Complex 4e8k
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 | 3.03 |
| System mass | 133.91 kDa |
| Deposition year | 2012 |
| Molecule type | RNA |
| # RNA entities | 1 |
| Organism | Oceanobacillus |
| RCSB PDB Entry | 4e8k |
| Reference | Marcia Marco, Pyle Anna Marie. 2012. Visualizing Group II Intron Catalysis through the Stages of Splicing Cell |
| Equivalence Class |
NR_all_35054.12
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 | EPE |
| Residue | . / 441 |
| Chain | QA / A |
| Non-redundant | False |
| Interacting RNA chains | A/A |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/A: ribozyme |
| RNA family global | ribozyme |
| Volume | - |
| Hydrophobicity | - |
| Hydrophilicity | - |
| Buriedness | - |
| Don/acc character | - |
| SiteScore | - |
| D Score | - |
| Kd | — |
| Compound | EPE |
| Residue | . / 443 |
| Chain | SA / A |
| Non-redundant | False |
| Interacting RNA chains | A/A |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/A: ribozyme |
| RNA family global | ribozyme |
| Volume | 69.29 Å3 |
| Hydrophobicity | 0.545 |
| Hydrophilicity | 0.709 |
| Buriedness | 0.661 |
| Don/acc character | 1.092 |
| SiteScore | 0.699 |
| D Score | 0.477 |
| Kd | — |
| Compound | EPE |
| Residue | . / 446 |
| Chain | VA / A |
| Non-redundant | False |
| Interacting RNA chains | A/A |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/A: ribozyme |
| RNA family global | ribozyme |
| Volume | 242.50 Å3 |
| Hydrophobicity | 0.063 |
| Hydrophilicity | 0.928 |
| Buriedness | 0.668 |
| Don/acc character | 1.611 |
| SiteScore | 0.865 |
| D Score | 0.670 |
| Kd | — |
| Compound | EPE |
| Residue | . / 447 |
| Chain | WA / A |
| Non-redundant | True |
| Interacting RNA chains | A/A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/A: ribozyme |
| RNA family global | ribozyme |
| Volume | 212.66 Å3 |
| Hydrophobicity | 0.016 |
| Hydrophilicity | 0.666 |
| Buriedness | 0.482 |
| Don/acc character | 3.106 |
| SiteScore | 1.078 |
| D Score | 1.012 |
| Kd | — |
| Compound | EPE |
| Residue | . / 448 |
| Chain | XA / A |
| Non-redundant | False |
| Interacting RNA chains | A/A |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/A: ribozyme |
| RNA family global | ribozyme |
| Volume | 116.96 Å3 |
| Hydrophobicity | 0.019 |
| Hydrophilicity | 0.819 |
| Buriedness | 0.535 |
| Don/acc character | 2.700 |
| SiteScore | 1.084 |
| D Score | 0.994 |
| Kd | — |
| Compound | SPM |
| Residue | . / 445 |
| Chain | UA / A |
| Non-redundant | False |
| Interacting RNA chains | A/A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/A: ribozyme |
| RNA family global | ribozyme |
| Volume | 254.51 Å3 |
| Hydrophobicity | 0.253 |
| Hydrophilicity | 1.124 |
| Buriedness | 0.701 |
| Don/acc character | 1.755 |
| SiteScore | 0.973 |
| D Score | 0.764 |
| Kd | — |