Complex 6e8t
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 | 2.90 |
| System mass | 48.17 kDa |
| Deposition year | 2018 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | N/A |
| RCSB PDB Entry | 6e8t |
| Reference | Trachman Robert J., Autour Alexis, Jeng Sunny C. Y., Abdolahzadeh Amir, Andreoni Alessio, Cojocaru Razvan, Garipov Ramil, Dolgosheina Elena V., Knutson Jay R., Ryckelynck Michael, Unrau Peter J., Ferré-D’Amaré Adrian R.. 2019. Structure and functional reselection of the Mango-III fluorogenic RNA aptamer Nature Chemical Biology |
| Equivalence Class |
NR_all_30516.3,
NR_all_14315.1
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 | HZG |
| Residue | . / 101 |
| Chain | E / D |
| Non-redundant | True |
| Interacting RNA chains | A/D |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/D: aptamer_rna |
| RNA family global | aptamer_rna |
| Volume | 600.59 Å3 |
| Hydrophobicity | 0.795 |
| Hydrophilicity | 0.874 |
| Buriedness | 0.707 |
| Don/acc character | 3.783 |
| SiteScore | 1.188 |
| D Score | 1.079 |
| Kd | 1.7nM |
| Compound | HZG |
| Residue | . / 101 |
| Chain | G / C |
| Non-redundant | False |
| Interacting RNA chains | B/C |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | B/C: aptamer_rna |
| RNA family global | aptamer_rna |
| Volume | 624.26 Å3 |
| Hydrophobicity | 0.963 |
| Hydrophilicity | 0.768 |
| Buriedness | 0.692 |
| Don/acc character | 3.677 |
| SiteScore | 1.198 |
| D Score | 1.105 |
| Kd | 1.7nM |
| Compound | HZG |
| Residue | . / 101 |
| Chain | J / B |
| Non-redundant | False |
| Interacting RNA chains | C/B |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | C/B: aptamer_rna |
| RNA family global | aptamer_rna |
| Volume | 771.41 Å3 |
| Hydrophobicity | 1.097 |
| Hydrophilicity | 0.800 |
| Buriedness | 0.721 |
| Don/acc character | 4.940 |
| SiteScore | 1.212 |
| D Score | 1.112 |
| Kd | 1.7nM |
| Compound | HZG |
| Residue | . / 101 |
| Chain | L / A |
| Non-redundant | False |
| Interacting RNA chains | D/A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | D/A: aptamer_rna |
| RNA family global | aptamer_rna |
| Volume | 582.76 Å3 |
| Hydrophobicity | 0.974 |
| Hydrophilicity | 0.801 |
| Buriedness | 0.693 |
| Don/acc character | 2.817 |
| SiteScore | 1.193 |
| D Score | 1.095 |
| Kd | 1.7nM |