MolNFT v1 · #138922 · protein
Crystal structure of human TLR8 in complex with cu-CPT8M
5WYX · Toll-like receptor 8: “Crystal structure of human TLR8 in complex with cu-CPT8M”. X-ray diffraction, 4 ligands (CU8, NAG, MAN), 10 pockets (best druggability 0.80). MolNFT v1 #138922 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5WYX
- Type
- protein
- Length
- 1,489 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 8
- UniProt
- Q9NR97
- Ligands
- CU8, NAG, MAN, BMA
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toll-like receptor 8 | protein | 750 | 10% helix, 16% strand | Q9NR97 |
| B | Toll-like receptor 8 | protein | 739 | 11% helix, 16% strand | Q9NR97 |
Ligands and binding sites
- CU8 · 7-(3-methylphenyl)pyrazolo[1,5-a]pyrimidine-3-carboxamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.80 | 0.82 | 115 | NAG, CU8 |
| 2 | 923 | 0.78 | 0.80 | 88 | CU8 |
| 3 | 456 | 0.66 | 0.78 | 65 | NAG |
| 4 | 343 | 0.60 | 0.77 | 43 | NAG |
| 5 | 395 | 0.58 | 0.74 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1510 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 5WYX · Crystal structure of human TLR8 in complex with CU-CPT8m · 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 5WYX · PDBe 5WYX · UniProt Q9NR97
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