Research workbench
Crystal structure of human TLR8 in complex with resiquimod (R848) crystal form 3
Analyse Crystal structure of human TLR8 in complex with resiquimod (R848) crystal form 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W3N
- Type
- protein
- Length
- 1,500 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 8
- UniProt
- Q9NR97
- Ligands
- RX8, NAG, MAN, BMA
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toll-like receptor 8 | protein | 751 | 11% helix, 15% strand | Q9NR97 |
| B | Toll-like receptor 8 | protein | 749 | 11% helix, 15% strand | Q9NR97 |
Ligands and binding sites
- RX8 · 1-[4-amino-2-(ethoxymethyl)-1H-imidazo[4,5-c]quinolin-1-yl]-2-methylpropan-2-ol · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 887 | 0.76 | 0.79 | 88 | NAG |
| 2 | 716 | 0.75 | 0.80 | 83 | NAG |
| 3 | 274 | 0.60 | 0.79 | 26 | empty |
| 4 | 139 | 0.59 | 0.84 | 25 | empty |
| 5 | 258 | 0.59 | 0.78 | 30 | RX8 |
Interfaces
1 interface between chains.
- A–B · 2054 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 glycan, 12 disulfide (N-glycosylation, disulfide).
Compared structures
- 3W3N · Crystal structure of human TLR8 in complex with Resiquimod (R848) crystal form 3 · 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 3W3N · PDBe 3W3N · UniProt Q9NR97
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