SMTL ID : 6oh6.1

Crystal structure of (E)-biformene synthase LrdC from Streptomyces sp. strain K155 in complex with Mg and PPi

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

2 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.1: 13 residues within 4Å: Chain A: D.90, E.95, R.184, T.187, N.230, S.234, R.237, E.238, R.316, Y.317 Ligands: MG.2, MG.3, MG.4 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:E.95, A:N.230, A:S.234, A:Y.317, A:Y.317 Water bridges: A:R.184, A:R.184, A:R.237, A:R.237, A:R.237, A:R.237, A:R.316, A:R.316, A:R.316, A:R.316 Salt bridges: A:R.184, A:R.237, A:R.316 PPV.9: 13 residues within 4Å: Chain B: D.90, E.95, R.184, T.187, N.230, S.234, R.237, E.238, R.316, Y.317 Ligands: MG.10, MG.11, MG.12 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:E.95, B:N.230, B:S.234, B:Y.317 Water bridges: B:R.184, B:R.184, B:R.237, B:R.237, B:R.237, B:R.237, B:R.316, B:R.316, B:R.316, B:R.316 Salt bridges: B:R.184, B:R.237, B:R.316

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: R.184, N.230, S.234, E.238 Ligands: PPV.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.234, A:E.238 MG.3: 6 residues within 4Å: Chain A: D.90, D.91, E.95, R.316 Ligands: PPV.1, MG.4 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.95, H2O.2, H2O.2 MG.4: 5 residues within 4Å: Chain A: D.90, E.95, E.165 Ligands: PPV.1, MG.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.90, A:E.95, H2O.1, H2O.1, H2O.1 MG.10: 5 residues within 4Å: Chain B: R.184, N.230, S.234, E.238 Ligands: PPV.9 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.234, B:E.238 MG.11: 6 residues within 4Å: Chain B: D.90, D.91, E.95, R.316 Ligands: PPV.9, MG.12 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.95, H2O.7, H2O.7 MG.12: 5 residues within 4Å: Chain B: D.90, E.95, E.165 Ligands: PPV.9, MG.11 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.90, B:E.95, H2O.6, H2O.6, H2O.7

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: V.115, H.133, L.136, A.137, R.140, Y.148 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.133, A:L.136, A:R.140, A:Y.148 GOL.13: 6 residues within 4Å: Chain B: V.115, H.133, L.136, A.137, R.140, Y.148 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.133, B:L.136, B:R.140

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 5 residues within 4Å: Chain A: L.116, A.117, H.149, A.152, R.156 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:D.157 Hydrogen bonds: A:H.149, A:R.156, A:R.156 PEG.7: 6 residues within 4Å: Chain A: L.181, A.182, P.185, K.191, A.223, N.224 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.191 Water bridges: A:K.191, A:N.224 PEG.8: 7 residues within 4Å: Chain A: A.18, T.19, F.20, P.21, R.280, E.302, R.306 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.18, A:P.21, A:R.280, A:R.306 PEG.14: 5 residues within 4Å: Chain B: L.116, A.117, H.149, A.152, R.156 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Water bridges: A:D.157, A:D.157 Hydrogen bonds: B:H.149, B:R.156, B:R.156 PEG.15: 6 residues within 4Å: Chain B: L.181, A.182, P.185, K.191, A.223, N.224 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.191 Water bridges: B:K.191, B:N.224 PEG.16: 7 residues within 4Å: Chain B: A.18, T.19, F.20, P.21, R.280, E.302, R.306 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.18, B:P.21, B:R.280, B:R.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Centeno-Leija, S. et al., The structure of (E)-biformene synthase provides insights into the biosynthesis of bacterial bicyclic labdane-related diterpenoids. J.Struct.Biol. (2019)

Release Date

2019-04-17

Peptides

Labdane-related diterpene synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Labdane-related diterpene synthase

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