Complex 6nd6
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 | 2.85 |
| System mass | 4572.35 kDa |
| Deposition year | 2018 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Thermus |
| RCSB PDB Entry | 6nd6 |
| Reference | Svetlov Maxim S., Plessa Elena, Chen Chih-Wei, Bougas Anthony, Krokidis Marios G., Dinos George P., Polikanov Yury S.. 2019. High-resolution crystal structures of ribosome-bound chloramphenicol and erythromycin provide the ultimate basis for their competition RNA |
| Equivalence Class |
NR_all_97519.80
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 | ERY |
| Residue | . / 4074 |
| Chain | PSA / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | 637.98 Å3 |
| Hydrophobicity | 0.355 |
| Hydrophilicity | 1.538 |
| Buriedness | 0.763 |
| Don/acc character | 0.519 |
| SiteScore | 1.193 |
| D Score | 0.896 |
| Kd | — |
| Compound | ERY |
| Residue | . / 3875 |
| Chain | VRC / 2A |
| Non-redundant | True |
| Interacting RNA chains | EB/2A |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | EB/2A: rRNA |
| RNA family global | rRNA |
| Volume | 137.54 Å3 |
| Hydrophobicity | 0.531 |
| Hydrophilicity | 1.228 |
| Buriedness | 0.618 |
| Don/acc character | 0.836 |
| SiteScore | 0.985 |
| D Score | 0.768 |
| Kd | — |