SMTL ID : 6b06.2 (1 other biounit)

Crystal structure of CfFPPS2, a lepidopteran type-II farnesyl diphosphate synthase, complexed with IPP and [2-(1-methylpyridin-2-yl)-1-phosphono-ethyl]phosphonic acid (inhibitor 1b)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x C6J: 2-(2,2-diphosphonoethyl)-1-methylpyridin-1-ium(Non-covalent)

C6J.1: 15 residues within 4Å: Chain A: L.87, D.91, D.95, R.100, Q.159, K.188, T.189, Y.192, Q.228, D.231, K.245 Ligands: MG.2, MG.3, MG.4, IPE.5 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.87, A:D.91, A:Y.192 Hydrogen bonds: A:D.95, A:R.100, A:R.100, A:D.231, A:K.245 Water bridges: A:D.91, A:D.95, A:S.97, A:Q.159, A:D.235, A:D.235, A:D.249, A:D.249 C6J.6: 15 residues within 4Å: Chain B: L.87, D.91, D.95, R.100, Q.159, K.188, T.189, Y.192, Q.228, D.231, K.245 Ligands: MG.7, MG.8, MG.9, IPE.10 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.87, B:D.91, B:Y.192 Hydrogen bonds: B:R.100, B:R.100, B:D.231, B:K.245 Water bridges: B:D.91, B:D.95, B:S.97, B:Q.159

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.91, D.95 Ligands: C6J.1, MG.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.91, A:D.95, H2O.1, H2O.1, H2O.1 MG.3: 5 residues within 4Å: Chain A: D.91, D.95, R.100 Ligands: C6J.1, MG.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.91, A:D.95, H2O.1, H2O.1 MG.4: 3 residues within 4Å: Chain A: D.231, D.235 Ligands: C6J.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.231, H2O.1, H2O.1, H2O.1 MG.7: 4 residues within 4Å: Chain B: D.91, D.95 Ligands: C6J.6, MG.8 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.91, B:D.95, H2O.1, H2O.1, H2O.1 MG.8: 5 residues within 4Å: Chain B: D.91, D.95, R.100 Ligands: C6J.6, MG.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.91, B:D.95, H2O.1, H2O.1 MG.9: 3 residues within 4Å: Chain B: D.231, D.235 Ligands: C6J.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.231, H2O.1, H2O.1, H2O.1

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

IPE.5: 9 residues within 4Å: Chain A: K.45, R.48, Q.84, R.101, Y.192, F.227, Q.228, D.231 Ligands: C6J.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.227, A:D.231 Hydrogen bonds: A:Q.84 Salt bridges: A:K.45, A:K.45, A:R.48 IPE.10: 9 residues within 4Å: Chain B: K.45, R.48, Q.84, R.101, Y.192, F.227, Q.228, D.231 Ligands: C6J.6 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.227, B:D.231 Hydrogen bonds: B:Q.84 Salt bridges: B:K.45, B:K.45, B:R.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Picard, M.E. et al., Structural characterization of a lepidopteran type-II farnesyl diphosphate synthase from the spruce budworm, Choristoneura fumiferana: Implications for inhibitor design. Insect Biochem. Mol. Biol. (2017)

Release Date

2017-12-13

Peptides

Farnesyl diphosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

Farnesyl diphosphate synthase

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