Research workbench
Crystal structure of monkey TLR7 in complex with imdq and gguugg
Analyse Crystal structure of monkey TLR7 in complex with imdq and gguugg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZSD
- Type
- protein + RNA
- Length
- 1,553 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toll-like receptor 7; RNA (5'-R(P*UP*UP*GP*A)-3')
- UniProt
- B3Y653
- Ligands
- IDQ, NAG, SO4
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Toll-like receptor 7 | protein | 774 | 13% helix, 15% strand | B3Y653 |
| A | Toll-like receptor 7 | protein | 773 | 12% helix, 15% strand | B3Y653 |
| C, D | RNA (5'-R(P*UP*UP*GP*A)-3') | rna | 3 | — | — |
Ligands and binding sites
- IDQ · 1-[[4-(aminomethyl)phenyl]methyl]-2-butyl-imidazo[4,5-c]quinolin-4-amine · ligand · 2 copies · chains B, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains B, A
- SO4 · Sulfate ion · ion · 14 copies · chains B, A, C
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 | 752 | 0.71 | 0.77 | 87 | NAG |
| 2 | 411 | 0.70 | 0.82 | 57 | SO4 |
| 3 | 50 | 0.68 | 0.97 | 15 | SO4 |
| 4 | 355 | 0.67 | 0.81 | 54 | empty |
| 5 | 52 | 0.65 | 0.95 | 16 | empty |
Interfaces
5 interfaces between chains.
- B–A · 2394 Ų buried · 47 hydrogen bonds · protein-protein
- B–D · 599 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–C · 569 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–C · 67 Ų buried · 1 hydrogen bond · protein-nucleic
- A–D · 43 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 18 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 5ZSD · Crystal structure of monkey TLR7 in complex with IMDQ and GGUUGG · the same entry in another collection · chain B against B, 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 5ZSD · PDBe 5ZSD · UniProt B3Y653
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