SMTL ID : 5afx.1

T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-1238

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.255, D.259, D.273 Ligands: PVZ.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.255 MG.2: 4 residues within 4Å: Chain A: D.103, D.107 Ligands: MG.3, PVZ.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.103, A:D.107 MG.3: 5 residues within 4Å: Chain A: D.103, D.107, Q.172 Ligands: MG.2, PVZ.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.103, A:D.107 MG.5: 4 residues within 4Å: Chain B: D.255, D.259, D.273 Ligands: PVZ.8 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.255, H2O.6 MG.6: 4 residues within 4Å: Chain B: D.103, D.107, S.109 Ligands: PVZ.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.103, B:D.107 MG.7: 6 residues within 4Å: Chain B: D.103, D.107, Q.172, D.175, K.278 Ligands: PVZ.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.103, B:D.107, H2O.5

2 x PVZ: [1-hydroxy-2-(1-nonyl-1H-3lambda~5~-imidazol-3-yl)ethane-1,1-diyl]bis(phosphonic acid)(Non-covalent)

PVZ.4: 21 residues within 4Å: Chain A: Y.99, L.100, D.103, M.106, D.107, R.112, K.137, D.165, T.168, A.169, Q.172, K.212, T.213, Y.216, D.255, K.269 Chain B: N.131, L.134 Ligands: MG.1, MG.2, MG.3 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.99, A:Y.99, A:Y.99, A:T.168, A:A.169, A:Q.172, B:L.134 Hydrogen bonds: A:R.112, A:R.112, A:Q.252, A:D.255, A:K.269 PVZ.8: 23 residues within 4Å: Chain A: N.131, L.134 Chain B: H.98, Y.99, L.100, D.103, M.106, D.107, R.112, K.137, D.165, T.168, A.169, Q.172, K.212, T.213, Y.216, Q.252, D.255, K.269 Ligands: MG.5, MG.6, MG.7 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.99, B:Y.99, B:Y.99, B:T.168, B:A.169, B:Q.172, A:L.134 Hydrogen bonds: B:R.112, B:R.112, B:K.212, B:Q.252, B:D.255, B:K.269 pi-Cation interactions: B:K.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, G. et al., Inhibition of Trypanosoma Brucei Cell Growth by Lipophilic Bisphosphonates: An in Vitro and in Vivo Investigation. Antimicrob.Agents Chemother. (2015)

Release Date

2015-10-28

Peptides

FARNESYL PYROPHOSPHATE SYNTHASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

FARNESYL PYROPHOSPHATE SYNTHASE

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