Complex 9dfe
Legend
Pocket colors by molecule type
RNA
Protein
DNA
These colors appear when a pocket is selected (the structure fades to show the pocket surface). Colors from the molecule-type palette (RNA / protein / DNA).
System information
| Experimental technique | X-ray |
| Experimental resolution | 2.60 |
| System mass | 4429.60 kDa |
| Deposition year | 2024 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Thermus |
| RCSB PDB Entry | 9dfe |
| Reference | Wright Gerard, Jangra Manoj, Travin Dmitrii, Aleksandrova Elena, Kaur Manpreet, Darwish Lena, Koteva Kalinka, Klepacki Dorota, Wang Wenliang, Tiffany Maya, Sokaribo Akosiererem, Coombes Brian, Vázquez-Laslop Nora, Polikanov Yury, Mankin Alexander. 2024. A Broad Spectrum Lasso Peptide Antibiotic Targeting the Bacterial Ribosome preprint (Research Square) |
| Equivalence Class |
NR_all_42622.80
BGSU version: 4.52 |
Pockets List
Legend
Cell colors for SiteScore and D Score:
Favourable
Intermediate
Unfavourable
Not available
| Score | Threshold | Meaning |
|---|---|---|
| SiteScore | < 0.8 | Non-drug binding site |
| SiteScore | 0.8 – 1.0 | Potential drug binding site |
| SiteScore | > 1.0 | Promising binding site |
| D Score | < 0.83 | Undruggable |
| D Score | 0.83 – 0.98 | Difficult |
| D Score | > 0.98 | Druggable |
Tick a pocket below to highlight it in the 3D structure above.
| Compound | ARG |
| Residue | . / 232 |
| Chain | VRA / 1B |
| Non-redundant | True |
| Interacting RNA chains | B/1B |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | B/1B: rRNA |
| RNA family global | rRNA |
| Volume | 193.45 Å3 |
| Hydrophobicity | 0.012 |
| Hydrophilicity | 2.147 |
| Buriedness | 0.610 |
| Don/acc character | 0.786 |
| SiteScore | 1.091 |
| D Score | 0.606 |
| Kd | — |