Complex 9i5t
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 | 2.60 |
| System mass | 1381.24 kDa |
| Deposition year | 2025 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Porphyromonas |
| RCSB PDB Entry | 9i5t |
| Reference | Hiregange Disha-Gajanan, Samiya Sarit, Mizgalska Danuta, Ben-Zeev Efrat, Waghalter Miriam, Rivalta Andre, Rajan K Shanmugha, Halfon Yehuda, Breiner-Goldstein Elinor, Kaczmarczyk Igor, Sroka Aneta, Taoka Masato, Nobe Yuko, Isobe Toshiaki, Paukner Susanne, Zimmerman Ella, Bashan Anat, Potempa Jan, Yonath Ada. 2025. Structural studies of ribosome from an anaerobic Bacteroidetes human pathogen Porphyromonas gingivalis Nucleic Acids Research |
| Equivalence Class |
NR_all_18178.1
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 | 62B |
| Residue | . / 2901 |
| Chain | IA / A |
| Non-redundant | True |
| Interacting RNA chains | J/A |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | J/A: rRNA |
| RNA family global | rRNA |
| Volume | 634.21 Å3 |
| Hydrophobicity | 0.307 |
| Hydrophilicity | 1.109 |
| Buriedness | 0.749 |
| Don/acc character | 1.682 |
| SiteScore | 1.184 |
| D Score | 1.028 |
| Kd | — |