SMTL ID : 6oh7.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-dimer

Ligands

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

PEG.1: 5 residues within 4Å: Chain A: L.116, A.117, H.149, A.152, R.156 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.149, A:R.156, A:R.156 PEG.2: 7 residues within 4Å: Chain A: L.181, A.182, P.185, K.191, T.220, A.223, N.224 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.191, A:K.191 Water bridges: A:A.182, A:N.224 PEG.3: 7 residues within 4Å: Chain A: A.18, T.19, F.20, P.21, R.280, E.302, R.306 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.18, A:P.21, A:R.306 PEG.8: 5 residues within 4Å: Chain B: L.116, A.117, H.149, A.152, R.156 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.157, B:H.149, B:R.156, B:R.156 PEG.9: 7 residues within 4Å: Chain B: L.181, A.182, P.185, K.191, T.220, A.223, N.224 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.191, B:K.191 Water bridges: B:A.182, B:N.224 PEG.10: 7 residues within 4Å: Chain B: A.18, T.19, F.20, P.21, R.280, E.302, R.306 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.18, B:P.21, B:R.306

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: D.90, E.95, E.165 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.3 MG.11: 3 residues within 4Å: Chain B: D.90, E.95, E.165 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.90, B:E.95, H2O.6, H2O.7, H2O.9

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: W.40, E.43, H.44, V.131, D.134, R.138 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.40, A:D.134, A:R.138 GOL.6: 6 residues within 4Å: Chain A: V.115, N.120, P.121, P.122, P.129, H.133 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.121, A:H.133 Water bridges: A:N.120 GOL.7: 3 residues within 4Å: Chain A: A.54, V.55, N.58 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.58 GOL.12: 6 residues within 4Å: Chain B: W.40, E.43, H.44, V.131, D.134, R.138 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.40, B:R.138 GOL.13: 6 residues within 4Å: Chain B: V.115, N.120, P.121, P.122, P.129, H.133 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.121 Water bridges: B:N.120 GOL.14: 3 residues within 4Å: Chain B: A.54, V.55, N.58 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.58

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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