SMTL ID : 4kpd.1

Crystal Structure of Human Farnesyl Pyrophosphate Synthase (Y204F) Mutant Complexed with Mg, Risedronate and Isopentenyl Pyrophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 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.5 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.5 MG.2: 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.3, H2O.3, H2O.4 MG.3: 5 residues within 4Å: Chain A: D.125, D.129, D.196 Ligands: MG.1, RIS.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.125, A:D.129, H2O.3, H2O.3, H2O.3 MG.6: 4 residues within 4Å: Chain B: D.125, D.129 Ligands: MG.8, RIS.10 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.10, H2O.10, H2O.11 MG.7: 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.10, H2O.10, H2O.10 MG.8: 5 residues within 4Å: Chain B: D.125, D.129, D.196 Ligands: MG.6, RIS.10 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.9, H2O.10, H2O.10

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

IPE.4: 13 residues within 4Å: Chain A: G.78, K.79, R.82, Q.118, R.135, T.223, F.226, S.227, F.261, Q.262, D.265, R.373 Ligands: RIS.5 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:T.223, A:F.226, A:F.261 Hydrogen bonds: A:K.79, A:R.82, A:Q.118, A:R.373 Water bridges: A:K.79, A:K.79, A:K.79, A:Y.80, A:Y.80, A:N.81, A:N.81, A:N.81, A:E.115, A:R.134, A:K.279, A:K.279, A:K.279 Salt bridges: A:K.79, A:K.79, A:R.82, A:R.135 IPE.9: 13 residues within 4Å: Chain B: G.78, K.79, R.82, Q.118, R.135, T.223, F.226, S.227, F.261, Q.262, D.265, R.373 Ligands: RIS.10 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:T.223, B:F.226, B:F.261 Hydrogen bonds: B:K.79, B:R.82, B:Q.118, B:R.373 Water bridges: B:K.79, B:K.79, B:K.79, B:Y.80, B:Y.80, B:N.81, B:N.81, B:N.81, B:E.115, B:R.134, B:K.279, B:K.279, B:K.279 Salt bridges: B:K.79, B:K.79, B:R.82, B:R.135

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

RIS.5: 15 residues within 4Å: Chain A: L.122, D.125, D.129, R.134, Q.193, K.222, T.223, F.226, Q.262, D.265, K.279 Ligands: MG.1, MG.2, MG.3, IPE.4 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.122, A:D.125 Hydrogen bonds: A:R.134, A:R.134, A:K.222, A:T.223, A:Q.262, A:D.265 Water bridges: A:D.125, A:S.131, A:S.131, A:S.131, A:Q.193, A:D.265, A:D.265, A:K.279 RIS.10: 15 residues within 4Å: Chain B: L.122, D.125, D.129, R.134, Q.193, K.222, T.223, F.226, Q.262, D.265, K.279 Ligands: MG.6, MG.7, MG.8, IPE.9 16 PLIP interactions: 16 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 Water bridges: B:D.125, B:S.131, B:S.131, B:S.131, B:Q.193, B:D.269, B:D.269, B:D.269, B:D.269

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsoumpra, M.K. et al., Crystal Structure of Human Farnesyl Pyrophosphate Synthase (Y204F) Mutant 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