Complex 6up0
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 | 2.80 |
| System mass | 25.50 kDa |
| Deposition year | 2019 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | N/A |
| RCSB PDB Entry | 6up0 |
| Reference | Jeng Sunny C.Y., Trachman Robert J., Weissenboeck Florian, Truong Lynda, Link Katie A., Jepsen Mette D.E., Knutson Jay R., Andersen Ebbe S., Ferré-D'Amaré Adrian R., Unrau Peter J.. 2021. Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET RNA |
| Equivalence Class |
NR_all_08239.3
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 | YO3 |
| Residue | . / 104 |
| Chain | F / C |
| Non-redundant | True |
| Interacting RNA chains | A/C |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/C: aptamer_rna |
| RNA family global | aptamer_rna |
| Volume | 202.71 Å3 |
| Hydrophobicity | 0.765 |
| Hydrophilicity | 0.759 |
| Buriedness | 0.575 |
| Don/acc character | 2.848 |
| SiteScore | 1.122 |
| D Score | 1.038 |
| Kd | — |
| Compound | YO3 |
| Residue | . / 104 |
| Chain | K / D |
| Non-redundant | True |
| Interacting RNA chains | B/D |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | B/D: aptamer_rna |
| RNA family global | aptamer_rna |
| Volume | 182.82 Å3 |
| Hydrophobicity | 1.094 |
| Hydrophilicity | 0.751 |
| Buriedness | 0.620 |
| Don/acc character | 1.881 |
| SiteScore | 1.088 |
| D Score | 0.983 |
| Kd | — |