Complex 3rkf
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 | 2.50 |
| System mass | 90.95 kDa |
| Deposition year | 2011 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | Bacillus |
| RCSB PDB Entry | 3rkf |
| Reference | Buck Janina, Wacker Anna, Warkentin Eberhart, Wöhnert Jens, Wirmer-Bartoschek Julia, Schwalbe Harald. 2011. Influence of ground-state structure and Mg 2+ binding on folding kinetics of the guanine-sensing riboswitch aptamer domain Nucleic Acids Research |
| Equivalence Class |
NR_all_76114.3
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 | DX4 |
| Residue | . / 91 |
| Chain | E / 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 | 149.55 Å3 |
| Hydrophobicity | 0.144 |
| Hydrophilicity | 1.680 |
| Buriedness | 0.837 |
| Don/acc character | 0.413 |
| SiteScore | 1.087 |
| D Score | 0.695 |
| Kd | — |
| Compound | DX4 |
| Residue | . / 91 |
| Chain | O / B |
| Non-redundant | False |
| Interacting RNA chains | B/B |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | B/B: riboswitch |
| RNA family global | riboswitch |
| Volume | 183.51 Å3 |
| Hydrophobicity | 0.181 |
| Hydrophilicity | 1.247 |
| Buriedness | 0.773 |
| Don/acc character | 0.909 |
| SiteScore | 1.080 |
| D Score | 0.844 |
| Kd | — |
| Compound | DX4 |
| Residue | . / 91 |
| Chain | U / C |
| Non-redundant | False |
| Interacting RNA chains | C/C |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | C/C: riboswitch |
| RNA family global | riboswitch |
| Volume | 172.19 Å3 |
| Hydrophobicity | 0.000 |
| Hydrophilicity | 1.607 |
| Buriedness | 0.813 |
| Don/acc character | 0.806 |
| SiteScore | 1.111 |
| D Score | 0.756 |
| Kd | — |
| Compound | DX4 |
| Residue | . / 91 |
| Chain | AA / D |
| Non-redundant | False |
| Interacting RNA chains | D/D |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | D/D: riboswitch |
| RNA family global | riboswitch |
| Volume | 198.94 Å3 |
| Hydrophobicity | 0.408 |
| Hydrophilicity | 1.433 |
| Buriedness | 0.824 |
| Don/acc character | 0.793 |
| SiteScore | 1.101 |
| D Score | 0.797 |
| Kd | — |