MolNFT v1 · #120854 · protein
Crystal structure of human TLR8 with an uncleaved Z-loop
5HDH · Toll-like receptor 8: “Crystal structure of human TLR8 with an uncleaved Z-loop”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 5 pockets (best druggability 0.69). MolNFT v1 #120854 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5HDH
- Type
- protein
- Length
- 751 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 8
- UniProt
- Q9NR97
- Ligands
- NAG, MAN, BMA, SO4
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toll-like receptor 8 | protein | 751 | 11% helix, 16% strand | Q9NR97 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.69 | 0.79 | 60 | NAG |
| 2 | 158 | 0.69 | 0.88 | 24 | empty |
| 3 | 150 | 0.50 | 0.78 | 22 | empty |
| 4 | 153 | 0.46 | 0.76 | 24 | empty |
| 5 | 61 | 0.33 | 0.76 | 16 | NAG |
Modifications
Observed in the structure: 9 glycan, 7 disulfide (N-glycosylation, disulfide).
Compared structures
- 5HDH · Crystal structure of human TLR8 with an uncleaved Z-loop · 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 5HDH · PDBe 5HDH · UniProt Q9NR97
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