Nucleotide-free cryo-EM structure of E.COLI LPTB2FG transporter

Structure

electron microscopy · 3 distinct chains · 47% helix, 10% strand (DSSP).

Ligands and binding sites

• 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}) · ligand · chains F, G

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• F–G · 1536 Ų buried · 4 hydrogen bonds · protein-protein
• G–A · 957 Ų buried · 3 hydrogen bonds · protein-protein
• F–B · 901 Ų buried · 7 hydrogen bonds · protein-protein
• A–B · 607 Ų buried · 7 hydrogen bonds · protein-protein

Compared structures

• 6MHU · Nucleotide-free Cryo-EM Structure of E.coli LptB2FG Transporter · the same entry in another collection · chain F against F, TM-score 1.00
• P0A9V1 · AlphaFold monomer V2.0 prediction for lipopolysaccharide export system ATP-binding… · a predicted model of the same protein · chain A against A, TM-score 0.94
• P0ADC6 · AlphaFold monomer V2.0 prediction for lipopolysaccharide export system permease protein… · a predicted model of the same protein · chain G against A, TM-score 0.90
• P0AF98 · AlphaFold monomer V2.0 prediction for lipopolysaccharide export system permease protein… · a predicted model of the same protein · chain F against A, TM-score 0.82

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P0AF98
• Every structure of UniProt P0ADC6
• Every structure of UniProt P0A9V1
• Elsewhere: RCSB PDB 6MHU · PDBe 6MHU · UniProt P0AF98 · UniProt P0ADC6 · UniProt P0A9V1