SMTL ID : 3icz.1

Trypanosoma cruzi farnesyl diphosphate synthase homodimer in complex with 1-(2,2-Bis-phosphono-ethyl)-3-butyl-pyridinium and isopentenyl pyrophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

IPE.1: 12 residues within 4Å: Chain A: G.47, K.48, R.51, Q.91, R.107, R.108, T.208, Y.211, F.246, Q.247, D.250 Ligands: PB6.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.246, A:D.250 Hydrogen bonds: A:K.48, A:R.51, A:Q.91, A:R.360 Water bridges: A:K.48, A:K.48, A:Y.49, A:R.107, A:R.107, A:R.107, A:K.264, A:K.264 Salt bridges: A:K.48, A:K.48, A:R.51, A:R.108, A:K.264 IPE.6: 12 residues within 4Å: Chain B: G.47, K.48, R.51, Q.91, R.107, R.108, T.208, Y.211, F.246, Q.247, D.250 Ligands: PB6.7 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:F.246, B:D.250 Hydrogen bonds: B:K.48, B:R.51, B:Q.91, B:R.360 Water bridges: B:K.48, B:K.48, B:Y.49, B:R.107, B:R.107, B:R.107, B:K.264, B:K.264 Salt bridges: B:K.48, B:K.48, B:R.51, B:R.108, B:K.264

2 x PB6: 3-[(1E)-but-1-en-1-yl]-1-(2,2-diphosphonoethyl)pyridinium(Non-covalent)

PB6.2: 16 residues within 4Å: Chain A: Y.94, D.98, M.101, D.102, R.107, T.163, Q.167, K.207, T.208, Q.247, D.250, K.264 Ligands: IPE.1, MG.3, MG.4, MG.5 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.94, A:Y.94, A:D.98, A:T.163, A:Q.167, A:Q.167, A:K.207, A:T.208 Hydrogen bonds: A:D.98, A:R.107, A:R.107, A:K.207, A:Q.247, A:K.264 Water bridges: A:D.98, A:S.104, A:S.104, A:S.104, A:D.170, A:D.254, A:K.273 PB6.7: 16 residues within 4Å: Chain B: Y.94, D.98, M.101, D.102, R.107, T.163, Q.167, K.207, T.208, Q.247, D.250, K.264 Ligands: IPE.6, MG.8, MG.9, MG.10 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:Y.94, B:Y.94, B:T.163, B:Q.167, B:Q.167, B:K.207, B:T.208 Hydrogen bonds: B:D.98, B:R.107, B:R.107, B:K.207, B:Q.247, B:K.264 Water bridges: B:D.98, B:D.99, B:D.102, B:S.104, B:S.104, B:D.170, B:K.264, B:K.273

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.98, D.102 Ligands: PB6.2, MG.5 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.4: 2 residues within 4Å: Chain A: D.250 Ligands: PB6.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.250, H2O.1, H2O.1, H2O.1 MG.5: 5 residues within 4Å: Chain A: D.98, D.102, D.170 Ligands: PB6.2, MG.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.98, A:D.102, H2O.1, H2O.1, H2O.1 MG.8: 4 residues within 4Å: Chain B: D.98, D.102 Ligands: PB6.7, 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 MG.9: 2 residues within 4Å: Chain B: D.250 Ligands: PB6.7 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.250, H2O.12, H2O.12, H2O.12 MG.10: 5 residues within 4Å: Chain B: D.98, D.102, D.170 Ligands: PB6.7, MG.8 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.98, B:D.102, H2O.12, 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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