MolNFT v1 · #138923 · protein
Crystal structure of human TLR8 in complex with cu-CPT9B
5WYZ · Toll-like receptor 8: “Crystal structure of human TLR8 in complex with cu-CPT9B”. X-ray diffraction, 4 ligands (7VF, NAG, MAN), 12 pockets (best druggability 0.82). MolNFT v1 #138923 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5WYZ
- Type
- protein
- Length
- 1,495 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 8
- UniProt
- Q9NR97
- Ligands
- 7VF, NAG, MAN, BMA
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toll-like receptor 8 | protein | 750 | 11% helix, 16% strand | Q9NR97 |
| B | Toll-like receptor 8 | protein | 745 | 10% helix, 16% strand | Q9NR97 |
Ligands and binding sites
- 7VF · 4-(3-methyl-4-oxidanyl-phenyl)quinolin-7-ol · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 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
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 778 | 0.82 | 0.85 | 111 | 7VF |
| 2 | 697 | 0.80 | 0.84 | 100 | 7VF |
| 3 | 339 | 0.63 | 0.79 | 51 | empty |
| 4 | 259 | 0.60 | 0.79 | 31 | NAG |
| 5 | 249 | 0.60 | 0.79 | 32 | NAG |
Interfaces
1 interface between chains.
- A–B · 1764 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 5WYZ · Crystal structure of human TLR8 in complex with CU-CPT9b · 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 5WYZ · PDBe 5WYZ · UniProt Q9NR97
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