Crystal structure of human TLR8 in complex with ORN06

Structure

x-ray diffraction · 4 distinct chains · 12% helix, 15% strand (DSSP).

Ligands and binding sites

• URI · Uridine · ligand · 4 copies · chains A, B, C, D
• UCG · 3'-O-[(R)-{[(2R,3aR,4R,6R,6aR)-6-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2-hydroxy-2-oxidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]methoxy}(hydroxy)phosphoryl]uridine 5'-(dihydrogen phosphate) · ligand · 4 copies · chains A, B, C, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 42 copies · chains A, B, C, D
• BMA · beta-D-mannopyranose · sugar · 9 copies · chains A, B, C, D
• MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A

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.

• A–B · 2311 Ų buried · 37 hydrogen bonds · protein-protein
• C–D · 2305 Ų buried · 37 hydrogen bonds · protein-protein
• A–C · 255 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 30 glycan, 24 disulfide (N-glycosylation, disulfide).

Compared structures

• 4R07 · Crystal structure of human TLR8 in complex with ORN06 · the same entry in another collection · chain D against D, TM-score 1.00
• Q9NR97 · AlphaFold monomer V2.0 prediction for toll-like receptor 8 (Q9NR97) · a predicted model of the same protein · chain B 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 4R07 · PDBe 4R07 · UniProt Q9NR97