Research workbench
Crystal structure of human TLR8 in complex with mb-343
Analyse Crystal structure of human TLR8 in complex with mb-343 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AZ5
- Type
- protein
- Length
- 2,991 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 8
- UniProt
- Q9NR97
- Ligands
- MBL, NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toll-like receptor 8 | protein | 748 | 12% helix, 15% strand | Q9NR97 |
| B | Toll-like receptor 8 | protein | 749 | 12% helix, 15% strand | Q9NR97 |
| C | Toll-like receptor 8 | protein | 748 | 11% helix, 16% strand | Q9NR97 |
| D | Toll-like receptor 8 | protein | 746 | 12% helix, 15% strand | Q9NR97 |
Ligands and binding sites
- MBL · 1-pentyl-4-phenyl-imidazol-2-amine · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 38 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 8 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.76 | 0.78 | 109 | NAG |
| 2 | 674 | 0.76 | 0.81 | 79 | NAG |
| 3 | 935 | 0.76 | 0.78 | 91 | NAG |
| 4 | 768 | 0.74 | 0.79 | 81 | NAG |
| 5 | 677 | 0.66 | 0.76 | 70 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2205 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2164 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 312 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 glycan, 24 disulfide (N-glycosylation, disulfide).
Compared structures
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 5AZ5 · PDBe 5AZ5 · UniProt Q9NR97
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