Complex 9mkk
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 | Electron Microscopy |
| Experimental resolution | 3.20 |
| System mass | 2146.72 kDa |
| Deposition year | 2024 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Escherichia |
| RCSB PDB Entry | 9mkk |
| Reference | Majumdar Soneya, Parajuli Narayan Prasad, Ge Xueliang, Sanyal Suparna. 2025. Structure–function comparison of Arbekacin with other aminoglycosides elucidates its higher potency as bacterial translation inhibitor Scientific Reports |
| Equivalence Class |
NR_all_35542.167,
NR_all_83717.187,
NR_all_56726.172
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 | 84G |
| Residue | . / 1601 |
| Chain | AB / A |
| Non-redundant | True |
| Interacting RNA chains | YA/A |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | YA/A: rRNA |
| RNA family global | rRNA |
| Volume | - |
| Hydrophobicity | - |
| Hydrophilicity | - |
| Buriedness | - |
| Don/acc character | - |
| SiteScore | - |
| D Score | - |
| Kd | — |
| Compound | 84G |
| Residue | . / 3001 |
| Chain | BB / a |
| Non-redundant | True |
| Interacting RNA chains | ZA/a, AA/Z |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | AA/Z: tRNA, ZA/a: rRNA |
| RNA family global | multiple |
| Volume | 429.78 Å3 |
| Hydrophobicity | 0.089 |
| Hydrophilicity | 0.921 |
| Buriedness | 0.679 |
| Don/acc character | 1.650 |
| SiteScore | 1.049 |
| D Score | 0.905 |
| Kd | — |