Complex 9v4u
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 | 2.54 |
| System mass | 23.11 kDa |
| Deposition year | 2025 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | Staphylococcus |
| RCSB PDB Entry | 9v4u |
| Reference | Li Hongcheng, Shen Xin, Xu Xiaochen, Tai Xiaoqing, He Mengqi, Zhang Jinzhu, Ren Aiming. 2025. Ligand specificity and adaptability revealed by the first Guanine-II riboswitch tertiary structure Nucleic Acids Research |
| Equivalence Class |
NR_all_84306.1
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 | NPR |
| Residue | . / 101 |
| Chain | B / A |
| Non-redundant | True |
| Interacting RNA chains | A/A |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/A: riboswitch |
| RNA family global | riboswitch |
| Volume | 244.90 Å3 |
| Hydrophobicity | 0.703 |
| Hydrophilicity | 1.323 |
| Buriedness | 0.818 |
| Don/acc character | 0.698 |
| SiteScore | 1.230 |
| D Score | 0.999 |
| Kd | — |