SMTL ID : 5uv2.1

Crystal Structure of (+)-Limonene Synthase Complexed with 2-Fluoroneryl Diphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: D.343, D.347 Ligands: MN.2, LA6.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.343, A:D.347, H2O.4, H2O.4 MN.2: 5 residues within 4Å: Chain A: D.343, D.347, E.422 Ligands: MN.1, LA6.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.343, A:D.347, H2O.1, H2O.3, H2O.6 MN.3: 2 residues within 4Å: Chain A: D.488 Ligands: LA6.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.488, H2O.2, H2O.7, H2O.7

1 x LA6: (2E)-2-fluoro-3,7-dimethylocta-2,6-dien-1-yl trihydrogen diphosphate(Non-covalent)

LA6.4: 16 residues within 4Å: Chain A: W.315, I.336, I.339, T.340, D.343, D.347, S.444, I.445, T.446, F.484, R.485, D.488, K.504 Ligands: MN.1, MN.2, MN.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:W.315, A:W.315, A:I.336, A:I.339, A:I.445, A:F.484 Hydrogen bonds: A:D.343 Water bridges: A:R.485, A:D.489, A:K.504, A:K.504, A:K.504, A:K.504, A:K.504 Salt bridges: A:R.485, A:K.504 Halogen bonds: A:T.340

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, R.P. et al., Structural Characterization of Early Michaelis Complexes in the Reaction Catalyzed by (+)-Limonene Synthase from Citrus sinensis Using Fluorinated Substrate Analogues. Biochemistry (2017)

Release Date

2017-03-22

Peptides

(+)-limonene synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

(+)-limonene synthase

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