SMTL ID : 3ick.1

Trypanosoma cruzi farnesyl diphosphate synthase homodimer in complex with minodronate and isopentenyl disphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.1: 6 residues within 4Å: Chain A: T.42, T.43, L.95, R.107, R.108, W.113 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.95 Hydrogen bonds: A:W.113 Water bridges: A:D.99 Salt bridges: A:R.108 ACY.9: 6 residues within 4Å: Chain B: T.42, T.43, L.95, R.107, R.108, W.113 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.95 Hydrogen bonds: B:W.113 Salt bridges: B:R.108

2 x M0N: (1-HYDROXY-2-IMIDAZO[1,2-A]PYRIDIN-3-YLETHANE-1,1-DIYL)BIS(PHOSPHONIC ACID)(Non-covalent)

M0N.2: 17 residues within 4Å: Chain A: Y.94, L.95, D.98, D.102, R.107, T.163, Q.167, K.207, T.208, Y.211, Q.247, D.250, K.264 Ligands: IPE.5, MG.6, MG.7, MG.8 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.94, A:D.98, A:T.163, A:Q.167, A:Y.211 Hydrogen bonds: A:D.98, A:R.107, A:R.107, A:Y.211, A:Q.247, A:Q.247, A:Q.247, A:D.250 Water bridges: A:S.104, A:S.104, A:S.104, A:S.104, A:Q.167, A:D.254 M0N.10: 17 residues within 4Å: Chain B: Y.94, L.95, D.98, D.102, R.107, T.163, Q.167, K.207, T.208, Y.211, Q.247, D.250, K.264 Ligands: IPE.13, MG.14, MG.15, MG.16 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.94, B:D.98, B:T.163, B:Q.167, B:Y.211 Hydrogen bonds: B:D.98, B:R.107, B:R.107, B:Q.247, B:Q.247, B:Q.247, B:D.250 Water bridges: B:D.102, B:S.104, B:S.104, B:S.104, B:Q.167, B:K.264

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

SO4.3: 5 residues within 4Å: Chain A: F.17, Q.21, K.25, H.141 Chain B: K.158 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.21 Water bridges: A:H.141, A:H.141, A:H.141, A:H.141, B:K.158, B:K.158 Salt bridges: A:K.25, A:H.141, B:K.158 SO4.4: 8 residues within 4Å: Chain A: G.47, K.48, Y.49, F.50, R.51, Q.91, R.108 Ligands: IPE.5 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.48, A:Y.49, A:F.50, A:Q.91, A:R.108 Water bridges: A:K.48, A:R.51, A:R.51 Salt bridges: A:K.48, A:R.51 SO4.11: 5 residues within 4Å: Chain A: K.158 Chain B: F.17, Q.21, K.25, H.141 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.21 Salt bridges: B:K.25, B:H.141, A:K.158 Water bridges: A:K.158, A:K.158 SO4.12: 8 residues within 4Å: Chain B: G.47, K.48, Y.49, F.50, R.51, Q.91, R.108 Ligands: IPE.13 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:K.48, B:Y.49, B:F.50, B:Q.91, B:R.108 Water bridges: B:K.48, 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.5: 14 residues within 4Å: Chain A: G.47, K.48, F.50, R.51, Q.91, R.108, T.208, Y.211, T.212, F.246, Q.247, D.250 Ligands: M0N.2, SO4.4 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.246, A:D.250 Hydrogen bonds: A:K.48 Water bridges: A:K.48, A:K.48, A:K.48, A:K.48, A:R.360 Salt bridges: A:K.48, A:K.48, A:R.51, A:R.51, A:R.108, A:K.264 IPE.13: 14 residues within 4Å: Chain B: G.47, K.48, F.50, R.51, Q.91, R.108, T.208, Y.211, T.212, F.246, Q.247, D.250 Ligands: M0N.10, SO4.12 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.246, B:D.250 Hydrogen bonds: B:K.48 Water bridges: B:K.48, B:K.48, B:K.48, B:K.48, B:R.360 Salt bridges: B:K.48, B:K.48, B:R.51, B:R.51, B:R.108, B:K.264

6 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain A: D.98, D.102 Ligands: M0N.2, MG.8 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.7: 4 residues within 4Å: Chain A: D.250, D.254, D.268 Ligands: M0N.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.8: 6 residues within 4Å: Chain A: D.98, D.102, D.170, K.273 Ligands: M0N.2, MG.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.1 MG.14: 4 residues within 4Å: Chain B: D.98, D.102 Ligands: M0N.10, MG.16 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.98, B:D.102, H2O.10, H2O.10 MG.15: 4 residues within 4Å: Chain B: D.250, D.254, D.268 Ligands: M0N.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.250, H2O.10, H2O.10, H2O.10 MG.16: 6 residues within 4Å: Chain B: D.98, D.102, D.170, K.273 Ligands: M0N.10, MG.14 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.98, B:D.102, H2O.9, H2O.10, H2O.10

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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