MolNFT v1 · #83584 · protein

Crystal structure of human TLR8 in complex with ds-877

3WN4 · Toll-like receptor 8: “Crystal structure of human TLR8 in complex with ds-877”. X-ray diffraction, 4 ligands (D87, NAG, BMA), 4 pockets (best druggability 0.64). MolNFT v1 #83584 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 3WN4
Type: protein
Length: 747 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Toll-like receptor 8
UniProt: Q9NR97
Ligands: D87, NAG, BMA, MAN
Pockets: 4 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 12% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Toll-like receptor 8	protein	747	12% helix, 15% strand	Q9NR97

Ligands and binding sites

D87 · 2-butylfuro[2,3-c]quinolin-4-amine · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A
BMA · beta-D-mannopyranose · sugar · 3 copies · chains A
MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	399	0.64	0.78	49	NAG
2	96	0.57	0.86	21	empty
3	170	0.50	0.77	22	empty
4	84	0.35	0.75	15	empty

Modifications

Observed in the structure: 12 glycan, 6 disulfide (N-glycosylation, disulfide).

Compared structures

3WN4 · Crystal structure of human TLR8 in complex with DS-877 · 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 3WN4 · PDBe 3WN4 · UniProt Q9NR97

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