SMTL ID : 4nkf.1

The effects of Lysine 200 and Phenylalanine 239 Farnesyl Pyrophosphate Synthase (FPPS) mutations on the catalytic activity, crystal structure and inhibition by nitrogen containing bisphosphonates

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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, 210.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.125, A:D.129, H2O.4, H2O.4 MG.2: 3 residues within 4Å: Chain A: D.265, D.269 Ligands: 210.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.265, H2O.4, H2O.4, H2O.4 MG.3: 4 residues within 4Å: Chain A: D.125, D.129 Ligands: MG.1, 210.4 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.4 MG.7: 4 residues within 4Å: Chain B: D.125, D.129 Ligands: MG.9, 210.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.11, H2O.11 MG.8: 3 residues within 4Å: Chain B: D.265, D.269 Ligands: 210.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.265, H2O.10, H2O.10, H2O.10 MG.9: 4 residues within 4Å: Chain B: D.125, D.129 Ligands: MG.7, 210.10 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.10, H2O.11, H2O.11

2 x 210: PAMIDRONATE(Non-covalent)

210.4: 12 residues within 4Å: Chain A: L.122, D.125, D.129, R.134, K.222, T.223, Q.262, D.265, K.279 Ligands: MG.1, MG.2, MG.3 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:L.122 Hydrogen bonds: A:R.134, A:R.134, A:K.222, A:Q.262, 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:R.134, A:Q.193, A:Q.193, A:Q.193, A:Y.226, A:D.269, A:K.279 210.10: 12 residues within 4Å: Chain B: L.122, D.125, D.129, R.134, K.222, T.223, Q.262, D.265, K.279 Ligands: MG.7, MG.8, MG.9 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:L.122 Hydrogen bonds: B:R.134, B:R.134, B:K.222, B:Q.262, B:Q.262, B:D.265 Water bridges: B:D.129, B:S.131, B:S.131, B:S.131, B:S.131, B:R.134, B:Q.193, B:Q.193, B:Q.193, B:D.265, B:D.265, B:D.269, B:K.279

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

EDO.5: 6 residues within 4Å: Chain A: E.180, L.183, Q.184 Chain B: Y.162, R.163, K.166 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.163, B:R.163 EDO.11: 6 residues within 4Å: Chain A: Y.162, R.163, K.166 Chain B: E.180, L.183, Q.184 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.163, A:R.163

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 5 residues within 4Å: Chain A: Y.141, Q.142, K.143, G.147 Chain B: L.148 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.142, A:G.147 PEG.12: 5 residues within 4Å: Chain A: L.148 Chain B: Y.141, Q.142, K.143, G.147 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.142, B:G.147 Water bridges: B:Y.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsoumpra, M.K. et al., The effects of Lysine 200 and Phenylalanine 239 Farnesyl Pyrophosphate Synthase (FPPS) mutations on the catalytic activity, crystal structure and inhibition by nitrogen containing bisphosphonates. To be Published

Release Date

2014-11-19

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Farnesyl pyrophosphate synthase

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