Crystal structure of human TLR8 in complex with resiquimod (R848) crystal form 1

Structure

x-ray diffraction · 1 distinct chain · 11% helix, 16% strand (DSSP).

Ligands and binding sites

• RX8 · 1-[4-amino-2-(ethoxymethyl)-1H-imidazo[4,5-c]quinolin-1-yl]-2-methylpropan-2-ol · ligand · 4 copies · chains B, C, A, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 39 copies · chains A, B, C, D
• MAN · alpha-D-mannopyranose · sugar · 16 copies · chains A, B, C, D
• BMA · beta-D-mannopyranose · sugar · 12 copies · chains A, B, C, D
• SO4 · Sulfate ion · ion · 8 copies · chains A, D, B, C

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• B–C · 2083 Ų buried · 28 hydrogen bonds · protein-protein
• A–D · 2039 Ų buried · 29 hydrogen bonds · protein-protein
• A–B · 516 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 27 glycan, 24 disulfide (N-glycosylation, disulfide).

Compared structures

• 3W3L · Crystal structure of human TLR8 in complex with Resiquimod (R848) crystal form 1 · the same entry in another collection · chain A against A, TM-score 1.00
• Q9NR97 · AlphaFold monomer V2.0 prediction for toll-like receptor 8 (Q9NR97) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q9NR97
• Elsewhere: RCSB PDB 3W3L · PDBe 3W3L · UniProt Q9NR97