SMTL ID : 4nke.1

The effects of Lysine 200 and Phenylalanine 239 Farnesyl Pyrophosphate Synthase (FPPS) mutations on the catalytic activity, crystal structure and inhibition by nitrogen containing bisphosphonates

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.125, D.129 Ligands: MG.3, RIS.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.125, A:D.129, H2O.10, H2O.10 MG.2: 3 residues within 4Å: Chain A: D.265, K.279 Ligands: RIS.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.265, H2O.10, H2O.11, H2O.11 MG.3: 4 residues within 4Å: Chain A: D.125, D.129 Ligands: MG.1, RIS.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.125, A:D.129, H2O.10, H2O.10, H2O.10 MG.8: 4 residues within 4Å: Chain B: D.125, D.129 Ligands: MG.10, RIS.11 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.26, H2O.26 MG.9: 3 residues within 4Å: Chain B: D.265, K.279 Ligands: RIS.11 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.265, H2O.26, H2O.26, H2O.26 MG.10: 4 residues within 4Å: Chain B: D.125, D.129 Ligands: MG.8, RIS.11 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.26, H2O.26, H2O.26

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

RIS.4: 15 residues within 4Å: Chain A: L.122, D.125, D.129, R.134, Q.193, K.222, T.223, Y.226, Q.262, D.265, K.279 Ligands: MG.1, MG.2, MG.3, IPE.5 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:L.122, A:D.125 Hydrogen bonds: A:R.134, A:R.134, A:K.222, A:Y.226, A:Q.262, A:D.265, A:K.279, A:K.279 Water bridges: A:D.125, A:D.129, A:D.129, A:D.129, A:S.131, A:Q.193, A:D.269, A:D.269, A:K.288 RIS.11: 15 residues within 4Å: Chain B: L.122, D.125, D.129, R.134, Q.193, K.222, T.223, Y.226, Q.262, D.265, K.279 Ligands: MG.8, MG.9, MG.10, IPE.12 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.122, B:D.125 Hydrogen bonds: B:R.134, B:R.134, B:K.222, B:Q.262, B:D.265, B:K.279, B:K.279 Water bridges: B:D.125, B:S.131, B:Q.193, B:K.288

2 x IPE: 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

IPE.5: 12 residues within 4Å: Chain A: G.78, K.79, R.82, Q.118, R.135, T.223, Y.226, S.227, Q.262, D.265 Ligands: RIS.4, EDO.6 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:T.223, A:D.265 Hydrogen bonds: A:K.79, A:Q.118 Water bridges: A:K.79, A:K.79, A:Y.80, A:Y.80, A:R.82, A:R.82 Salt bridges: A:K.79, A:K.79, A:R.82, A:R.135 IPE.12: 12 residues within 4Å: Chain B: G.78, K.79, R.82, Q.118, R.135, T.223, Y.226, S.227, Q.262, D.265 Ligands: RIS.11, EDO.13 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:T.223, B:D.265 Hydrogen bonds: B:K.79, B:Q.118 Water bridges: B:K.79, B:K.79, B:Y.80, B:Y.80, B:R.82, B:R.82 Salt bridges: B:K.79, B:K.79, B:R.82, B:R.135

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 5 residues within 4Å: Chain A: G.78, K.79, V.276, T.277 Ligands: IPE.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.79, A:K.79, A:V.276 EDO.7: 4 residues within 4Å: Chain A: L.183, Q.184 Chain B: Y.162, R.163 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.162, A:L.183 EDO.13: 5 residues within 4Å: Chain B: G.78, K.79, V.276, T.277 Ligands: IPE.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.79, B:K.79, B:V.276 EDO.14: 4 residues within 4Å: Chain A: Y.162, R.163 Chain B: L.183, Q.184 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.183, A:Y.162

Links

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Citation

Tsoumpra, M.K. et al., The effects of Lysine 200 and Phenylalanine 239 Farnesyl Pyrophosphate Synthase (FPPS) mutations on the catalytic activity, crystal structure and inhibition by nitrogen containing bisphosphonates. To be Published

Release Date

2014-11-19

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Farnesyl pyrophosphate synthase

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