SMTL ID : 5nx6.1

Crystal structure of 1,8-cineole synthase from Streptomyces clavuligerus in complex with 2-fluoroneryl diphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-dimer

Ligands

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

LA6.1: 20 residues within 4Å: Chain A: F.74, F.77, F.78, D.81, R.174, F.179, M.180, I.216, N.217, N.220, S.224, K.227, E.228, N.305, W.308, C.309, R.314, Y.315 Ligands: MG.2, MG.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.74, A:F.77, A:F.78, A:I.216, A:N.220, A:W.308 Hydrogen bonds: A:R.174, A:S.224, A:E.228 Water bridges: A:D.81, A:D.81, A:R.174, A:K.227, A:K.227 Salt bridges: A:K.227, A:R.314 LA6.7: 20 residues within 4Å: Chain B: F.74, F.77, F.78, D.81, R.174, F.179, M.180, I.216, N.217, N.220, S.224, K.227, E.228, N.305, W.308, C.309, R.314, Y.315 Ligands: MG.8, MG.9 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.74, B:F.78, B:I.216, B:N.220, B:W.308 Hydrogen bonds: B:R.174, B:N.220, B:S.224, B:Y.315, B:Y.315 Water bridges: B:R.174, B:K.227, B:K.227, B:D.233 Salt bridges: B:K.227, B:R.314

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: N.220, S.224, E.228 Ligands: LA6.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.224, A:E.228, H2O.1 MG.3: 2 residues within 4Å: Chain A: D.81 Ligands: LA6.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.81, H2O.1, H2O.1, H2O.1, H2O.1 MG.8: 4 residues within 4Å: Chain B: N.220, S.224, E.228 Ligands: LA6.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.224, B:E.228, H2O.16 MG.9: 2 residues within 4Å: Chain B: D.81 Ligands: LA6.7 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.81, H2O.16, H2O.16, H2O.17, H2O.17

2 x 9D2: 2-ethyl-2-(hydroxymethyl)propane-1,3-diol(Non-covalent)

9D2.4: 5 residues within 4Å: Chain A: E.6, Q.250, L.253, A.254, R.257 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.253, A:R.257 Water bridges: A:R.257 9D2.10: 5 residues within 4Å: Chain B: E.6, Q.250, L.253, A.254, R.257 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.253, B:R.257 Water bridges: B:R.257

2 x NDS: ETHYL DIMETHYL AMMONIO PROPANE SULFONATE(Non-covalent)

NDS.5: 7 residues within 4Å: Chain A: F.19, R.22, R.26, Q.63, G.64 Chain B: P.18, R.22 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.64 Salt bridges: A:R.22, A:R.26 NDS.11: 6 residues within 4Å: Chain A: P.18 Chain B: F.19, R.22, R.26, Q.63, G.64 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.64 Salt bridges: B:R.22, B:R.26

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: G.282, I.283, P.284, R.288 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.283, A:R.288 Water bridges: A:L.285, A:R.288 GOL.12: 4 residues within 4Å: Chain B: G.282, I.283, L.285, R.288 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.288 Water bridges: B:G.279, B:L.285, B:R.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Karuppiah, V. et al., Structural Basis of Catalysis in the Bacterial Monoterpene Synthases Linalool Synthase and 1,8-Cineole Synthase. ACS Catal (2017)

Release Date

2017-09-20

Peptides

Pentalenene synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pentalenene synthase

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