SMTL ID : 4q23.1

The role of threonine 201 and tyrosine 204 in the human farnesyl pyrophosphate synthase catalytic mechanism and the mode of inhibition by the nitrogen-containing bisphosphonates

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

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

RIS.1: 13 residues within 4Å: Chain A: L.122, D.125, D.129, R.134, Q.193, K.222, Y.226, Q.262, D.265, K.279 Ligands: MG.2, MG.3, MG.4 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:D.125 Hydrogen bonds: A:D.125, A:R.134, A:R.134, A:Q.262, A:D.265, A:K.279 Water bridges: A:S.131, A:S.131, A:S.131, A:S.131, A:S.131, A:R.134, A:Q.193, A:K.222, A:K.222, A:K.222, A:K.222, A:D.265, A:D.265, A:K.279, A:K.279 RIS.6: 13 residues within 4Å: Chain B: L.122, D.125, D.129, R.134, Q.193, K.222, Y.226, Q.262, D.265, K.279 Ligands: MG.7, MG.8, MG.9 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:D.125 Hydrogen bonds: B:D.125, B:R.134, B:R.134, B:Y.226, B:Q.262, B:D.265, B:K.279 Water bridges: B:D.129, B:D.129, B:S.131, B:S.131, B:S.131, B:S.131, B:R.134, B:Q.193, B:K.222, B:K.222, B:K.222, B:K.222, B:D.269, B:D.269, B:D.269, B:D.269, B:D.269

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.4, H2O.4 MG.3: 3 residues within 4Å: Chain A: D.265, D.269 Ligands: RIS.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.265, H2O.4, H2O.4, H2O.4 MG.4: 5 residues within 4Å: Chain A: D.125, D.129, D.196 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.4, H2O.4, H2O.4 MG.7: 4 residues within 4Å: Chain B: D.125, D.129 Ligands: RIS.6, MG.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.9, H2O.9 MG.8: 3 residues within 4Å: Chain B: D.265, D.269 Ligands: RIS.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.265, H2O.9, H2O.9, H2O.9 MG.9: 5 residues within 4Å: Chain B: D.125, D.129, D.196 Ligands: RIS.6, MG.7 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.9, H2O.9, H2O.9

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 5 residues within 4Å: Chain A: G.78, K.79, R.82, Q.118, R.135 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.79, A:R.82 Water bridges: A:Y.80, A:R.134 Salt bridges: A:R.135 SO4.10: 5 residues within 4Å: Chain B: G.78, K.79, R.82, Q.118, R.135 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.79, B:R.82 Water bridges: B:Y.80, B:R.134 Salt bridges: B:R.135

Links

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Citation

Tsoumpra, M.K. et al., The role of threonine 201 and tyrosine 204 in the human farnesyl pyrophosphate synthase catalytic mechanism and the mode of inhibition by the nitrogen-containing bisphosphonates. To be Published

Release Date

2015-03-18

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Farnesyl pyrophosphate synthase

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