SMTL ID : 4n9u.1

The role of lysine 200 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 2.11 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.4 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.4 MG.2: 3 residues within 4Å: Chain A: D.265, D.269 Ligands: RIS.4 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.265, H2O.2, H2O.2, H2O.2, H2O.4 MG.3: 5 residues within 4Å: Chain A: D.125, D.129, D.196 Ligands: MG.1, RIS.4 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.7: 4 residues within 4Å: Chain B: D.125, D.129 Ligands: MG.9, RIS.10 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.7, H2O.7, H2O.8 MG.8: 3 residues within 4Å: Chain B: D.265, D.269 Ligands: RIS.10 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.265, H2O.7, H2O.7, H2O.7, H2O.8 MG.9: 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.7, H2O.7, H2O.7

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

RIS.4: 15 residues within 4Å: Chain A: L.122, D.125, D.129, R.134, T.189, Q.193, G.222, T.223, Y.226, Q.262, D.265, K.279 Ligands: MG.1, MG.2, MG.3 19 PLIP interactions: 19 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:D.129, A:S.131, A:S.131, A:S.131, A:S.131, A:Q.193, A:T.223, A:D.269, A:D.269, A:D.269, A:D.269 RIS.10: 15 residues within 4Å: Chain B: L.122, D.125, D.129, R.134, T.189, Q.193, G.222, T.223, Y.226, Q.262, D.265, K.279 Ligands: MG.7, MG.8, MG.9 14 PLIP interactions: 14 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.125, B:D.129, B:S.131, B:S.131, B:S.131, B:S.131, B:Q.193, B:D.265

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 7 residues within 4Å: Chain A: E.158, L.183, S.186 Chain B: E.158, A.159, Y.162 Ligands: EDO.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.183 EDO.6: 5 residues within 4Å: Chain A: Y.162, R.163, K.166 Chain B: L.183, Q.184 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.163, A:R.163 Water bridges: A:Y.162, A:R.163, A:K.166 EDO.11: 7 residues within 4Å: Chain A: E.158, A.159, Y.162 Chain B: E.158, L.183, S.186 Ligands: EDO.5 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.183 Water bridges: B:Y.162, A:E.158 EDO.12: 5 residues within 4Å: Chain A: L.183, Q.184 Chain B: Y.162, R.163, K.166 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.163, B:R.163 Water bridges: B:Y.162, B:R.163, B:K.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsoumpra, M.K. et al., The role of lysine 200 in the human farnesyl pyrophosphate synthase catalytic mechanism and the mode of inhibition by the nitrogen-containing bisphosphonates. TO BE PUBLISHED

Release Date

2014-10-22

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Farnesyl pyrophosphate synthase