)

Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Risedronate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.84, D.90, D.92 Ligands: MG.3, RIS.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.84, A:D.90, H2O.1, H2O.2 MG.2: 2 residues within 4Å: Chain A: D.223 Ligands: RIS.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.223, H2O.1, H2O.5, H2O.5 MG.3: 4 residues within 4Å: Chain A: D.84, D.90 Ligands: MG.1, RIS.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.84, A:D.90, H2O.1, H2O.1, H2O.5 MG.6: 3 residues within 4Å: Chain B: D.223, D.227 Ligands: RIS.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.223, H2O.9, H2O.12, H2O.12 MG.7: 4 residues within 4Å: Chain B: D.84, D.90 Ligands: MG.8, RIS.10 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.84, B:D.90, H2O.8, H2O.12, H2O.12 MG.8: 4 residues within 4Å: Chain B: D.84, D.90 Ligands: MG.7, RIS.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.84, B:D.90, H2O.10, H2O.12

2 x IPE: 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

IPE.4: 12 residues within 4Å: Chain A: G.44, K.45, R.48, H.77, L.81, R.96, T.182, F.219, Q.220, D.223, R.297 Ligands: RIS.5 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:L.81, A:T.182, A:F.219, A:D.223 Hydrogen bonds: A:K.45, A:R.297 Water bridges: A:K.45, A:K.45, A:R.46, A:R.48, A:R.48, A:R.95, A:K.237, A:K.299, A:K.299 Salt bridges: A:K.45, A:K.45, A:R.48, A:H.77, A:H.77, A:R.96 IPE.9: 12 residues within 4Å: Chain B: G.44, K.45, R.48, H.77, L.81, R.96, T.182, F.219, Q.220, D.223, R.297 Ligands: RIS.10 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:L.81, B:T.182, B:F.219, B:D.223 Hydrogen bonds: B:K.45, B:R.297 Water bridges: B:K.45, B:K.45, B:K.45, B:R.48, B:R.48, B:H.77, B:R.95, B:R.96 Salt bridges: B:K.45, B:K.45, B:R.48, B:H.77, B:H.77, B:R.96

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

RIS.5: 15 residues within 4Å: Chain A: S.80, L.81, D.84, D.90, R.95, Q.158, K.181, T.182, Q.220, D.223, K.237 Ligands: MG.1, MG.2, MG.3, IPE.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:D.84 Hydrogen bonds: A:R.95, A:R.95, A:Q.220, A:D.223 Water bridges: A:Q.158, A:D.161, A:K.181, A:K.181, A:K.181, A:K.181, A:D.227 RIS.10: 15 residues within 4Å: Chain B: S.80, L.81, D.84, D.90, R.95, Q.158, K.181, T.182, Q.220, D.223, K.237 Ligands: MG.6, MG.7, MG.8, IPE.9 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:D.84 Hydrogen bonds: B:R.95, B:R.95, B:T.182, B:Q.220, B:D.223 Water bridges: B:D.90, B:D.90, B:D.90, B:D.92, B:Q.158, B:Q.158, B:D.161, B:K.181, B:K.181, B:K.181, B:K.181, B:K.237, B:K.237

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

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