SMTL ID : 8frl.1

Acinetobacter baylyi LptB2FG bound to lipopolysaccharide and a macrocyclic peptide

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-mer

Ligands

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)

Y75.1: 13 residues within 4Å: Chain C: E.58, E.249, W.271, V.314, I.317, A.318, R.320, T.321 Chain D: L.36, L.39, S.40 Ligands: JSG.2, LMT.3 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:V.314, C:I.317, C:I.317, D:L.36 Hydrogen bonds: C:E.58, C:E.58, C:T.321 pi-Stacking: C:W.271

1 x JSG: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-5-[(2~{S},3~{S},4~{R},5~{R},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},3~{S},4~{R},5~{S},6~{R})-6-[(1~{S})-2-[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-1-oxidanyl-ethyl]-3,4-bis(oxidanyl)-5-phosphonooxy-oxan-2-yl]oxy-3-oxidanyl-5-phosphonooxy-oxan-2-yl]oxy-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanyltetradecanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid(Non-covalent)

JSG.2: 31 residues within 4Å: Chain C: L.22, I.25, M.26, R.30, K.33, R.55, E.58, F.59, T.61, L.62, L.66, M.117, W.271, G.275, T.278, A.310, I.313, L.316, I.317 Chain D: Q.30, F.33, T.34, E.65, I.66, L.309, F.310, L.313, Y.316, Y.317 Ligands: Y75.1, LMT.3 30 PLIP interactions: 11 interactions with chain D, 19 interactions with chain C Hydrophobic interactions: D:Q.30, D:F.33, D:F.33, D:I.66, D:L.309, D:L.309, D:F.310, D:L.313, D:Y.316, C:L.22, C:F.59, C:L.62, C:L.62, C:L.62, C:W.271, C:W.271, C:A.310, C:I.313, C:L.316 Hydrogen bonds: D:Q.30, D:T.34, C:R.42 Salt bridges: C:R.30, C:R.30, C:R.30, C:K.33, C:K.33, C:K.33, C:R.55, C:R.55

1 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.3: 11 residues within 4Å: Chain C: A.310, V.314 Chain D: F.33, T.34, G.37, E.38, N.41, Y.54, K.135 Ligands: Y75.1, JSG.2 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.33, D:F.33, C:A.310, C:V.314 Hydrogen bonds: D:E.38, D:E.38, D:N.41, D:Y.54, D:K.135

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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