MolNFT v1 · #105483 · protein

Crystal structure of human TLR8 in complex with hybrid-2

4R6A · Toll-like receptor 8: “Crystal structure of human TLR8 in complex with hybrid-2”. X-ray diffraction, 4 ligands (HB2, NAG, BMA), 16 pockets (best druggability 0.77). MolNFT v1 #105483 on GenesisL1: 3D structure, binding sites and…

PDB: 4R6A
Type: protein
Length: 1,486 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Toll-like receptor 8
UniProt: Q9NR97
Ligands: HB2, NAG, BMA, MAN
Pockets: 16 · best druggability 0.77

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	746	12% helix, 15% strand	Q9NR97
B	Toll-like receptor 8	protein	740	12% helix, 15% strand	Q9NR97

Ligands and binding sites

HB2 · 1-(4-amino-2-butyl-1H-imidazo[4,5-c]quinolin-1-yl)-2-methylpropan-2-ol · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 6 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

16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	729	0.77	0.81	79	NAG
2	694	0.76	0.81	78	NAG
3	110	0.60	0.86	26	empty
4	279	0.59	0.79	24	empty
5	162	0.58	0.82	20	HB2

Interfaces

1 interface between chains.

A–B · 2201 Å² buried · 27 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 glycan, 12 disulfide (N-glycosylation, disulfide).

Compared structures

4R6A · Crystal structure of human TLR8 in complex with Hybrid-2 · 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 4R6A · PDBe 4R6A · UniProt Q9NR97

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