SMTL ID : 7d79.2 (1 other biounit)

The structure of DcsB complex with its substrate analogue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 6 residues within 4Å: Chain A: G.59, F.60, N.61, I.90, I.101, Q.106 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: G.59, F.60, C.62, S.134, F.135, F.194, A.205, M.269 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.60, A:S.134, A:S.134, A:F.135

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

NA.3: 5 residues within 4Å: Chain A: D.178, S.181, Q.182, E.187, F.189 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.178, A:F.189

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

EDO.4: 4 residues within 4Å: Chain A: L.183 Chain B: T.115, H.116, S.119 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.116, B:S.119, B:S.119 Water bridges: B:K.33, B:H.116

1 x GYF: methyl 3-sulfanylpropanoate(Non-covalent)

GYF.5: 10 residues within 4Å: Chain B: G.59, F.60, C.62, S.134, F.135, F.194, A.205, M.269, H.296, L.297 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.297 Hydrogen bonds: B:F.60, B:S.134, B:F.135 Salt bridges: B:H.296

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
C

B
B

DltD domain-containing protein

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