SMTL ID : 5cg6.1

Neutron crystal structure of human farnesyl pyrophosphate synthase in complex with risedronate and isopentenyl pyrophosphate

Coordinates

PDB Format

Method

NEUTRON DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 7 residues within 4Å: Chain A: D.97, D.101, Q.165, D.168, K.260 Ligands: MG.2, RIS.4 8 PLIP interactions: 2 interactions with chain A, 6 Ligand-Water interactions Metal complexes: A:D.97, A:D.101, H2O.1, H2O.1, H2O.1, H2O.1, H2O.2, H2O.2 MG.2: 5 residues within 4Å: Chain A: D.97, D.101, R.106 Ligands: MG.1, RIS.4 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.97, A:D.101, H2O.1, H2O.1, H2O.2, H2O.2 MG.3: 5 residues within 4Å: Chain A: Q.234, D.237, D.241, K.251 Ligands: RIS.4 7 PLIP interactions: 1 interactions with chain A, 6 Ligand-Water interactions Metal complexes: A:D.237, H2O.1, H2O.1, H2O.1, H2O.1, H2O.1, H2O.1 MG.6: 7 residues within 4Å: Chain B: D.97, D.101, Q.165, D.168, K.260 Ligands: MG.7, RIS.9 8 PLIP interactions: 2 interactions with chain B, 6 Ligand-Water interactions Metal complexes: B:D.97, B:D.101, H2O.2, H2O.2, H2O.3, H2O.3, H2O.4, H2O.4 MG.7: 5 residues within 4Å: Chain B: D.97, D.101, R.106 Ligands: MG.6, RIS.9 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.97, B:D.101, H2O.3, H2O.3, H2O.4, H2O.4 MG.8: 5 residues within 4Å: Chain B: Q.234, D.237, D.241, K.251 Ligands: RIS.9 7 PLIP interactions: 1 interactions with chain B, 6 Ligand-Water interactions Metal complexes: B:D.237, H2O.3, H2O.3, H2O.3, H2O.3, H2O.3, H2O.3

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

RIS.4: 17 residues within 4Å: Chain A: F.93, L.94, D.97, D.101, R.106, T.161, Q.165, K.194, T.195, Y.198, Q.234, D.237, K.251 Ligands: MG.1, MG.2, MG.3, IPE.5 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.94, A:D.97 Hydrogen bonds: A:R.106, A:R.106, A:K.194, A:T.195, A:T.195, A:Q.234, A:Q.234, A:Q.234, A:K.251 Water bridges: A:D.98, A:S.103, A:Q.165 RIS.9: 17 residues within 4Å: Chain B: F.93, L.94, D.97, D.101, R.106, T.161, Q.165, K.194, T.195, Y.198, Q.234, D.237, K.251 Ligands: MG.6, MG.7, MG.8, IPE.10 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.94, B:D.97 Hydrogen bonds: B:R.106, B:R.106, B:K.194, B:T.195, B:T.195, B:Y.198, B:Q.234, B:Q.234, B:Q.234, B:K.251 Water bridges: B:Q.165, B:D.238, B:D.241, B:D.241

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

IPE.5: 16 residues within 4Å: Chain A: G.50, K.51, Y.52, R.54, Q.90, L.94, R.106, R.107, T.195, Y.198, S.199, F.233, Q.234, D.237, K.251 Ligands: RIS.4 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:T.195, A:F.233, A:D.237 Hydrogen bonds: A:K.51, A:R.54, A:Q.90 Water bridges: A:K.51, A:Y.52, A:N.53, A:N.53, A:E.87, A:K.251 Salt bridges: A:K.51, A:K.51, A:R.54, A:R.107 IPE.10: 16 residues within 4Å: Chain B: G.50, K.51, Y.52, R.54, Q.90, L.94, R.106, R.107, T.195, Y.198, S.199, F.233, Q.234, D.237, K.251 Ligands: RIS.9 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:T.195, B:F.233, B:D.237 Hydrogen bonds: B:K.51, B:R.54, B:Q.90 Water bridges: B:K.51, B:Y.52, B:Y.52, B:E.87, B:R.107, B:R.107, B:K.251 Salt bridges: B:K.51, B:K.51, B:R.54, B:R.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yokoyama, T. et al., Protonation State and Hydration of Bisphosphonate Bound to Farnesyl Pyrophosphate Synthase. J.Med.Chem. (2015)

Release Date

2015-10-14

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Farnesyl pyrophosphate synthase

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