SMTL ID : 3id0.1

Trypanosoma cruzi farnesyl diphosphate synthase homodimer in complex with 3-Fluoro-1-(2-hydroxy-2,2-bisphosphono-ethyl)pyridinium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

homo-dimer

Ligands

2 x NI9: 3-FLUORO-1-(2-HYDROXY-2,2-DIPHOSPHONOETHYL)PYRIDINIUM(Non-covalent)

NI9.1: 14 residues within 4Å: Chain A: Y.94, D.98, D.102, R.107, Q.167, K.207, T.208, Y.211, Q.247, D.250, K.264 Ligands: MG.2, MG.3, MG.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.211 Hydrogen bonds: A:R.107, A:R.107, A:Q.247, A:Q.247, A:D.250 NI9.7: 14 residues within 4Å: Chain B: Y.94, D.98, D.102, R.107, Q.167, K.207, T.208, Y.211, Q.247, D.250, K.264 Ligands: MG.8, MG.9, MG.10 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.211 Hydrogen bonds: B:R.107, B:R.107, B:Q.247, B:Q.247

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.98, D.99, D.102, S.104 Ligands: NI9.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.98, A:D.102 MG.3: 4 residues within 4Å: Chain A: D.250, D.251, D.268 Ligands: NI9.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.250 MG.4: 5 residues within 4Å: Chain A: D.98, D.102, Q.167, D.170 Ligands: NI9.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.98, A:D.102, A:D.170 MG.8: 5 residues within 4Å: Chain B: D.98, D.99, D.102, S.104 Ligands: NI9.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.98, B:D.102 MG.9: 4 residues within 4Å: Chain B: D.250, D.251, D.268 Ligands: NI9.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.250 MG.10: 5 residues within 4Å: Chain B: D.98, D.102, Q.167, D.170 Ligands: NI9.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.98, B:D.102, B:D.170

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

SO4.5: 4 residues within 4Å: Chain A: F.17, K.25, H.141 Chain B: K.158 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.25, A:H.141, B:K.158 SO4.6: 7 residues within 4Å: Chain A: G.47, K.48, Y.49, F.50, R.51, Q.91, R.108 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.48, A:Y.49, A:F.50, A:Q.91 Water bridges: A:K.48, A:R.51, A:R.108, A:R.108, A:K.362 Salt bridges: A:K.48, A:R.51, A:R.108 SO4.11: 4 residues within 4Å: Chain A: K.158 Chain B: F.17, K.25, H.141 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:K.158, B:K.25, B:H.141 SO4.12: 7 residues within 4Å: Chain B: G.47, K.48, Y.49, F.50, R.51, Q.91, R.108 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:K.48, B:Y.49, B:F.50, B:Q.91 Water bridges: B:K.48, B:R.51, B:R.108, B:R.108, B:K.362 Salt bridges: B:K.48, B:R.51, B:R.108

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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