SMTL ID : 4kqs.1

Crystal Structure of Farnesyl Pyrophosphate Synthase Mutant (Y204A) Complexed with Mg, Risedronate and Isopentenyl Pyrophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.125, D.129, D.196 Ligands: MG.2, RIS.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.125, A:D.129, H2O.2, H2O.2, H2O.2 MG.2: 4 residues within 4Å: Chain A: D.125, D.129 Ligands: MG.1, RIS.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.125, A:D.129, H2O.1, H2O.1 MG.3: 3 residues within 4Å: Chain A: D.265, D.269 Ligands: RIS.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.265, H2O.1, H2O.1, H2O.1 MG.6: 5 residues within 4Å: Chain B: D.125, D.129, D.196 Ligands: MG.7, RIS.10 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.18, H2O.18, H2O.18 MG.7: 4 residues within 4Å: Chain B: D.125, D.129 Ligands: MG.6, RIS.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.17, H2O.17 MG.8: 3 residues within 4Å: Chain B: D.265, D.269 Ligands: RIS.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.265, H2O.17, H2O.17, H2O.17

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

IPE.4: 11 residues within 4Å: Chain A: G.78, K.79, R.82, Q.118, R.135, T.223, S.227, F.261, Q.262, D.265 Ligands: RIS.5 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:T.223, A:F.261, A:D.265 Hydrogen bonds: A:K.79, A:Q.118 Water bridges: A:K.79, A:K.79, A:K.79, A:K.79, A:Y.80, A:Y.80, A:N.81, A:N.81, A:R.82, A:R.82, A:E.115, A:K.279, A:K.279, A:K.279 Salt bridges: A:K.79, A:K.79, A:R.82, A:R.82, A:R.135 IPE.9: 11 residues within 4Å: Chain B: G.78, K.79, R.82, Q.118, R.135, T.223, S.227, F.261, Q.262, D.265 Ligands: RIS.10 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:T.223, B:F.261, B:D.265 Hydrogen bonds: B:K.79, B:Q.118 Water bridges: B:K.79, B:K.79, B:K.79, B:K.79, B:Y.80, B:Y.80, B:N.81, B:N.81, B:R.82, B:R.82, B:E.115, B:K.279, B:K.279, B:K.279 Salt bridges: B:K.79, B:K.79, B:R.82, B:R.82, B:R.135

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

RIS.5: 14 residues within 4Å: Chain A: L.122, D.125, D.129, R.134, Q.193, K.222, T.223, Q.262, D.265, K.279 Ligands: MG.1, MG.2, MG.3, IPE.4 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.122, A:D.125 Hydrogen bonds: A:R.134, A:R.134, A:Q.262, A:D.265 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:D.269, A:D.269, A:D.283 RIS.10: 14 residues within 4Å: Chain B: L.122, D.125, D.129, R.134, Q.193, K.222, T.223, Q.262, D.265, K.279 Ligands: MG.6, MG.7, MG.8, IPE.9 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:L.122, B:D.125 Hydrogen bonds: B:R.134, B:R.134, B:Q.262, B:D.265 Water bridges: B:D.129, 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, B:K.279, B:D.283

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsoumpra, M.K. et al., Crystal Structure of Farnesyl Pyrophosphate Synthase Mutant (Y204A) Complexed with Mg, Risedronate and Isopentenyl Pyrophosphate. To be Published

Release Date

2014-04-30

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Farnesyl pyrophosphate synthase

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