Complex 9pgm
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 | 3.18 |
| System mass | 3083.92 kDa |
| Deposition year | 2025 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Homo |
| RCSB PDB Entry | 9pgm |
| Reference | Wang Shuhui, Brischigliaro Michele, Zhang Yuekang, Wu Chunxiang, Zheng Wei, Barrientos Antoni, Xiong Yong. 2026. Structural basis of TACO1-mediated efficient mitochondrial translation Nature Communications |
| Equivalence Class |
NR_all_93855.32
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 | NAD |
| Residue | . / 1701 |
| Chain | YJ / AA |
| Non-redundant | True |
| Interacting RNA chains | CC/AA |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | CC/AA: rRNA |
| RNA family global | rRNA |
| Volume | 923.01 Å3 |
| Hydrophobicity | 0.073 |
| Hydrophilicity | 1.621 |
| Buriedness | 0.820 |
| Don/acc character | 0.626 |
| SiteScore | 1.082 |
| D Score | 0.904 |
| Kd | — |
| Compound | SPM |
| Residue | . / 1702 |
| Chain | ZJ / AA |
| Non-redundant | True |
| Interacting RNA chains | CC/AA |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | CC/AA: rRNA |
| RNA family global | rRNA |
| Volume | 775.52 Å3 |
| Hydrophobicity | 0.217 |
| Hydrophilicity | 1.115 |
| Buriedness | 0.807 |
| Don/acc character | 3.276 |
| SiteScore | 1.223 |
| D Score | 1.061 |
| Kd | — |
| Compound | SPM |
| Residue | . / 1780 |
| Chain | ZM / AA |
| Non-redundant | True |
| Interacting RNA chains | CC/AA |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | CC/AA: rRNA |
| RNA family global | rRNA |
| Volume | 734.02 Å3 |
| Hydrophobicity | 0.242 |
| Hydrophilicity | 1.093 |
| Buriedness | 0.769 |
| Don/acc character | 4.375 |
| SiteScore | 1.197 |
| D Score | 1.045 |
| Kd | — |