Complex 8syk
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 | 3.06 |
| System mass | 143.42 kDa |
| Deposition year | 2023 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | N/A |
| RCSB PDB Entry | 8syk |
| 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 | . / 202 |
| Chain | F / A |
| Non-redundant | False |
| Interacting RNA chains | A/A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/A: synthetic construct |
| RNA family global | synthetic construct |
| Volume | 419.49 Å3 |
| Hydrophobicity | 0.413 |
| Hydrophilicity | 1.060 |
| Buriedness | 0.697 |
| Don/acc character | 1.149 |
| SiteScore | 1.149 |
| D Score | 1.012 |
| Kd | — |
| Compound | TAC |
| Residue | . / 202 |
| Chain | CA / B |
| Non-redundant | False |
| Interacting RNA chains | B/B |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | B/B: synthetic construct |
| RNA family global | synthetic construct |
| Volume | 407.83 Å3 |
| Hydrophobicity | 0.406 |
| Hydrophilicity | 0.959 |
| Buriedness | 0.659 |
| Don/acc character | 1.777 |
| SiteScore | 1.140 |
| D Score | 1.023 |
| Kd | — |
| Compound | TAC |
| Residue | . / 202 |
| Chain | QA / C |
| Non-redundant | False |
| Interacting RNA chains | C/C |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | C/C: synthetic construct |
| RNA family global | synthetic construct |
| Volume | 498.04 Å3 |
| Hydrophobicity | 0.256 |
| Hydrophilicity | 1.079 |
| Buriedness | 0.691 |
| Don/acc character | 1.273 |
| SiteScore | 1.145 |
| D Score | 1.003 |
| Kd | — |
| Compound | TAC |
| Residue | . / 202 |
| Chain | IB / D |
| Non-redundant | False |
| Interacting RNA chains | D/D |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | D/D: synthetic construct |
| RNA family global | synthetic construct |
| Volume | 344.72 Å3 |
| Hydrophobicity | 0.428 |
| Hydrophilicity | 0.990 |
| Buriedness | 0.696 |
| Don/acc character | 1.151 |
| SiteScore | 1.158 |
| D Score | 1.035 |
| Kd | — |