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Crystal structure of human TLR8 in complex with CL097

Analyse Crystal structure of human TLR8 in complex with CL097 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3W3J
Type: protein
Length: 1,493 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Toll-like receptor 8
UniProt: Q9NR97
Ligands: C09, NAG, BMA, MAN, SO4
Pockets: 13 · best druggability 0.76

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	747	13% helix, 15% strand	Q9NR97
B	Toll-like receptor 8	protein	746	12% helix, 15% strand	Q9NR97

Ligands and binding sites

C09 · 2-(ethoxymethyl)-1H-imidazo[4,5-c]quinolin-4-amine · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B
MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 16 copies · chains A, B
GOL · Glycerol · additive · chains B

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

Pockets

13 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	816	0.76	0.80	83	NAG, SO4, GOL
2	817	0.75	0.79	87	NAG, SO4
3	129	0.57	0.83	24	empty
4	293	0.57	0.77	28	empty
5	157	0.56	0.81	20	C09, SO4

Interfaces

1 interface between chains.

A–B · 2389 Å² buried · 34 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 glycan, 12 disulfide (N-glycosylation, disulfide).

Compared structures

3W3J · Crystal structure of human TLR8 in complex with CL097 · 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 3W3J · PDBe 3W3J · UniProt Q9NR97

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