SMTL ID : 1yhl.1

Structure of the complex of Trypanosoma cruzi farnesyl diphosphate synthase with risedronate, dmapp and mg+2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 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, RIS.6 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.2: 2 residues within 4Å: Chain A: D.250 Ligands: RIS.6 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.250, H2O.1, H2O.1, H2O.5 MG.3: 5 residues within 4Å: Chain A: D.98, D.102, D.170 Ligands: MG.1, RIS.6 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.5 MG.7: 4 residues within 4Å: Chain B: D.98, D.102 Ligands: MG.9, RIS.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.98, B:D.102, H2O.16, H2O.16 MG.8: 2 residues within 4Å: Chain B: D.250 Ligands: RIS.12 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.250, H2O.16, H2O.16, H2O.20 MG.9: 5 residues within 4Å: Chain B: D.98, D.102, D.170 Ligands: MG.7, RIS.12 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.98, B:D.102, H2O.16, H2O.16, H2O.20

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

SO4.4: 3 residues within 4Å: Chain A: F.17, Q.21, H.141 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.21 Water bridges: A:H.141, B:K.158, B:K.158, B:K.158 Salt bridges: A:H.141, B:K.158 SO4.10: 3 residues within 4Å: Chain B: F.17, Q.21, H.141 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Water bridges: A:K.158, A:K.158, A:K.158, B:H.141 Salt bridges: A:K.158, B:H.141 Hydrogen bonds: B:Q.21

2 x DMA: DIMETHYLALLYL DIPHOSPHATE(Non-covalent)

DMA.5: 13 residues within 4Å: Chain A: G.47, K.48, Y.49, F.50, R.51, Q.91, L.95, R.108, Y.211, F.246, K.264, K.362 Ligands: RIS.6 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.95, A:F.246 Hydrogen bonds: A:K.48, A:Y.49, A:F.50 Water bridges: A:Q.91, A:Q.91, A:Q.91, A:R.108 Salt bridges: A:R.51, A:R.108, A:K.362, A:K.362 DMA.11: 13 residues within 4Å: Chain B: G.47, K.48, Y.49, F.50, R.51, Q.91, L.95, R.108, Y.211, F.246, K.264, K.362 Ligands: RIS.12 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.95, B:F.246 Hydrogen bonds: B:K.48, B:Y.49, B:F.50, B:Q.91 Salt bridges: B:R.51, B:R.108, B:K.362, B:K.362

2 x RIS: 1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID(Non-covalent)

RIS.6: 15 residues within 4Å: Chain A: L.95, 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, DMA.5 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.95, A:D.98 Hydrogen bonds: A:D.102, A:R.107, A:R.107, A:Q.247, A:D.250 Water bridges: A:S.104, A:S.104, A:S.104, A:S.104, A:Q.167, A:K.207, A:K.207, A:D.250, A:K.264, A:K.264, A:D.268 RIS.12: 15 residues within 4Å: Chain B: L.95, 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, DMA.11 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:L.95, B:D.98 Hydrogen bonds: B:R.107, B:R.107, B:Y.211, B:Q.247, B:D.250 Water bridges: B:S.104, B:S.104, B:S.104, B:S.104, B:Q.167, B:K.207, B:K.207, B:D.254, B:D.254, B:D.254, B:D.268

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
A

B
A

farnesyl pyrophosphate synthase

Related Entries With Identical Sequence