Complex 8p8b
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 | Electron Microscopy |
| Experimental resolution | 2.90 |
| System mass | 2044.19 kDa |
| Deposition year | 2023 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Mycoplasmoides |
| RCSB PDB Entry | 8p8b |
| Reference | Xue Liang, Spahn Christian M. T., Schacherl Magdalena, Mahamid Julia. 2025. Structural insights into context-dependent inhibitory mechanisms of chloramphenicol in cells Nature Structural & Molecular Biology |
| Equivalence Class |
NR_all_06181.4
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 | CLM |
| Residue | . / 3001 |
| Chain | NA / 3 |
| Non-redundant | True |
| Interacting RNA chains | D/3 |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | D/3: rRNA |
| RNA family global | rRNA |
| Volume | 734.02 Å3 |
| Hydrophobicity | 0.545 |
| Hydrophilicity | 1.160 |
| Buriedness | 0.797 |
| Don/acc character | 1.042 |
| SiteScore | 1.216 |
| D Score | 1.040 |
| Kd | — |
| Compound | SPM |
| Residue | . / 3227 |
| Chain | FJ / 3 |
| Non-redundant | True |
| Interacting RNA chains | D/3 |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | D/3: rRNA |
| RNA family global | rRNA |
| Volume | 693.20 Å3 |
| Hydrophobicity | 0.453 |
| Hydrophilicity | 1.441 |
| Buriedness | 0.824 |
| Don/acc character | 0.836 |
| SiteScore | 1.085 |
| D Score | 0.965 |
| Kd | — |
| Compound | SPM |
| Residue | . / 3241 |
| Chain | TJ / 3 |
| Non-redundant | True |
| Interacting RNA chains | D/3 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | D/3: rRNA |
| RNA family global | rRNA |
| Volume | 404.40 Å3 |
| Hydrophobicity | 0.702 |
| Hydrophilicity | 1.019 |
| Buriedness | 0.807 |
| Don/acc character | 1.593 |
| SiteScore | 1.227 |
| D Score | 1.092 |
| Kd | — |
| Compound | SPM |
| Residue | . / 3249 |
| Chain | BK / 3 |
| Non-redundant | True |
| Interacting RNA chains | D/3 |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | D/3: rRNA |
| RNA family global | rRNA |
| Volume | 707.95 Å3 |
| Hydrophobicity | 0.396 |
| Hydrophilicity | 1.192 |
| Buriedness | 0.755 |
| Don/acc character | 1.129 |
| SiteScore | 1.188 |
| D Score | 1.004 |
| Kd | — |
| Compound | SPM |
| Residue | . / 303 |
| Chain | LK / b |
| Non-redundant | True |
| Interacting RNA chains | D/3 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | D/3: rRNA |
| RNA family global | rRNA |
| Volume | 383.47 Å3 |
| Hydrophobicity | 0.216 |
| Hydrophilicity | 1.148 |
| Buriedness | 0.856 |
| Don/acc character | 1.106 |
| SiteScore | 1.041 |
| D Score | 0.996 |
| Kd | — |