Complex 8t5o
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 | 2.98 |
| System mass | 40.81 kDa |
| Deposition year | 2023 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | N/A |
| RCSB PDB Entry | 8t5o |
| Reference | Stagno Jason R, Deme Justin C, Dwivedi Vibha, Lee Yun-Tzai, Lee Hyun Kyung, Yu Ping, Chen Szu-Yun, Fan Lixin, Degenhardt Maximilia F S, Chari Raj, Young Howard A, Lea Susan M, Wang Yun-Xing. 2025. Structural investigation of an RNA device that regulates PD-1 expression in mammalian cells Nucleic Acids Research |
| Equivalence Class |
NR_all_24709.3
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 | TAC |
| Residue | . / 301 |
| Chain | B / A |
| Non-redundant | True |
| Interacting RNA chains | A/A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/A: ribozyme |
| RNA family global | ribozyme |
| Volume | 266.85 Å3 |
| Hydrophobicity | 0.374 |
| Hydrophilicity | 0.983 |
| Buriedness | 0.627 |
| Don/acc character | 0.974 |
| SiteScore | 1.113 |
| D Score | 0.995 |
| Kd | — |