SMTL ID : 2ogd.1

T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-527

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 7 residues within 4Å: Chain A: K.70, R.73, Q.119, F.274, R.388 Ligands: ACT.2, SUF.6 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.73, A:K.292, A:K.292 Salt bridges: A:K.70, A:R.73, A:R.388 ACT.2: 6 residues within 4Å: Chain A: G.69, K.70, R.73, Q.119, R.136 Ligands: ACT.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:R.136 Hydrogen bonds: A:K.70, A:Q.119 Water bridges: A:Y.71, A:Y.71, A:R.73, A:R.73, A:R.73 Salt bridges: A:K.70, A:R.73, A:R.136 ACT.9: 8 residues within 4Å: Chain B: K.70, R.73, Q.119, R.135, F.274, R.388, K.390 Ligands: ACT.10 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.274 Hydrogen bonds: B:Q.119, B:R.135, B:R.388 Water bridges: B:K.292, B:K.292, B:K.292 Salt bridges: B:K.70, B:R.73, B:K.292, B:K.390 ACT.10: 6 residues within 4Å: Chain B: G.69, K.70, R.73, Q.119, R.136 Ligands: ACT.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.70 Water bridges: B:Y.71, B:R.73 Salt bridges: B:K.70, B:R.136

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.126, D.130 Ligands: MG.5, SUF.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.126, A:D.130, H2O.7, H2O.9 MG.4: 2 residues within 4Å: Chain A: D.278 Ligands: SUF.6 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.278, H2O.1, H2O.7, H2O.9 MG.5: 5 residues within 4Å: Chain A: D.126, D.130, D.198 Ligands: MG.3, SUF.6 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.126, A:D.130, H2O.1, H2O.7, H2O.9 MG.11: 4 residues within 4Å: Chain B: D.126, D.130 Ligands: MG.13, SUF.14 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.126, B:D.130, H2O.18, H2O.21 MG.12: 4 residues within 4Å: Chain B: D.278, D.282, K.292 Ligands: SUF.14 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.278, H2O.18, H2O.18, H2O.21 MG.13: 6 residues within 4Å: Chain B: D.126, D.130, D.198, K.301 Ligands: MG.11, SUF.14 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.126, B:D.130, H2O.18, H2O.18, H2O.21

2 x SUF: [2-(DIMETHYL-LAMBDA~4~-SULFANYL)-1-HYDROXYETHANE-1,1-DIYL]BIS(PHOSPHONIC ACID)(Non-covalent)

SUF.6: 14 residues within 4Å: Chain A: L.123, D.126, D.130, R.135, K.235, T.236, Y.239, Q.275, D.278, K.292 Ligands: ACT.1, MG.3, MG.4, MG.5 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.135, A:R.135, A:Q.275, A:D.278 Water bridges: A:D.126, A:S.132, A:S.132, A:S.132, A:Q.195, A:K.235, A:K.235, A:T.236, A:D.282, A:K.292 Salt bridges: A:D.126 SUF.14: 13 residues within 4Å: Chain B: L.123, D.126, D.130, R.135, K.235, T.236, Y.239, Q.275, D.278, K.292 Ligands: MG.11, MG.12, MG.13 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:D.126, B:R.135, B:R.135, B:Q.275, B:D.278 Water bridges: B:D.126, B:D.130, B:D.130, B:S.132, B:S.132, B:D.198, B:K.235, B:K.235, B:D.282, B:K.292, B:K.292 Salt bridges: B:D.126

3 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.7: 4 residues within 4Å: Chain A: D.179, C.182, R.183, R.186 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.179 BME.15: 3 residues within 4Å: Chain B: C.182, R.183, R.186 No protein-ligand interaction detected (PLIP) BME.16: 1 residues within 4Å: Chain B: C.370 No protein-ligand interaction detected (PLIP)

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.8: 6 residues within 4Å: Chain A: R.186, V.187, T.190, Y.238, L.242 Chain B: K.47 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:R.186, A:V.187, A:T.190, A:L.242 Hydrogen bonds: A:R.186, A:R.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., Bisphosphonates: Teaching Old Drugs with New Tricks. TO BE PUBLISHED

Release Date

2007-10-02

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Farnesyl pyrophosphate synthase

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