Complex 6c65
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 | 36.97 kDa |
| Deposition year | 2018 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | N/A |
| RCSB PDB Entry | 6c65 |
| Reference | Trachman Robert J., Abdolahzadeh Amir, Andreoni Alessio, Cojocaru Razvan, Knutson Jay R., Ryckelynck Michael, Unrau Peter J., Ferré-D’Amaré Adrian R.. 2018. Crystal Structures of the Mango-II RNA Aptamer Reveal Heterogeneous Fluorophore Binding and Guide Engineering of Variants with Improved Selectivity and Brightness Biochemistry |
| Equivalence Class |
NR_all_82829.3
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 | EKJ |
| Residue | . / 101 |
| Chain | D / A |
| Non-redundant | True |
| Interacting RNA chains | A/A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/A: aptamer_rna |
| RNA family global | aptamer_rna |
| Volume | 387.93 Å3 |
| Hydrophobicity | 0.700 |
| Hydrophilicity | 0.690 |
| Buriedness | 0.619 |
| Don/acc character | 4.689 |
| SiteScore | 1.164 |
| D Score | 1.086 |
| Kd | 0.9nM |
| Compound | EKJ |
| Residue | . / 101 |
| Chain | H / B |
| Non-redundant | False |
| Interacting RNA chains | B/B |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | B/B: aptamer_rna |
| RNA family global | aptamer_rna |
| Volume | 373.18 Å3 |
| Hydrophobicity | 0.651 |
| Hydrophilicity | 0.735 |
| Buriedness | 0.621 |
| Don/acc character | 3.108 |
| SiteScore | 1.157 |
| D Score | 1.073 |
| Kd | 0.9nM |
| Compound | EKJ |
| Residue | . / 101 |
| Chain | L / C |
| Non-redundant | False |
| Interacting RNA chains | C/C |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | C/C: aptamer_rna |
| RNA family global | aptamer_rna |
| Volume | 353.98 Å3 |
| Hydrophobicity | 0.699 |
| Hydrophilicity | 0.785 |
| Buriedness | 0.640 |
| Don/acc character | 2.508 |
| SiteScore | 1.161 |
| D Score | 1.068 |
| Kd | 0.9nM |