SMTL ID : 7zrn.1

Crystal structure of 10-epi-cubebol synthase from Sorangium cellulosum (ScCubS) in complex with Pyrophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-dimer

Ligands

2 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.1: 14 residues within 4Å: Chain A: D.107, E.111, R.202, T.205, S.206, N.248, S.252, K.255, E.256, R.336, Y.337 Ligands: MG.2, MG.3, MG.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:T.205, A:N.248, A:Y.337 Water bridges: A:E.111, A:R.202, A:R.202, A:T.207, A:K.255, A:K.255, A:K.255 Salt bridges: A:R.202, A:K.255, A:R.336 PPV.5: 15 residues within 4Å: Chain B: F.104, D.107, E.111, R.202, T.205, S.206, N.248, S.252, K.255, E.256, R.336, Y.337 Ligands: MG.7, MG.8, MG.9 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:D.107, B:S.252, B:E.256 Water bridges: B:D.107, B:R.202, B:N.248, B:K.255, B:K.255, B:K.255, B:R.336, B:R.336 Salt bridges: B:R.202, B:K.255, B:R.336

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: R.202, N.248, D.249, S.252, E.256 Ligands: PPV.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.252, A:E.256, H2O.1 MG.3: 5 residues within 4Å: Chain A: D.107, E.111, K.255 Ligands: PPV.1, MG.4 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.111, H2O.1, H2O.5 MG.4: 4 residues within 4Å: Chain A: D.107, E.111 Ligands: PPV.1, MG.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.107, A:E.111, H2O.1, H2O.4, H2O.7 MG.7: 6 residues within 4Å: Chain B: R.202, N.248, D.249, S.252, E.256 Ligands: PPV.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.252, B:E.256, H2O.9 MG.8: 4 residues within 4Å: Chain B: D.107, E.111 Ligands: PPV.5, MG.9 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.107, B:E.111, H2O.10, H2O.12, H2O.12 MG.9: 6 residues within 4Å: Chain B: D.107, E.111, K.255, R.336 Ligands: PPV.5, MG.8 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.111, H2O.9, H2O.11, H2O.14

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 8 residues within 4Å: Chain B: C.110, E.111, S.114, V.123, C.180, E.183, A.184, R.187 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.111 Hydrogen bonds: B:A.184 Salt bridges: B:R.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Whitehead, J.N. et al., How a 10- epi-Cubebol Synthase Avoids Premature Reaction Quenching to Form a Tricyclic Product at High Purity. Acs Catalysis (2022)

Release Date

2022-11-02

Peptides

10-epi-cubebol synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

10-epi-cubebol synthase