Complex 7oax
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 | 2.24 |
| System mass | 73.12 kDa |
| Deposition year | 2021 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | N/A |
| RCSB PDB Entry | 7oax |
| 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 | SPM |
| Residue | . / 103 |
| Chain | G / A |
| Non-redundant | True |
| Interacting RNA chains | A/A, C/C |
| RNA environment detailled | ion, other |
| RNA environment global | RNA/Other |
| RNA family chains | A/A: aptamer_rna, C/C: aptamer_rna |
| RNA family global | aptamer_rna |
| Volume | 715.50 Å3 |
| Hydrophobicity | 0.465 |
| Hydrophilicity | 1.006 |
| Buriedness | 0.716 |
| Don/acc character | 2.244 |
| SiteScore | 1.169 |
| D Score | 1.042 |
| Kd | — |
| Compound | SPM |
| Residue | . / 102 |
| Chain | N / 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 | 694.92 Å3 |
| Hydrophobicity | 0.405 |
| Hydrophilicity | 1.028 |
| Buriedness | 0.708 |
| Don/acc character | 2.276 |
| SiteScore | 1.159 |
| D Score | 1.030 |
| Kd | — |
| Compound | SPM |
| Residue | . / 102 |
| Chain | V / C |
| Non-redundant | True |
| Interacting RNA chains | A/A, C/C |
| RNA environment detailled | ion, other |
| RNA environment global | RNA/Other |
| RNA family chains | A/A: aptamer_rna, C/C: aptamer_rna |
| RNA family global | aptamer_rna |
| Volume | 748.08 Å3 |
| Hydrophobicity | 0.588 |
| Hydrophilicity | 1.034 |
| Buriedness | 0.733 |
| Don/acc character | 2.178 |
| SiteScore | 1.175 |
| D Score | 1.043 |
| Kd | — |
| Compound | SPM |
| Residue | . / 102 |
| Chain | CA / 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 | 794.39 Å3 |
| Hydrophobicity | 0.420 |
| Hydrophilicity | 1.045 |
| Buriedness | 0.731 |
| Don/acc character | 2.295 |
| SiteScore | 1.172 |
| D Score | 1.038 |
| Kd | — |
| Compound | V5Z |
| Residue | . / 102 |
| Chain | F / A |
| Non-redundant | True |
| Interacting RNA chains | A/A, C/C |
| 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 | 247.65 Å3 |
| Hydrophobicity | 0.834 |
| Hydrophilicity | 0.882 |
| Buriedness | 0.732 |
| Don/acc character | 1.289 |
| SiteScore | 1.061 |
| D Score | 0.909 |
| Kd | — |
| Compound | V5Z |
| Residue | . / 103 |
| Chain | O / 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 | 241.82 Å3 |
| Hydrophobicity | 0.694 |
| Hydrophilicity | 0.958 |
| Buriedness | 0.730 |
| Don/acc character | 1.582 |
| SiteScore | 0.852 |
| D Score | 0.918 |
| Kd | — |
| Compound | V5Z |
| Residue | . / 103 |
| Chain | W / C |
| Non-redundant | True |
| Interacting RNA chains | A/A, C/C |
| 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 | 489.12 Å3 |
| Hydrophobicity | 0.869 |
| Hydrophilicity | 0.962 |
| Buriedness | 0.753 |
| Don/acc character | 1.827 |
| SiteScore | 1.202 |
| D Score | 1.078 |
| Kd | — |
| Compound | V5Z |
| Residue | . / 103 |
| Chain | DA / 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 | 755.97 Å3 |
| Hydrophobicity | 0.423 |
| Hydrophilicity | 1.013 |
| Buriedness | 0.729 |
| Don/acc character | 2.283 |
| SiteScore | 1.176 |
| D Score | 1.047 |
| Kd | — |