SMTL ID : 5nx7.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

homo-dimer

Ligands

2 x 0FV: (2Z)-2-fluoro-3,7-dimethylocta-2,6-dien-1-yl trihydrogen diphosphate(Non-covalent)

0FV.1: 20 residues within 4Å: Chain A: F.77, D.81, R.174, F.179, M.180, L.183, I.216, N.217, N.220, S.224, K.227, E.228, N.305, W.308, R.314, Y.315 Ligands: LA6.2, MG.3, MG.4, MG.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.77, A:F.179, A:L.183, A:N.220, A:W.308 Hydrogen bonds: A:N.220, A:S.224 Water bridges: A:K.227, A:K.227, A:R.314 Salt bridges: A:R.174, A:K.227, A:R.314 0FV.8: 21 residues within 4Å: Chain B: F.74, F.77, F.78, D.81, R.174, F.179, M.180, L.183, I.216, N.217, N.220, S.224, K.227, E.228, N.305, R.314, Y.315 Ligands: LA6.9, MG.10, MG.11, MG.12 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.74, B:F.77, B:F.78, B:L.183, B:I.216, B:N.220 Hydrogen bonds: B:N.220, B:N.220, B:S.224, B:Y.315, B:Y.315 Water bridges: B:R.174, B:K.227, B:K.227, B:R.314 Salt bridges: B:R.174, B:K.227, B:R.314

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

LA6.2: 21 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, C.309, R.314, Y.315 Ligands: 0FV.1, MG.3, MG.4, MG.5 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.74, A:F.78, A:F.179, A:I.216, A:N.220 Hydrogen bonds: A:N.220, A:S.224 Water bridges: A:R.174, A:K.227, A:K.227, A:K.227 Salt bridges: A:R.174, A:K.227, A:R.314 LA6.9: 22 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: 0FV.8, MG.10, MG.11, MG.12 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:F.74, B:F.77, B:F.78, B:I.216, B:N.220, B:W.308 Hydrogen bonds: B:N.220, B:S.224, B:Y.315, B:Y.315 Water bridges: B:R.174, B:R.174, B:K.227, B:K.227, B:K.227, B:R.314 Salt bridges: B:R.174, B:K.227, B:R.314

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: N.220, S.224, E.228 Ligands: 0FV.1, LA6.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.224, A:E.228, H2O.2 MG.4: 4 residues within 4Å: Chain A: D.81 Ligands: 0FV.1, LA6.2, MG.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.81, H2O.2, H2O.3, H2O.3 MG.5: 4 residues within 4Å: Chain A: D.81 Ligands: 0FV.1, LA6.2, MG.4 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.81, H2O.1, H2O.1, H2O.3, H2O.3 MG.10: 5 residues within 4Å: Chain B: N.220, S.224, E.228 Ligands: 0FV.8, LA6.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.224, B:E.228, H2O.17 MG.11: 5 residues within 4Å: Chain B: D.81, K.227 Ligands: 0FV.8, LA6.9, MG.12 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.81, H2O.17, H2O.17, H2O.20 MG.12: 4 residues within 4Å: Chain B: D.81 Ligands: 0FV.8, LA6.9, MG.11 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)

9D2.6: 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:R.257 Water bridges: A:E.6, A:R.257 9D2.13: 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:R.257 Water bridges: B:E.6, B:R.257

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

NDS.7: 8 residues within 4Å: Chain A: F.19, R.22, R.26, Q.63, G.64 Chain B: P.18, F.19, R.22 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.19 Hydrogen bonds: A:G.64 Salt bridges: A:R.22, A:R.26 NDS.14: 8 residues within 4Å: Chain A: P.18, F.19, R.22 Chain B: F.19, R.22, R.26, Q.63, G.64 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.64 Salt bridges: B:R.22, B:R.26 Hydrophobic interactions: A:F.19

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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