Research workbench
Crystal structure of human TLR8 in complex with cu-CPT9A
Analyse Crystal structure of human TLR8 in complex with cu-CPT9A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z14
- Type
- protein
- Length
- 1,477 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 8
- UniProt
- Q9NR97
- Ligands
- 7VC, NAG, MAN, BMA
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toll-like receptor 8 | protein | 743 | 10% helix, 17% strand | Q9NR97 |
| B | Toll-like receptor 8 | protein | 734 | 10% helix, 17% strand | Q9NR97 |
Ligands and binding sites
- 7VC · 4-(7-methoxyquinolin-4-yl)-2-methyl-phenol · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains B
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 881 | 0.81 | 0.83 | 115 | 7VC |
| 2 | 587 | 0.70 | 0.78 | 66 | empty |
| 3 | 125 | 0.70 | 0.90 | 27 | 7VC |
| 4 | 228 | 0.64 | 0.82 | 29 | NAG |
| 5 | 319 | 0.62 | 0.79 | 42 | NAG |
Interfaces
1 interface between chains.
- A–B · 1709 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 5Z14 · Crystal structure of human TLR8 in complex with CU-CPT9a · 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 5Z14 · PDBe 5Z14 · UniProt Q9NR97
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