Complex 5ndk
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 | 2.95 |
| System mass | 4521.81 kDa |
| Deposition year | 2017 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Escherichia |
| RCSB PDB Entry | 5ndk |
| Reference | Prokhorova Irina, Altman Roger B., Djumagulov Muminjon, Shrestha Jaya P., Urzhumtsev Alexandre, Ferguson Angelica, Chang Cheng-Wei Tom, Yusupov Marat, Blanchard Scott C., Yusupova Gulnara. 2017. Aminoglycoside interactions and impacts on the eukaryotic ribosome Proceedings of the National Academy of Sciences |
| Equivalence Class |
NR_all_65795.87
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 | 8UZ |
| Residue | . / 2201 |
| Chain | ED / 13 |
| Non-redundant | True |
| Interacting RNA chains | A/13 |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/13: rRNA |
| RNA family global | rRNA |
| Volume | 44.59 Å3 |
| Hydrophobicity | 0.132 |
| Hydrophilicity | 0.830 |
| Buriedness | 0.551 |
| Don/acc character | 4.673 |
| SiteScore | 0.696 |
| D Score | 0.491 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 2202 |
| Chain | FD / 13 |
| Non-redundant | True |
| Interacting RNA chains | A/13 |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | A/13: rRNA |
| RNA family global | rRNA |
| Volume | 177.67 Å3 |
| Hydrophobicity | 0.011 |
| Hydrophilicity | 1.248 |
| Buriedness | 0.720 |
| Don/acc character | 1.882 |
| SiteScore | 0.804 |
| D Score | 0.620 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 2201 |
| Chain | OK / 1G |
| Non-redundant | True |
| Interacting RNA chains | J/1G |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | J/1G: rRNA |
| RNA family global | rRNA |
| Volume | 250.05 Å3 |
| Hydrophobicity | 0.069 |
| Hydrophilicity | 1.151 |
| Buriedness | 0.693 |
| Don/acc character | 2.420 |
| SiteScore | 0.972 |
| D Score | 0.757 |
| Kd | — |
| Compound | 8UZ |
| Residue | . / 2202 |
| Chain | PK / 1G |
| Non-redundant | True |
| Interacting RNA chains | J/1G |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | J/1G: rRNA |
| RNA family global | rRNA |
| Volume | 173.90 Å3 |
| Hydrophobicity | 0.033 |
| Hydrophilicity | 1.045 |
| Buriedness | 0.676 |
| Don/acc character | 3.118 |
| SiteScore | 0.774 |
| D Score | 0.526 |
| Kd | — |