SMTL ID : 3icm.1

Trypanosoma cruzi farnesyl diphosphate synthase homodimer in complex with isopentenyl pyrophosphate, Mg2+ and 1-(2-Hydroxy-2,2-bis-phosphono-ethyl)-3-phenyl-pyridinium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x P2H: 1-(2-hydroxy-2,2-diphosphonoethyl)-3-phenylpyridinium(Non-covalent)

P2H.1: 16 residues within 4Å: Chain A: Y.94, D.98, D.102, R.107, T.163, Q.167, K.207, T.208, Y.211, Q.247, D.250, K.264 Ligands: IPE.3, MG.4, MG.5, MG.6 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.94, A:Y.94, A:Y.94, A:D.98, A:T.163, A:Q.167, A:Q.167, A:K.207, A:Y.211 Hydrogen bonds: A:D.98, A:R.107, A:R.107, A:Q.247 Water bridges: A:Q.167, A:K.207, A:K.207, A:K.207, A:K.207, A:K.207, A:D.254 P2H.7: 16 residues within 4Å: Chain B: Y.94, D.98, D.102, R.107, T.163, Q.167, K.207, T.208, Y.211, Q.247, D.250, K.264 Ligands: IPE.9, MG.10, MG.11, MG.12 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:Y.94, B:Y.94, B:Y.94, B:D.98, B:T.163, B:Q.167, B:Q.167, B:K.207, B:Y.211 Hydrogen bonds: B:D.98, B:R.107, B:R.107, B:Q.247 Water bridges: B:D.102, B:D.102, B:D.102, B:Q.167, B:K.207, B:K.207, B:K.207, B:K.207, B:K.207, B:K.264

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 8 residues within 4Å: Chain A: G.47, K.48, Y.49, F.50, R.51, Q.91, R.108 Ligands: IPE.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.48, A:Y.49, A:F.50, A:R.51, A:Q.91 Water bridges: A:K.48 Salt bridges: A:K.48, A:R.108 SO4.8: 8 residues within 4Å: Chain B: G.47, K.48, Y.49, F.50, R.51, Q.91, R.108 Ligands: IPE.9 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:K.48, B:Y.49, B:F.50, B:R.51, B:Q.91 Water bridges: B:K.48 Salt bridges: B:K.48, B:R.108

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

IPE.3: 14 residues within 4Å: Chain A: G.47, K.48, R.51, Q.91, R.108, T.208, Y.211, T.212, F.246, Q.247, D.250, R.360 Ligands: P2H.1, SO4.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.246 Hydrogen bonds: A:K.48, A:Q.91, A:Q.91, A:R.360 Water bridges: A:K.48, A:Y.49, A:R.51, A:R.51, A:K.264 Salt bridges: A:K.48, A:K.48, A:R.51, A:R.108, A:K.264 IPE.9: 14 residues within 4Å: Chain B: G.47, K.48, R.51, Q.91, R.108, T.208, Y.211, T.212, F.246, Q.247, D.250, R.360 Ligands: P2H.7, SO4.8 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.246 Hydrogen bonds: B:K.48, B:Q.91, B:Q.91, B:R.360 Water bridges: B:K.48, B:Y.49, B:R.51, B:R.51, B:K.264 Salt bridges: B:K.48, B:K.48, B:R.51, B:R.108, B:K.264

6 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: D.98, D.102 Ligands: P2H.1, MG.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.98, A:D.102, H2O.5, H2O.8 MG.5: 2 residues within 4Å: Chain A: D.250 Ligands: P2H.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.250, H2O.1, H2O.1, H2O.1 MG.6: 6 residues within 4Å: Chain A: D.98, D.102, Q.167, D.170 Ligands: P2H.1, MG.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.98, A:D.102, H2O.1, H2O.1 MG.10: 4 residues within 4Å: Chain B: D.98, D.102 Ligands: P2H.7, MG.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.98, B:D.102, H2O.17, H2O.19 MG.11: 2 residues within 4Å: Chain B: D.250 Ligands: P2H.7 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.250, H2O.12, H2O.12, H2O.12 MG.12: 6 residues within 4Å: Chain B: D.98, D.102, Q.167, D.170 Ligands: P2H.7, MG.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.98, B:D.102, H2O.12, H2O.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, C.H. et al., Binding of nitrogen-containing bisphosphonates (N-BPs) to the Trypanosoma cruzi farnesyl diphosphate synthase homodimer. Proteins (2010)

Release Date

2010-02-09

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Farnesyl pyrophosphate synthase

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