SMTL ID : 5cg5.1

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

Coordinates

PDB Format Compare

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

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

RIS.4: 16 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 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:D.97 Hydrogen bonds: A:R.106, A:K.194, A:Q.234, A:Q.234, A:D.237, A:K.251 Water bridges: A:S.103, A:R.106, A:Q.165, A:T.195, A:D.237, A:D.237 RIS.8: 16 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.5, MG.6, MG.7 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:D.97 Hydrogen bonds: B:R.106, B:R.106, B:K.194, B:Q.234, B:Q.234, B:D.237 Water bridges: B:S.103, B:Q.165, B:T.195, B:D.241, B:D.241, B:K.251, B:K.251

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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