Complex 8fc5
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 | 2.65 |
| System mass | 4427.72 kDa |
| Deposition year | 2022 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Thermus |
| RCSB PDB Entry | 8fc5 |
| Reference | Chen Chih-Wei, Leimer Nadja, Syroegin Egor A., Dunand Clémence, Bulman Zackery P., Lewis Kim, Polikanov Yury S., Svetlov Maxim S.. 2023. Structural insights into the mechanism of overcoming Erm-mediated resistance by macrolides acting together with hygromycin-A Nature Communications |
| Equivalence Class |
NR_all_97519.80,
NR_all_42622.80
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 | ARG |
| Residue | . / 230 |
| Chain | ZRA / 1B |
| Non-redundant | True |
| Interacting RNA chains | B/1B |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | B/1B: rRNA |
| RNA family global | rRNA |
| Volume | 218.83 Å3 |
| Hydrophobicity | 0.015 |
| Hydrophilicity | 1.851 |
| Buriedness | 0.576 |
| Don/acc character | 1.070 |
| SiteScore | 1.042 |
| D Score | 0.649 |
| Kd | — |
| Compound | ARG |
| Residue | . / 319 |
| Chain | UTA / 1F |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | - |
| Hydrophobicity | - |
| Hydrophilicity | - |
| Buriedness | - |
| Don/acc character | - |
| SiteScore | - |
| D Score | - |
| Kd | — |
| Compound | HGR |
| Residue | . / 4032 |
| Chain | TQA / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | ion, other |
| RNA environment global | RNA/Other |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | 498.38 Å3 |
| Hydrophobicity | 1.017 |
| Hydrophilicity | 0.939 |
| Buriedness | 0.801 |
| Don/acc character | 0.852 |
| SiteScore | 1.238 |
| D Score | 1.114 |
| Kd | — |
| Compound | HGR |
| Residue | . / 3712 |
| Chain | SKC / 2A |
| Non-redundant | True |
| Interacting RNA chains | BB/2A |
| RNA environment detailled | ion, other |
| RNA environment global | RNA/Other |
| RNA family chains | BB/2A: rRNA |
| RNA family global | rRNA |
| Volume | 507.30 Å3 |
| Hydrophobicity | 0.834 |
| Hydrophilicity | 1.407 |
| Buriedness | 0.773 |
| Don/acc character | 0.540 |
| SiteScore | 1.200 |
| D Score | 0.945 |
| Kd | — |
| Compound | ZIT |
| Residue | . / 4033 |
| Chain | UQA / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | protein, ion, other |
| RNA environment global | RNA/Other |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | 370.78 Å3 |
| Hydrophobicity | 0.319 |
| Hydrophilicity | 0.994 |
| Buriedness | 0.729 |
| Don/acc character | 0.791 |
| SiteScore | 1.142 |
| D Score | 1.005 |
| Kd | — |
| Compound | ZIT |
| Residue | . / 3713 |
| Chain | TKC / 2A |
| Non-redundant | True |
| Interacting RNA chains | BB/2A |
| RNA environment detailled | protein, ion, other |
| RNA environment global | RNA/Other |
| RNA family chains | BB/2A: rRNA |
| RNA family global | rRNA |
| Volume | 350.55 Å3 |
| Hydrophobicity | 0.913 |
| Hydrophilicity | 0.719 |
| Buriedness | 0.724 |
| Don/acc character | 1.325 |
| SiteScore | 1.210 |
| D Score | 1.116 |
| Kd | — |