SMTL ID : 8h6u.1

Class I sesquiterpene synthase BCBOT2 (complex)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.78 Å

Oligo State

homo-tetramer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 8 residues within 4Å: Chain A: D.108, D.109, D.112, E.113, K.259, R.340 Ligands: MG.2, POP.4 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.112, H2O.1, H2O.4 MG.2: 4 residues within 4Å: Chain A: D.108, D.112 Ligands: MG.1, POP.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.108, A:D.112, H2O.1, H2O.2 MG.3: 5 residues within 4Å: Chain A: R.206, N.252, S.256, D.260 Ligands: POP.4 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.256, H2O.1, H2O.2 MG.6: 5 residues within 4Å: Chain B: D.108, D.112, Q.185, T.209 Ligands: POP.9 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.108, B:D.112, H2O.6, H2O.7, H2O.8 MG.7: 4 residues within 4Å: Chain B: N.252, S.256, D.260 Ligands: POP.9 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.256, H2O.7 MG.8: 6 residues within 4Å: Chain B: D.109, D.112, E.113, K.259, R.340 Ligands: POP.9 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.112, H2O.7, H2O.7 MG.11: 4 residues within 4Å: Chain C: N.252, S.256, D.260 Ligands: POP.14 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.256, H2O.10 MG.12: 6 residues within 4Å: Chain C: D.108, D.112, R.206, T.209 Ligands: POP.14, BTM.15 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.108, C:D.112, H2O.11, H2O.11 MG.13: 6 residues within 4Å: Chain C: D.109, D.112, E.113, K.259, R.340 Ligands: POP.14 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.112, H2O.10 MG.16: 4 residues within 4Å: Chain D: N.252, S.256, D.260 Ligands: POP.19 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.256, H2O.15 MG.17: 6 residues within 4Å: Chain D: D.108, D.109, D.112, R.340 Ligands: MG.18, POP.19 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.112, H2O.14, H2O.15 MG.18: 5 residues within 4Å: Chain D: D.108, D.112, R.206 Ligands: MG.17, POP.19 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.108, D:D.112, H2O.14, H2O.15

4 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.4: 14 residues within 4Å: Chain A: D.108, D.112, R.206, T.209, I.210, N.252, S.256, K.259, R.340, Y.341 Ligands: MG.1, MG.2, MG.3, BTM.5 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:T.209, A:N.252, A:S.256, A:Y.341 Water bridges: A:R.206, A:K.259, A:K.259, A:K.259, A:R.340 Salt bridges: A:R.206, A:K.259, A:R.340 POP.9: 14 residues within 4Å: Chain B: D.108, D.112, R.206, T.209, I.210, N.252, S.256, K.259, R.340, Y.341 Ligands: MG.6, MG.7, MG.8, BTM.10 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:D.108, B:S.256, B:Y.341 Water bridges: B:D.112, B:D.112, B:R.206, B:D.253, B:D.253, B:K.259, B:K.259, B:R.340, B:R.340 Salt bridges: B:R.206, B:K.259, B:R.340 POP.14: 14 residues within 4Å: Chain C: D.108, D.112, R.206, T.209, I.210, N.252, S.256, K.259, R.340, Y.341 Ligands: MG.11, MG.12, MG.13, BTM.15 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.252, C:S.256 Water bridges: C:D.108, C:R.340 Salt bridges: C:R.206, C:K.259, C:R.340 POP.19: 13 residues within 4Å: Chain D: D.108, D.112, R.206, I.210, N.252, S.256, K.259, R.340, Y.341 Ligands: MG.16, MG.17, MG.18, BTM.20 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:D.108, D:N.252, D:S.256, D:Y.341 Water bridges: D:D.112, D:D.112, D:R.206, D:D.260, D:R.340 Salt bridges: D:R.206, D:K.259, D:R.340

4 x BTM: N-benzyl-N,N-diethylethanaminium(Non-covalent)

BTM.5: 14 residues within 4Å: Chain A: W.85, V.104, F.105, D.108, T.209, I.210, G.211, V.212, A.215, V.248, N.252, N.331, Y.341 Ligands: POP.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.85, A:W.85, A:F.105, A:D.108, A:V.212, A:A.215, A:V.248 pi-Cation interactions: A:F.105 BTM.10: 14 residues within 4Å: Chain B: W.85, V.104, F.105, D.108, T.209, I.210, G.211, V.212, A.215, V.248, N.252, N.331, Y.341 Ligands: POP.9 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.85, B:W.85, B:F.105, B:V.212, B:A.215, B:V.248 pi-Cation interactions: B:F.105 BTM.15: 13 residues within 4Å: Chain C: W.85, V.104, F.105, D.108, T.209, I.210, G.211, V.212, A.215, V.248, N.252 Ligands: MG.12, POP.14 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:W.85, C:W.85, C:V.104, C:F.105, C:D.108, C:I.210, C:V.212, C:A.215, C:V.248 Salt bridges: C:D.108 pi-Cation interactions: C:F.105 BTM.20: 12 residues within 4Å: Chain D: W.85, V.104, F.105, T.209, I.210, G.211, V.212, A.215, N.252, N.331, Y.341 Ligands: POP.19 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:W.85, D:W.85, D:V.104, D:F.105, D:V.212, D:A.215 pi-Cation interactions: D:F.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lou, T. et al., Structural Insights into Three Sesquiterpene Synthases for the Biosynthesis of Tricyclic Sesquiterpenes and Chemical Space Expansion by Structure-Based Mutagenesis. J.Am.Chem.Soc. (2023)

Release Date

2023-08-23

Peptides

Presilphiperfolan-8-beta-ol synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Presilphiperfolan-8-beta-ol synthase

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