MolNFT v1 · #86012 · protein + RNA
New insights into the mechanism of bacterial type III toxin-antitoxin systems: selective toxin inhibition by a non-coding RNA pseudoknot
4ATO · Toxn: “New insights into the mechanism of bacterial type III toxin-antitoxin systems: selective toxin inhibition by…”. X-ray diffraction, 3 pockets (best druggability 0.49). MolNFT v1 #86012 on GenesisL1: 3D structure, binding sites…
- PDB
- 4ATO
- Type
- protein + RNA
- Length
- 202 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toxn; Toxi
- UniProt
- Q3YN09
- Pockets
- 3 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toxn | protein | 168 | 45% helix, 19% strand | Q3YN09 |
| G | Toxi | rna | 34 | — | — |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.49 | 0.78 | 21 | empty |
| 2 | 233 | 0.48 | 0.75 | 24 | empty |
| 3 | 103 | 0.37 | 0.75 | 18 | MPD |
Interfaces
1 interface between chains.
- A–G · 1159 Ų buried · 39 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4ATO · New insights into the mechanism of bacterial Type III toxin-antitoxin systems: selective… · the same entry in another collection · chain A against A, TM-score 1.00
- Q3YN09 · AlphaFold monomer V2.0 prediction for endoribonuclease toxn (Q3YN09) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q3YN09
- Elsewhere: RCSB PDB 4ATO · PDBe 4ATO · UniProt Q3YN09
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