Research workbench
Crystal structure of human TLR8 ectodomain bound to small molecule antagonist 21
Analyse Crystal structure of human TLR8 ectodomain bound to small molecule antagonist 21 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RC9
- Type
- protein
- Length
- 1,474 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 8
- UniProt
- Q9NR97
- Ligands
- RQY, NAG, MAN, BMA
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Toll-like receptor 8 | protein | 737 | 11% helix, 15% strand | Q9NR97 |
Ligands and binding sites
- RQY · 2-(2,6-dimethylpyridin-4-yl)-5-(piperidin-4-yl)-3-(propan-2-yl)-1H-indole · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 26 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains B
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1061 | 0.79 | 0.80 | 111 | RQY |
| 2 | 223 | 0.61 | 0.81 | 29 | NAG |
| 3 | 224 | 0.60 | 0.80 | 31 | NAG |
| 4 | 67 | 0.50 | 0.85 | 19 | empty |
| 5 | 240 | 0.49 | 0.74 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 1319 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 glycan, 12 disulfide (N-glycosylation, disulfide).
Compared structures
- 7RC9 · Crystal structure of human TLR8 ectodomain bound to small molecule antagonist 21 · the same entry in another collection · chain A against A, TM-score 1.00
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 7RC9 · PDBe 7RC9 · UniProt Q9NR97
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