Research workbench
Human TLR8 bound to the potent agonist, gs-9688 (selgantolimod)
Analyse Human TLR8 bound to the potent agonist, gs-9688 (selgantolimod) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WML
- Type
- protein
- Length
- 2,883 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 8
- UniProt
- Q9NR97
- Ligands
- U57, NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toll-like receptor 8 | protein | 743 | 11% helix, 15% strand | Q9NR97 |
| B | Toll-like receptor 8 | protein | 751 | 11% helix, 16% strand | Q9NR97 |
| C | Toll-like receptor 8 | protein | 681 | 11% helix, 16% strand | Q9NR97 |
| D | Toll-like receptor 8 | protein | 708 | 9% helix, 15% strand | Q9NR97 |
Ligands and binding sites
- U57 · (2R)-2-[(2-amino-7-fluoropyrido[3,2-d]pyrimidin-4-yl) amino]-2-methylhexan-1-ol · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 39 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 15 copies · chains C, D, A, B
- BMA · beta-D-mannopyranose · sugar · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 551 | 0.77 | 0.84 | 79 | empty |
| 2 | 900 | 0.76 | 0.79 | 82 | NAG |
| 3 | 1148 | 0.76 | 0.78 | 99 | NAG |
| 4 | 826 | 0.74 | 0.79 | 87 | NAG |
| 5 | 794 | 0.72 | 0.78 | 89 | NAG |
Interfaces
3 interfaces between chains.
- C–D · 2030 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2025 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 496 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 glycan, 23 disulfide (N-glycosylation, disulfide).
Compared structures
- 6WML · Human TLR8 bound to the potent agonist, GS-9688 (Selgantolimod) · 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 6WML · PDBe 6WML · UniProt Q9NR97
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