SMTL ID : 4nua.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 1.43 Å

Oligo State

homo-dimer

Ligands

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

RIS.1: 14 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.2, MG.3, MG.4 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:D.125 Hydrogen bonds: A:R.134, A:R.134, A:Q.262, A:D.265, A:K.279, A:K.279 Water bridges: A:D.129, A:D.129, A:S.131, A:S.131, A:Q.193, A:K.222, A:K.222, A:K.222, A:K.222, A:Y.226, A:Y.226, A:D.269 RIS.12: 14 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.13, MG.14, MG.15 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:D.125 Hydrogen bonds: B:R.134, B:R.134, B:Q.262, B:D.265, B:K.279, B:K.279 Water bridges: B:S.131, B:S.131, B:S.131, B:Q.193, B:K.222, B:K.222, B:K.222, B:K.222, B:D.265, B:D.265

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.125, D.129 Ligands: RIS.1, MG.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.125, A:D.129, H2O.13, H2O.13 MG.3: 4 residues within 4Å: Chain A: D.265, D.269, K.279 Ligands: RIS.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.265, H2O.13, H2O.13, H2O.13 MG.4: 4 residues within 4Å: Chain A: D.125, D.129 Ligands: RIS.1, MG.2 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.125, A:D.129, H2O.14, H2O.14, H2O.14 MG.13: 4 residues within 4Å: Chain B: D.125, D.129 Ligands: RIS.12, MG.15 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.28, H2O.28 MG.14: 4 residues within 4Å: Chain B: D.265, D.269, K.279 Ligands: RIS.12 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.265, H2O.28, H2O.28, H2O.28 MG.15: 4 residues within 4Å: Chain B: D.125, D.129 Ligands: RIS.12, MG.13 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.28, H2O.28, H2O.28

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

EDO.5: 4 residues within 4Å: Chain A: L.93, I.241, P.357, L.358 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.93, A:P.357 EDO.6: 4 residues within 4Å: Chain A: K.213, R.214, S.217 Chain B: E.59 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.213, A:S.217, A:S.217 Water bridges: A:T.211, A:R.214 EDO.7: 4 residues within 4Å: Chain A: Q.264, F.336, L.337, E.340 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.264 EDO.8: 5 residues within 4Å: Chain A: Y.162, K.166 Chain B: E.180, L.183, Q.184 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.163, A:K.166 EDO.9: 9 residues within 4Å: Chain A: F.120, F.121, A.124, M.128, E.190, Q.193 Chain B: I.151, N.152, N.155 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:I.151, B:N.155 Water bridges: A:Q.193 EDO.10: 7 residues within 4Å: Chain A: E.256, E.259, F.260, Y.339, S.343, H.346, I.347 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.259, A:Y.339, A:S.343 EDO.16: 4 residues within 4Å: Chain B: L.93, I.241, P.357, L.358 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.93, B:P.357 EDO.17: 4 residues within 4Å: Chain A: E.59 Chain B: K.213, R.214, S.217 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.213, B:S.217, B:S.217 Water bridges: B:R.214 EDO.18: 4 residues within 4Å: Chain B: Q.264, F.336, L.337, E.340 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.264 EDO.19: 5 residues within 4Å: Chain A: E.180, L.183, Q.184 Chain B: Y.162, K.166 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.163, B:K.166 EDO.20: 9 residues within 4Å: Chain A: I.151, N.152, N.155 Chain B: F.120, F.121, A.124, M.128, E.190, Q.193 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.151, A:N.155 Water bridges: B:Q.193 EDO.21: 7 residues within 4Å: Chain B: E.256, E.259, F.260, Y.339, S.343, H.346, I.347 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.259, B:E.259, B:S.343

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.11: 4 residues within 4Å: Chain A: G.78, K.79, Q.118, R.135 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.79, A:Q.118, A:Q.118 Water bridges: A:Y.80, A:Y.80, A:R.82, A:R.82, A:R.82 Salt bridges: A:R.135 PO4.22: 4 residues within 4Å: Chain B: G.78, K.79, Q.118, R.135 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.79, B:Q.118, B:Q.118 Water bridges: B:Y.80, B:Y.80, B:R.82, B:R.82, B:R.82 Salt bridges: B:R.135

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