Research workbench
Crystal structure of monkey TLR7 in complex with R848
Analyse Crystal structure of monkey TLR7 in complex with R848 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GMH
- Type
- protein
- Length
- 1,544 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 7
- UniProt
- B3Y653
- Ligands
- RX8, NAG, SO4
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Toll-like receptor 7 | protein | 772 | 13% helix, 15% strand | B3Y653 |
Ligands and binding sites
- RX8 · 1-[4-amino-2-(ethoxymethyl)-1H-imidazo[4,5-c]quinolin-1-yl]-2-methylpropan-2-ol · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, B
- SO4 · Sulfate ion · ion · 28 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.70 | 0.81 | 66 | empty |
| 2 | 477 | 0.70 | 0.80 | 66 | SO4 |
| 3 | 257 | 0.69 | 0.85 | 43 | empty |
| 4 | 539 | 0.66 | 0.77 | 58 | NAG |
| 5 | 194 | 0.64 | 0.84 | 24 | RX8, SO4 |
Interfaces
1 interface between chains.
- A–B · 2409 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 5GMH · Crystal structure of monkey TLR7 in complex with R848 · 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 B3Y653
- Elsewhere: RCSB PDB 5GMH · PDBe 5GMH · UniProt B3Y653
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