Complex 8cgd
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 | 1.98 |
| System mass | 1353.56 kDa |
| Deposition year | 2023 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Escherichia |
| RCSB PDB Entry | 8cgd |
| Reference | Paternoga Helge, Crowe-McAuliffe Caillan, Bock Lars V., Koller Timm O., Morici Martino, Beckert Bertrand, Myasnikov Alexander G., Grubmüller Helmut, Nováček Jiří, Wilson Daniel N.. 2023. Structural conservation of antibiotic interaction with ribosomes Nature Structural & Molecular Biology |
| Equivalence Class |
NR_all_83717.187
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 | AM2 |
| Residue | . / 3003 |
| Chain | HA / a |
| Non-redundant | True |
| Interacting RNA chains | E/a |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | E/a: rRNA |
| RNA family global | rRNA |
| Volume | 247.65 Å3 |
| Hydrophobicity | 0.194 |
| Hydrophilicity | 0.811 |
| Buriedness | 0.790 |
| Don/acc character | 1.369 |
| SiteScore | 0.616 |
| D Score | 0.522 |
| Kd | — |
| Compound | CLY |
| Residue | . / 3002 |
| Chain | GA / a |
| Non-redundant | True |
| Interacting RNA chains | E/a |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | E/a: rRNA |
| RNA family global | rRNA |
| Volume | 585.50 Å3 |
| Hydrophobicity | 0.419 |
| Hydrophilicity | 1.163 |
| Buriedness | 0.786 |
| Don/acc character | 1.514 |
| SiteScore | 1.209 |
| D Score | 1.032 |
| Kd | — |