Complex 5d5l
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 | 2.50 |
| System mass | 104.74 kDa |
| Deposition year | 2015 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | Lacticaseibacillus |
| RCSB PDB Entry | 5d5l |
| Equivalence Class |
NR_all_55964.3
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 | PRF |
| Residue | . / 117 |
| Chain | U / A |
| Non-redundant | False |
| Interacting RNA chains | A/A |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/A: riboswitch |
| RNA family global | riboswitch |
| Volume | 98.10 Å3 |
| Hydrophobicity | 0.899 |
| Hydrophilicity | 0.946 |
| Buriedness | 0.644 |
| Don/acc character | 1.702 |
| SiteScore | 0.814 |
| D Score | 0.610 |
| Kd | — |
| Compound | PRF |
| Residue | . / 109 |
| Chain | JA / B |
| Non-redundant | False |
| Interacting RNA chains | B/B |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | B/B: riboswitch |
| RNA family global | riboswitch |
| Volume | 99.47 Å3 |
| Hydrophobicity | 0.576 |
| Hydrophilicity | 0.845 |
| Buriedness | 0.604 |
| Don/acc character | 2.229 |
| SiteScore | 0.826 |
| D Score | 0.643 |
| Kd | — |
| Compound | PRF |
| Residue | . / 104 |
| Chain | QA / C |
| Non-redundant | False |
| Interacting RNA chains | C/C |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | C/C: riboswitch |
| RNA family global | riboswitch |
| Volume | 87.81 Å3 |
| Hydrophobicity | 0.577 |
| Hydrophilicity | 0.936 |
| Buriedness | 0.616 |
| Don/acc character | 1.373 |
| SiteScore | 0.828 |
| D Score | 0.636 |
| Kd | — |
| Compound | PRF |
| Residue | . / 106 |
| Chain | ZA / D |
| Non-redundant | False |
| Interacting RNA chains | D/D |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | D/D: riboswitch |
| RNA family global | riboswitch |
| Volume | 87.81 Å3 |
| Hydrophobicity | 0.705 |
| Hydrophilicity | 0.835 |
| Buriedness | 0.627 |
| Don/acc character | 2.007 |
| SiteScore | 0.811 |
| D Score | 0.619 |
| Kd | — |