SMTL ID : 3iba.1

Crystal structure of the complex of Trypanosoma cruzi farnesyl diphosphate synthase with zoledronate, IPP and Mg2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.98, D.102 Ligands: MG.3, ZOL.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.98, A:D.102, H2O.1, H2O.4 MG.2: 3 residues within 4Å: Chain A: Q.247, D.250 Ligands: ZOL.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.250, H2O.1, H2O.1, H2O.3 MG.3: 6 residues within 4Å: Chain A: D.98, D.102, D.170, K.273 Ligands: MG.1, ZOL.4 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.6 MG.7: 4 residues within 4Å: Chain B: D.98, D.102 Ligands: MG.9, ZOL.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.98, B:D.102, H2O.12, H2O.15 MG.8: 3 residues within 4Å: Chain B: Q.247, D.250 Ligands: ZOL.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.250, H2O.12, H2O.12, H2O.14 MG.9: 6 residues within 4Å: Chain B: D.98, D.102, D.170, K.273 Ligands: MG.7, ZOL.10 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.17

2 x ZOL: ZOLEDRONIC ACID(Non-covalent)

ZOL.4: 14 residues within 4Å: Chain A: D.98, D.102, R.107, Q.167, K.207, T.208, Y.211, Q.247, D.250, K.264 Ligands: MG.1, MG.2, MG.3, IPE.6 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.107, A:R.107, A:K.207, A:K.207, A:Y.211, A:Q.247, A:D.250, A:K.264 Water bridges: A:S.104, A:Q.167, A:D.254, A:D.254 pi-Cation interactions: A:K.207 ZOL.10: 14 residues within 4Å: Chain B: D.98, D.102, R.107, Q.167, K.207, T.208, Y.211, Q.247, D.250, K.264 Ligands: MG.7, MG.8, MG.9, IPE.12 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:R.107, B:R.107, B:K.207, B:K.207, B:Q.247, B:D.250, B:D.250, B:K.264 Water bridges: B:D.99, B:D.102, B:D.102, B:S.104, B:Q.167 pi-Cation interactions: B:K.207

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

SO4.5: 7 residues within 4Å: Chain A: G.47, K.48, Y.49, F.50, R.51, Q.91 Ligands: IPE.6 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.48, A:Y.49, A:F.50, A:Q.91 Water bridges: A:R.51, A:R.51, A:R.51, A:R.51 Salt bridges: A:K.48, A:R.51 SO4.11: 7 residues within 4Å: Chain B: G.47, K.48, Y.49, F.50, R.51, Q.91 Ligands: IPE.12 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:K.48, B:Y.49, B:F.50, B:Q.91 Water bridges: B:R.51, B:R.51, B:R.51, B:R.51 Salt bridges: B:K.48, B:R.51

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

IPE.6: 13 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 Ligands: ZOL.4, SO4.5 13 PLIP interactions: 13 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:R.51, A:K.264, A:K.264, A:K.264 Salt bridges: A:R.51, A:R.108 IPE.12: 13 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 Ligands: ZOL.10, SO4.11 13 PLIP interactions: 13 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:R.51, B:K.264, B:K.264, B:K.264 Salt bridges: 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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