SMTL ID : 6b04.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-dimer

Ligands

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

C6J.1: 13 residues within 4Å: Chain A: 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 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:D.91 Hydrogen bonds: A:R.100, A:R.100, A:K.188, A:Q.228, A:D.231 Water bridges: A:S.97, A:Q.159, A:K.188, A:K.188, A:K.188, A:K.188, A:D.235 C6J.6: 13 residues within 4Å: Chain B: 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 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:D.91, B:Y.192 Hydrogen bonds: B:R.100, B:R.100, B:K.188, B:Q.228, B:K.245 Water bridges: B:S.97, B:Q.159, B:K.188, B:K.188, B:K.188, B:K.188, B:D.235, B:D.235, B:D.235

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.91, D.95, D.162 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.2, H2O.2, H2O.9 MG.3: 4 residues within 4Å: Chain A: D.91, D.95 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.2, H2O.8 MG.4: 2 residues within 4Å: Chain A: D.231 Ligands: C6J.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.231, H2O.3, H2O.3, H2O.6 MG.7: 5 residues within 4Å: Chain B: D.91, D.95, D.162 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.13, H2O.14, H2O.19 MG.8: 4 residues within 4Å: Chain B: D.91, D.95 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.13, H2O.18 MG.9: 2 residues within 4Å: Chain B: D.231 Ligands: C6J.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.231, H2O.14, H2O.16, H2O.18

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

EDO.5: 4 residues within 4Å: Chain A: E.28 Chain B: L.161, R.180, A.183 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Water bridges: B:E.179, B:E.179, B:R.180 Hydrogen bonds: A:E.28, A:E.28 EDO.10: 4 residues within 4Å: Chain B: L.320, P.321, S.322, E.323 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.319, B:S.322, B:S.322 EDO.11: 5 residues within 4Å: Chain A: L.161, E.179, R.180, A.183 Chain B: E.28 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:E.179, A:R.180 Hydrogen bonds: B:E.28

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
A

B
B

Farnesyl diphosphate synthase

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