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Crystal structure of human TLR8 in complex with CL075

Analyse Crystal structure of human TLR8 in complex with CL075 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3W3K
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: L07, NAG, MAN, BMA
Pockets: 12 · best druggability 0.75

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	747	12% helix, 15% strand	Q9NR97

Ligands and binding sites

L07 · 2-propyl[1,3]thiazolo[4,5-c]quinolin-4-amine · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, B
MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 5 copies · chains A, B

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

Pockets

12 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	779	0.75	0.79	85	NAG
2	257	0.65	0.82	32	empty
3	353	0.63	0.78	46	NAG
4	190	0.59	0.81	27	NAG
5	125	0.59	0.85	26	empty

Interfaces

1 interface between chains.

A–B · 2060 Å² buried · 36 hydrogen bonds · protein-protein

Modifications

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

Compared structures

3W3K · Crystal structure of human TLR8 in complex with CL075 · 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 3W3K · PDBe 3W3K · UniProt Q9NR97

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