SMTL ID : 3efq.1

T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-714

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.126, D.130 Ligands: MG.3, 714.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.126, A:D.130, H2O.1, H2O.5 MG.2: 3 residues within 4Å: Chain A: D.278, D.282 Ligands: 714.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.278, H2O.3, H2O.3, H2O.6 MG.3: 4 residues within 4Å: Chain A: D.126, D.130 Ligands: MG.1, 714.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.126, A:D.130, H2O.1, H2O.5, H2O.5 MG.5: 4 residues within 4Å: Chain B: D.126, D.130 Ligands: MG.7, 714.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.126, B:D.130, H2O.6, H2O.6 MG.6: 3 residues within 4Å: Chain B: D.278, D.282 Ligands: 714.8 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.278, H2O.6, H2O.6 MG.7: 5 residues within 4Å: Chain B: D.126, D.130, D.198 Ligands: MG.5, 714.8 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.126, B:D.130, H2O.7, H2O.10, H2O.10

2 x 714: 1-(2,2-diphosphonoethyl)-3-(octyloxy)pyridinium(Non-covalent)

714.4: 22 residues within 4Å: Chain A: H.121, Y.122, L.123, E.125, D.126, M.129, D.130, R.135, T.191, Q.195, K.235, T.236, Y.239, Q.275, D.278, K.292 Chain B: I.153, N.154, L.157 Ligands: MG.1, MG.2, MG.3 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.122, A:E.125, A:Q.195, A:Q.195, A:Y.239, B:I.153, B:L.157, B:L.157 Hydrogen bonds: A:R.135, A:R.135, A:K.235, A:Q.275, A:K.292 Water bridges: A:S.132, A:S.132, A:Q.195, A:D.278, A:D.278 714.8: 19 residues within 4Å: Chain A: N.154, L.157 Chain B: H.121, Y.122, E.125, D.126, M.129, D.130, R.135, T.191, Q.195, K.235, T.236, Q.275, D.278, K.292 Ligands: MG.5, MG.6, MG.7 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.122, B:E.125, B:E.125, B:Q.195, B:Q.195, B:K.235, A:L.157, A:L.157 Hydrogen bonds: B:R.135, B:R.135, B:Q.275 Water bridges: B:S.132, B:S.132, B:S.132, B:Q.195, B:K.235, B:K.235, B:K.235, B:K.235, B:K.292

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., Lipophilic bisphosphonates as dual farnesyl/geranylgeranyl diphosphate synthase inhibitors: an X-ray and NMR investigation. J.Am.Chem.Soc. (2009)

Release Date

2009-05-05

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Farnesyl pyrophosphate synthase

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