Complex 7oav
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 | 2.99 |
| System mass | 72.60 kDa |
| Deposition year | 2021 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | N/A |
| RCSB PDB Entry | 7oav |
| Reference | Mieczkowski Mateusz, Steinmetzger Christian, Bessi Irene, Lenz Ann-Kathrin, Schmiedel Alexander, Holzapfel Marco, Lambert Christoph, Pena Vladimir, Höbartner Claudia. 2021. Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine Nature Communications |
| Equivalence Class |
NR_all_84656.3
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 | GTP |
| Residue | . / 102 |
| Chain | Q / C |
| Non-redundant | False |
| Interacting RNA chains | C/C |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | C/C: aptamer_rna |
| RNA family global | aptamer_rna |
| Volume | 24.70 Å3 |
| Hydrophobicity | 0.005 |
| Hydrophilicity | 0.734 |
| Buriedness | 0.400 |
| Don/acc character | 3.362 |
| SiteScore | 0.612 |
| D Score | 0.431 |
| Kd | — |
| Compound | V5Z |
| Residue | . / 101 |
| Chain | E / A |
| Non-redundant | False |
| Interacting RNA chains | C/C, A/A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/A: aptamer_rna, C/C: aptamer_rna |
| RNA family global | aptamer_rna |
| Volume | 520.67 Å3 |
| Hydrophobicity | 0.961 |
| Hydrophilicity | 0.993 |
| Buriedness | 0.767 |
| Don/acc character | 1.389 |
| SiteScore | 1.205 |
| D Score | 1.076 |
| Kd | — |
| Compound | V5Z |
| Residue | . / 101 |
| Chain | K / B |
| Non-redundant | False |
| Interacting RNA chains | D/D, B/B |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | B/B: aptamer_rna, D/D: aptamer_rna |
| RNA family global | aptamer_rna |
| Volume | 501.47 Å3 |
| Hydrophobicity | 0.841 |
| Hydrophilicity | 0.925 |
| Buriedness | 0.754 |
| Don/acc character | 1.349 |
| SiteScore | 1.210 |
| D Score | 1.091 |
| Kd | — |
| Compound | V5Z |
| Residue | . / 101 |
| Chain | P / C |
| Non-redundant | False |
| Interacting RNA chains | C/C, A/A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/A: aptamer_rna, C/C: aptamer_rna |
| RNA family global | aptamer_rna |
| Volume | 753.91 Å3 |
| Hydrophobicity | 0.375 |
| Hydrophilicity | 1.187 |
| Buriedness | 0.738 |
| Don/acc character | 1.786 |
| SiteScore | 1.176 |
| D Score | 0.996 |
| Kd | — |
| Compound | V5Z |
| Residue | . / 101 |
| Chain | T / D |
| Non-redundant | False |
| Interacting RNA chains | D/D, B/B |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | B/B: aptamer_rna, D/D: aptamer_rna |
| RNA family global | aptamer_rna |
| Volume | 489.46 Å3 |
| Hydrophobicity | 0.802 |
| Hydrophilicity | 0.908 |
| Buriedness | 0.726 |
| Don/acc character | 1.649 |
| SiteScore | 1.195 |
| D Score | 1.080 |
| Kd | — |