SMTL ID : 8ufh.1

Acinetobacter baylyi LptB2FG bound to Acinetobacter baylyi lipopolysaccharide and a macrocyclic peptide

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-mer

Ligands

1 x WJW: (2~{R},4~{R},5~{R},6~{R})-2-[(2~{R},4~{R},5~{R},6~{R})-5-[(2~{S},4~{R},5~{R},6~{R})-4-[(2~{R},3~{R},4~{R},5~{S},6~{S})-3-acetamido-6-carboxy-4,5-bis(oxidanyl)oxan-2-yl]oxy-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-carboxy-5-oxidanyl-oxan-2-yl]oxy-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-4-[(3~{S})-3-dodecanoyloxydodecanoyl]oxy-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-heptanoyloxynonanoyl]amino]-3-oxidanyl-4-[(3~{R})-3-oxidanyloctanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-5-[[(3~{S})-3-[(3~{R})-3-oxidanyldodecanoyl]oxydecanoyl]amino]-3-phosphonooxy-oxan-2-yl]methoxy]oxan-4-yl]oxy-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-4,5-bis(oxidanyl)oxane-2-carboxylic acid(Non-covalent)

WJW.1: 32 residues within 4Å: Chain C: L.22, M.26, G.29, R.30, K.33, V.37, R.42, R.55, E.58, F.59, T.61, L.62, L.66, Q.113, W.271, G.275, T.278, I.306, I.313, I.317 Chain D: L.26, Q.30, F.33, T.34, N.41, R.61, I.66, K.135, L.313, Y.316, Y.317 Ligands: Y75.2 32 PLIP interactions: 10 interactions with chain D, 22 interactions with chain C Hydrophobic interactions: D:L.26, D:Q.30, D:F.33, D:F.33, D:F.33, D:I.66, D:L.313, C:L.22, C:E.58, C:F.59, C:L.62, C:L.62, C:L.66, C:W.271, C:T.278, C:I.306, C:I.313, C:I.317 Hydrogen bonds: D:N.41, D:R.61, D:Y.317, C:K.33, C:Y.34 Salt bridges: C:R.30, C:R.30, C:R.30, C:K.33, C:K.33, C:K.33, C:R.42, C:R.55, C:R.55

1 x Y75: (7S,10S,13S,17P)-10-(4-aminobutyl)-7-(3-aminopropyl)-17-(6-aminopyridin-3-yl)-20-chloro-13-[(1H-indol-3-yl)methyl]-12-methyl-6,7,9,10,12,13,15,16-octahydropyrido[2,3-b][1,5,8,11,14]benzothiatetraazacycloheptadecine-8,11,14(5H)-trione(Non-covalent)

Y75.2: 13 residues within 4Å: Chain C: E.58, L.125, E.249, W.271, V.314, I.317, A.318, R.320, T.321 Chain D: L.36, L.39, S.40 Ligands: WJW.1 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:W.271, C:V.314, C:I.317, C:I.317, C:T.321 Hydrogen bonds: C:E.58, C:E.249, C:T.321, D:S.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pahil, K.S. et al., A new antibiotic traps lipopolysaccharide in its intermembrane transporter. Nature (2024)

Release Date

2024-01-03

Peptides

Lipopolysaccharide export system ATP-binding protein LptB: AB
Lipopolysaccharide export system permease protein LptF: C
LPS export ABC transporter permease LptG: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
F

D
G

Membrane

We predict this structure to be a membrane protein.
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Lipopolysaccharide export system ATP-binding protein LptB

Lipopolysaccharide export system permease protein LptF

LPS export ABC transporter permease LptG

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