Research workbench

Crystal structure of human TLR8 in complex with ds-802

Analyse Crystal structure of human TLR8 in complex with ds-802 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4QBZ
Type: protein
Length: 1,505 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Toll-like receptor 8
UniProt: Q9NR97
Ligands: D80, NAG, BMA, MAN
Pockets: 15 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 12% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Toll-like receptor 8	protein	754	12% helix, 15% strand	Q9NR97
B	Toll-like receptor 8	protein	751	13% helix, 15% strand	Q9NR97

Ligands and binding sites

D80 · 2-butyl[1,3]oxazolo[4,5-c]quinolin-4-amine · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 5 copies · chains A, B
MAN · alpha-D-mannopyranose · sugar · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1017	0.79	0.80	97	NAG
2	860	0.76	0.79	83	NAG
3	354	0.64	0.80	40	empty
4	121	0.60	0.85	26	empty
5	184	0.59	0.81	23	D80

Interfaces

1 interface between chains.

A–B · 2388 Å² buried · 31 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 17 glycan, 12 disulfide (N-glycosylation, disulfide).

Compared structures

4QBZ · Crystal structure of human TLR8 in complex with DS-802 · 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 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 4QBZ · PDBe 4QBZ · UniProt Q9NR97

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.