Determinants of lipid substrate and membrane binding for the tetraacyldisaccharide-1-phosphate 4 -kinase lpxk

Structure

x-ray diffraction · 3 distinct chains · 30% helix, 26% strand (DSSP).

Ligands and binding sites

• LP4 · 2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose · ligand · 2 copies · chains A, C
• LP5 · (R)-((2R,3S,4R,5R,6R)-3-hydroxy-2-(hydroxymethyl)-5-((R)-3-hydroxytetradecanamido)-6-(phosphonooxy) tetrahydro-2H-pyran-4-yl) 3-hydroxytetradecanoate · ligand · 2 copies · chains A, C
• EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A

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

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–C · 429 Ų buried · 6 hydrogen bonds · protein-protein
• A–D · 362 Ų buried · 6 hydrogen bonds · protein-protein
• B–C · 198 Ų buried · 1 hydrogen bond · protein-protein
• B–D · 109 Ų buried · 1 hydrogen bond · protein-protein
• A–B · 92 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 4LKV · Determinants of lipid substrate and membrane binding for the… · the same entry in another collection · chain A against A, TM-score 1.00
• O67572 · AlphaFold monomer V2.0 prediction for tetraacyldisaccharide 4'-kinase (O67572) · a predicted model of the same protein · chain B against A, TM-score 0.95

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 O67572
• Elsewhere: RCSB PDB 4LKV · PDBe 4LKV · UniProt O67572