MolNFT v1 · #175460 · protein
Crystal structure of human TLR8 in complex with cu-CPD107
7CRF · Toll-like receptor 8: “Crystal structure of human TLR8 in complex with cu-CPD107”. X-ray diffraction, 4 ligands (GD0, NAG, MAN), 11 pockets (best druggability 0.75). MolNFT v1 #175460 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7CRF
- 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
- GD0, NAG, MAN, BMA
- Pockets
- 11 · best druggability 0.75
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 | 744 | 10% helix, 16% strand | Q9NR97 |
| B | Toll-like receptor 8 | protein | 751 | 10% helix, 16% strand | Q9NR97 |
Ligands and binding sites
- GD0 · 1-[2-(ethoxymethyl)-4-iodanyl-5-phenyl-imidazol-1-yl]-2-methyl-propan-2-ol · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 33 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 14 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 820 | 0.75 | 0.79 | 93 | NAG, GD0 |
| 2 | 564 | 0.72 | 0.80 | 73 | NAG, GD0 |
| 3 | 477 | 0.66 | 0.78 | 51 | empty |
| 4 | 334 | 0.60 | 0.77 | 43 | NAG |
| 5 | 237 | 0.59 | 0.79 | 30 | NAG |
Interfaces
1 interface between chains.
- A–B · 1166 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 glycan, 13 disulfide (N-glycosylation, disulfide).
Compared structures
- 7CRF · Crystal structure of human TLR8 in complex with CU-CPD107 · 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 7CRF · PDBe 7CRF · UniProt Q9NR97
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