Crystal structure of mouse TLR4/MD-2/LIPID iva complex

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 28% 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, B, D
• 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, B, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B

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

Pockets

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

Interfaces

5 interfaces between chains.

• B–D · 1193 Ų buried · 21 hydrogen bonds · protein-protein
• A–C · 1174 Ų buried · 22 hydrogen bonds · protein-protein
• A–B · 676 Ų buried · 7 hydrogen bonds · protein-protein
• A–D · 482 Ų buried · 3 hydrogen bonds · protein-protein
• C–B · 453 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

• 3VQ1 · Crystal structure of mouse TLR4/MD-2/lipid IVa complex · the same entry in another collection · chain A against A, TM-score 1.00
• Q9QUK6 · AlphaFold monomer V2.0 prediction for toll-like receptor 4 (Q9QUK6) · a predicted model of the same protein · chain A against A, TM-score 0.99
• Q9JHF9 · AlphaFold monomer V2.0 prediction for lymphocyte antigen 96 (Q9JHF9) · a predicted model of the same protein · chain C against A, TM-score 0.94

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 Q9QUK6
• Every structure of UniProt Q9JHF9
• Elsewhere: RCSB PDB 3VQ1 · PDBe 3VQ1 · UniProt Q9QUK6 · UniProt Q9JHF9