MolNFT v1 · #113916 · protein
Crystal structure of human TLR8 in complex with N1-4-aminomethylbenzyl (imdq)
5AWD · Toll-like receptor 8: “Crystal structure of human TLR8 in complex with N1-4-aminomethylbenzyl (imdq)”. X-ray diffraction, 4 ligands (IDQ, NAG, BMA), 3 pockets (best druggability 0.68). MolNFT v1 #113916 on GenesisL1: 3D structure…
- PDB
- 5AWD
- Type
- protein
- Length
- 750 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 8
- UniProt
- Q9NR97
- Ligands
- IDQ, NAG, BMA, MAN
- Pockets
- 3 · best druggability 0.68
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 | 750 | 12% helix, 15% strand | Q9NR97 |
Ligands and binding sites
- IDQ · 1-[[4-(aminomethyl)phenyl]methyl]-2-butyl-imidazo[4,5-c]quinolin-4-amine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.68 | 0.78 | 58 | NAG |
| 2 | 117 | 0.57 | 0.84 | 23 | empty |
| 3 | 56 | 0.32 | 0.77 | 21 | NAG |
Modifications
Observed in the structure: 10 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 5AWD · Crystal structure of human TLR8 in complex with N1-4-aminomethylbenzyl (IMDQ) · 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 5AWD · PDBe 5AWD · UniProt Q9NR97
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