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Crystal structure of human TLR8 in complex with XG-1-236

Analyse Crystal structure of human TLR8 in complex with XG-1-236 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4QC0
Type: protein
Length: 1,491 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.1
Source: Homo sapiens
Molecule: Toll-like receptor 8
UniProt: Q9NR97
Ligands: XG1, NAG, BMA, MAN
Pockets: 14 · best druggability 0.77

Structure

x-ray diffraction · resolution 2.1 · 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	745	11% helix, 15% strand	Q9NR97

Ligands and binding sites

XG1 · 2-butyl-2H-pyrazolo[3,4-c]quinolin-4-amine · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B
MAN · alpha-D-mannopyranose · sugar · chains B

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

Pockets

14 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	924	0.77	0.80	84	NAG
2	646	0.76	0.81	67	NAG
3	435	0.59	0.75	43	empty
4	174	0.59	0.82	21	XG1
5	126	0.56	0.83	25	empty

Interfaces

1 interface between chains.

A–B · 2243 Å² buried · 28 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 9 glycan (disulfide, N-glycosylation).

Compared structures

4QC0 · Crystal structure of human TLR8 in complex with xg-1-236 · 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 4QC0 · PDBe 4QC0 · UniProt Q9NR97

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