MolNFT v1 · #142081 · protein + RNA
Crystal structure of monkey TLR7 in complex with gguugg
5ZSL · Toll-like receptor 7: “Crystal structure of monkey TLR7 in complex with gguugg”. X-ray diffraction, 3 ligands (9K9, NAG, SO4), 18 pockets (best druggability 0.72). MolNFT v1 #142081 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5ZSL
- Type
- protein + RNA
- Length
- 1,556 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
- 9K9, NAG, SO4
- Pockets
- 18 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Toll-like receptor 7 | protein | 777 | 13% helix, 15% strand | B3Y653 |
| A | Toll-like receptor 7 | protein | 773 | 13% helix, 15% strand | B3Y653 |
| D, E | RNA (5'-R(P*UP*UP*GP*A)-3') | rna | 3 | — | — |
Ligands and binding sites
- 9K9 · 2-amino-9-[(2s,3ar,4r,6r,6ar)-2-hydroxy-6-(hydroxymethyl)-2-oxotetrahydro-2H-2lambda~5~-furo[3, 4-d][1,3,2]dioxaphosphol-4-yl]-3,9-dihydro-6H-purin-6-one · ligand · 2 copies · chains B, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains B, A
- SO4 · Sulfate ion · ion · 7 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 716 | 0.72 | 0.78 | 83 | NAG |
| 2 | 399 | 0.68 | 0.81 | 55 | empty |
| 3 | 328 | 0.67 | 0.82 | 49 | empty |
| 4 | 245 | 0.62 | 0.81 | 41 | empty |
| 5 | 216 | 0.62 | 0.82 | 37 | empty |
Interfaces
5 interfaces between chains.
- B–A · 2344 Ų buried · 41 hydrogen bonds · protein-protein
- B–E · 616 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–D · 554 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–D · 75 Ų buried · 1 hydrogen bond · protein-nucleic
- A–E · 27 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 18 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 5ZSL · Crystal structure of monkey TLR7 in complex with 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 5ZSL · PDBe 5ZSL · UniProt B3Y653
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