SMTL ID : 6b07.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

2 x C6M: 2-(2,2-diphosphonoethyl)-1-propylpyridin-1-ium(Non-covalent)

C6M.1: 14 residues within 4Å: Chain A: D.91, D.95, R.100, Q.159, K.188, T.189, Y.192, F.227, Q.228, D.231, K.245 Ligands: MG.2, MG.3, MG.4 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:D.91, A:T.189, A:Y.192, A:F.227 Hydrogen bonds: A:R.100, A:R.100, A:K.188, A:Q.228, A:K.245 Water bridges: A:D.91, A:D.91, A:D.95, A:S.97, A:Q.159, A:D.162, A:K.188, A:K.188, A:D.235, A:D.235, A:K.254 C6M.8: 14 residues within 4Å: Chain B: D.91, D.95, R.100, Q.159, K.188, T.189, Y.192, F.227, Q.228, D.231, K.245 Ligands: MG.9, MG.10, MG.11 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:D.91, B:T.189, B:Y.192, B:F.227 Hydrogen bonds: B:R.100, B:R.100, B:K.188, B:Q.228, B:K.245 Water bridges: B:D.91, B:D.91, B:D.95, B:S.97, B:Q.159, B:D.162, B:K.188, B:K.188, B:K.254

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.91, D.95, Q.159, D.162 Ligands: C6M.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.3, H2O.7 MG.3: 4 residues within 4Å: Chain A: D.91, D.95 Ligands: C6M.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.7 MG.4: 2 residues within 4Å: Chain A: D.231 Ligands: C6M.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.231, H2O.3, H2O.3, H2O.4 MG.9: 6 residues within 4Å: Chain B: D.91, D.95, Q.159, D.162 Ligands: C6M.8, MG.10 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.91, B:D.95, H2O.13, H2O.15, H2O.18 MG.10: 4 residues within 4Å: Chain B: D.91, D.95 Ligands: C6M.8, MG.9 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.11: 2 residues within 4Å: Chain B: D.231 Ligands: C6M.8 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.231, H2O.15, H2O.15, H2O.15

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

EDO.5: 7 residues within 4Å: Chain A: Y.39, N.40, M.89, D.92, P.104, C.105, W.106 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.88, A:D.92, A:P.104, A:W.106 Water bridges: A:Y.107 EDO.6: 4 residues within 4Å: Chain A: E.28 Chain B: L.161, R.180, A.183 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.28, B:R.180 EDO.7: 6 residues within 4Å: Chain A: E.146, N.149, E.150 Chain B: F.128, Y.129, H.132 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.149 EDO.12: 7 residues within 4Å: Chain B: Y.39, N.40, M.89, D.92, P.104, C.105, W.106 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.88, B:P.104, B:W.106 Water bridges: B:Y.107 EDO.13: 4 residues within 4Å: Chain A: L.161, R.180, A.183 Chain B: E.28 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.180 EDO.14: 6 residues within 4Å: Chain A: F.128, Y.129, H.132 Chain B: E.146, N.149, E.150 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.150 Water bridges: B:N.149

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

Related Entries With Identical Sequence