Cryo-EM structure of the multiple peptide resistance factor (mprf) loaded with two lysyl-phosphatidylglycerol molecules

Structure

electron microscopy · 1 distinct chain · 64% helix, 11% strand (DSSP).

Ligands and binding sites

• EV9 · [(2~{R})-3-[[(2~{S})-3-[(2~{S})-2,6-bis(azanyl) hexanoyl]oxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxy-2-hexadecanoyloxy-propyl] hexadecanoate · ligand · 4 copies · chains A, B
• LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole · ligand · 2 copies · chains A, B
• PGT · (1S)-2-{[{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · 2 copies · chains A, B
• J4U · (2~{R},3~{S},4~{S},5~{S},6~{S})-2-(hydroxymethyl)-6-[(2~{R},3~{S},4~{R},5~{R},6~{R})-2-(hydroxymethyl)-6-[2-[[(2~{R},3~{S},4~{R},5~{R},6~{S})-6-(hydroxymethyl)-5-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxymethyl]-4-[(1~{R},2~{R}, 4~{S},5'~{R},6~{R},7~{R},8~{R},9~{S},12~{S},13~{R}, 16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxy-butoxy]-4,5-bis(oxidanyl)oxa · ligand · 2 copies · chains A, B
• LMT · Dodecyl-beta-D-maltoside · additive · 2 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 649 Ų buried · 11 hydrogen bonds · protein-protein

Compared structures

• 7DUW · Cryo-EM structure of the multiple peptide resistance factor (MprF) loaded with two… · the same entry in another collection · chain A against A, TM-score 1.00

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 A0A6P1C618
• Elsewhere: RCSB PDB 7DUW · PDBe 7DUW · UniProt A0A6P1C618