SMTL ID : 7d78.1

The structure of thioesterase DcsB

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

1 x NA: SODIUM ION(Non-functional Binders)

NA.1: 5 residues within 4Å: Chain A: E.166, K.167, R.168, D.169, K.170 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.166, A:D.169, A:K.170 Water bridges: A:R.168

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: G.59, F.60, C.62, S.134, F.194, M.219, M.269, H.296, L.297 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.60, A:S.134, A:S.134, A:F.135 Water bridges: A:G.59 GOL.5: 5 residues within 4Å: Chain B: S.125, S.126, R.148, R.149, K.151 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.125, B:R.148, B:K.151, B:K.151 Water bridges: B:S.126 GOL.6: 7 residues within 4Å: Chain B: G.59, F.60, C.62, S.134, F.194, M.269, L.297 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.60, B:S.134, B:F.135

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: G.49, S.122 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: K.50, V.123, D.124, S.125 Ligand excluded by PLIP

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 6 residues within 4Å: Chain A: A.144, A.145, D.147, R.148, T.257 Chain B: D.169 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.144, B:D.169, B:D.169 Water bridges: A:K.256, A:K.256, A:T.257

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, D.W. et al., A Polyketide Cyclase That Forms Medium-Ring Lactones. J.Am.Chem.Soc. (2021)

Release Date

2021-01-27

Peptides

DltD domain-containing protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

DltD domain-containing protein

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