SMTL ID : 7d79.1 (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

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

CL.1: 2 residues within 4Å: Chain A: N.229, R.231 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain B: K.50, V.123, D.124, S.125 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Ligands: EDO.9 Ligand excluded by PLIP

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

EDO.2: 7 residues within 4Å: Chain A: K.50, S.118, S.119, L.120, V.123, D.124, S.125 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.50, A:L.120, A:S.125, A:S.125 EDO.3: 5 residues within 4Å: Chain A: S.125, S.126, R.148, R.149, K.151 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.151 EDO.4: 7 residues within 4Å: Chain A: A.144, A.145, D.147, R.148, T.257 Chain B: D.169, F.172 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.169, B:D.169, A:A.144 Water bridges: A:T.257 EDO.9: 3 residues within 4Å: Chain B: A.321, G.322 Ligands: CL.7 4 PLIP interactions: 4 interactions with chain B Water bridges: B:D.124, B:K.127, B:K.127, B:G.322 EDO.10: 3 residues within 4Å: Chain B: G.185, N.186, E.187 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.187

1 x GY0: methyl 3-[(E,3R,9R)-3,9-bis(oxidanyl)dec-4-enoyl]sulfanylpropanoate(Non-covalent)

GY0.5: 15 residues within 4Å: Chain A: P.58, G.59, F.60, C.62, M.66, L.67, M.133, S.134, F.135, F.218, M.219, M.269, H.296, L.297, S.301 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.60, A:F.218, A:L.297 Hydrogen bonds: A:G.59, A:F.60, A:S.134, A:F.135

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 6 residues within 4Å: Chain B: G.59, F.60, C.62, S.134, F.194, M.219 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.60, B:S.134, B:S.134, B:F.135

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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