SMTL ID : 1yhm.2 (1 other biounit)

Structure of the complex of Trypanosoma cruzi farnesyl disphosphate synthase with alendronate, Isopentenyl diphosphate and mg+2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: F.17, Q.21, K.25, H.141 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.21 Salt bridges: A:K.25, A:H.141, B:K.158 SO4.7: 4 residues within 4Å: Chain B: F.17, Q.21, K.25, H.141 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.21 Salt bridges: B:K.25, B:H.141, A:K.158

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.250 Ligands: AHD.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.250, H2O.1, H2O.1, H2O.1 MG.3: 4 residues within 4Å: Chain A: D.98, D.102 Ligands: MG.4, AHD.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: 4 residues within 4Å: Chain A: D.98, D.102 Ligands: MG.3, AHD.5 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: 2 residues within 4Å: Chain B: D.250 Ligands: AHD.11 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.250, H2O.2, H2O.2, H2O.2 MG.9: 4 residues within 4Å: Chain B: D.98, D.102 Ligands: MG.10, AHD.11 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.98, B:D.102, H2O.2, H2O.2 MG.10: 4 residues within 4Å: Chain B: D.98, D.102 Ligands: MG.9, AHD.11 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.98, B:D.102, H2O.2, H2O.2, H2O.2

2 x AHD: 4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE(Non-covalent)

AHD.5: 13 residues within 4Å: Chain A: D.98, D.102, R.107, Q.167, K.207, Y.211, Q.247, D.250, K.264 Ligands: MG.2, MG.3, MG.4, IPE.6 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:D.98, A:D.98, A:R.107, A:R.107, A:K.207, A:Y.211, A:Q.247, A:D.250 Water bridges: A:D.102, A:S.104, A:Q.167, A:D.254, A:D.254, A:D.254, A:D.254 AHD.11: 13 residues within 4Å: Chain B: D.98, D.102, R.107, Q.167, K.207, Y.211, Q.247, D.250, K.264 Ligands: MG.8, MG.9, MG.10, IPE.12 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:D.98, B:D.98, B:R.107, B:R.107, B:K.207, B:Q.247, B:D.250, B:D.250 Water bridges: B:S.104, B:Q.167, B:K.264, B:K.264

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, F.246, Q.247, D.250, K.264, K.362 Ligands: AHD.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:T.208, A:F.246, A:D.250 Hydrogen bonds: A:K.48, A:Y.49, A:Q.91, A:Q.91 Salt bridges: A:R.51, A:R.108, A:K.264, A:K.362, A:K.362 IPE.12: 13 residues within 4Å: Chain B: G.47, K.48, R.51, Q.91, R.108, T.208, Y.211, F.246, Q.247, D.250, K.264, K.362 Ligands: AHD.11 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:T.208, B:F.246, B:D.250 Hydrogen bonds: B:K.48, B:Y.49, B:Q.91, B:Q.91 Salt bridges: B:R.51, B:R.108, B:K.264, B:K.362, B:K.362

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gabelli, S.B. et al., Structure and mechanism of the farnesyl diphosphate synthase from Trypanosoma cruzi: Implications for drug design. Proteins (2005)

Release Date

2005-12-20

Peptides

farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

farnesyl pyrophosphate synthase

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