Complex 5v3f
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 | 1.70 |
| System mass | 22.43 kDa |
| Deposition year | 2017 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | N/A |
| RCSB PDB Entry | 5v3f |
| Reference | Trachman Robert J, Demeshkina Natalia A, Lau Matthew W L, Panchapakesan Shanker Shyam S, Jeng Sunny C Y, Unrau Peter J, Ferré-D'Amaré Adrian R. 2017. Structural basis for high-affinity fluorophore binding and activation by RNA Mango Nature Chemical Biology |
| Equivalence Class |
NR_all_93701.3
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 | 74G |
| Residue | . / 104 |
| Chain | F / 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 | 256.91 Å3 |
| Hydrophobicity | 0.966 |
| Hydrophilicity | 0.642 |
| Buriedness | 0.608 |
| Don/acc character | 3.574 |
| SiteScore | 1.167 |
| D Score | 1.095 |
| Kd | ~3nM |
| Compound | 74G |
| Residue | . / 104 |
| Chain | J / 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 | 250.73 Å3 |
| Hydrophobicity | 0.813 |
| Hydrophilicity | 0.634 |
| Buriedness | 0.587 |
| Don/acc character | 3.501 |
| SiteScore | 1.154 |
| D Score | 1.086 |
| Kd | ~3nM |