SMTL ID : 6onm.1

Crystal Structure of (+)-Limonene Synthase Complexed with 8,9-Difluorolinalyl Diphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

6 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: D.343, D.347 Ligands: MN.2, MWG.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.343, A:D.347 MN.2: 6 residues within 4Å: Chain A: D.343, D.347, Y.419, E.422 Ligands: MN.1, MWG.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.343, A:D.347 MN.3: 2 residues within 4Å: Chain A: D.488 Ligands: MWG.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.488 MN.5: 4 residues within 4Å: Chain B: D.343, D.347 Ligands: MN.6, MWG.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.343, B:D.347 MN.6: 6 residues within 4Å: Chain B: D.343, D.347, Y.419, E.422 Ligands: MN.5, MWG.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.343, B:D.347 MN.7: 2 residues within 4Å: Chain B: D.488 Ligands: MWG.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.488

2 x MWG: (3R)-8-fluoro-7-(fluoromethyl)-3-methylocta-1,6-dien-3-yl trihydrogen diphosphate(Non-covalent)

MWG.4: 13 residues within 4Å: Chain A: W.315, I.336, I.339, D.343, D.347, S.444, T.446, R.485, D.488, K.504 Ligands: MN.1, MN.2, MN.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.315 Hydrogen bonds: A:D.343 Water bridges: A:Y.419 Salt bridges: A:R.485, A:K.504 Halogen bonds: A:T.446 MWG.8: 13 residues within 4Å: Chain B: W.315, I.336, I.339, D.343, D.347, S.444, T.446, R.485, D.488, K.504 Ligands: MN.5, MN.6, MN.7 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.315 Hydrogen bonds: B:D.343 Salt bridges: B:R.485, B:K.504 Halogen bonds: B:T.446

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morehouse, B.R. et al., Direct Evidence of an Enzyme-Generated LPP Intermediate in (+)-Limonene Synthase Using a Fluorinated GPP Substrate Analog. Acs Chem.Biol. (2019)

Release Date

2019-09-04

Peptides

(+)-limonene synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

(+)-limonene synthase

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