Complex 5dm7
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 | 3.00 |
| System mass | 1360.56 kDa |
| Deposition year | 2015 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Deinococcus |
| RCSB PDB Entry | 5dm7 |
| Reference | Kaminishi Tatsuya, Schedlbauer Andreas, Fabbretti Attilio, Brandi Letizia, Ochoa-Lizarralde Borja, He Cheng-Guang, Milón Pohl, Connell Sean R., Gualerzi Claudio O., Fucini Paola. 2015. Crystallographic characterization of the ribosomal binding site and molecular mechanism of action of Hygromycin A Nucleic Acids Research |
| Equivalence Class |
NR_all_88987.11
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 | HGR |
| Residue | . / 6178 |
| Chain | DH / X |
| Non-redundant | True |
| Interacting RNA chains | CA/X |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | CA/X: rRNA |
| RNA family global | rRNA |
| Volume | 372.84 Å3 |
| Hydrophobicity | 0.979 |
| Hydrophilicity | 0.763 |
| Buriedness | 0.764 |
| Don/acc character | 1.847 |
| SiteScore | 1.218 |
| D Score | 1.111 |
| Kd | — |