Complex 8k82
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 | 3.00 |
| System mass | 3288.58 kDa |
| Deposition year | 2023 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Saccharomyces |
| RCSB PDB Entry | 8k82 |
| Reference | Li Xiang, Wang Mengjiao, Denk Timo, Buschauer Robert, Li Yi, Beckmann Roland, Cheng Jingdong. 2024. Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline Nature Communications |
| Equivalence Class |
NR_all_90506.85,
NR_all_03510.74
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 | T1C |
| Residue | . / 1990 |
| Chain | SF / C2 |
| Non-redundant | True |
| Interacting RNA chains | A/C2 |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/C2: rRNA |
| RNA family global | rRNA |
| Volume | 302.87 Å3 |
| Hydrophobicity | 0.022 |
| Hydrophilicity | 1.125 |
| Buriedness | 0.716 |
| Don/acc character | 2.229 |
| SiteScore | 1.072 |
| D Score | 0.888 |
| Kd | — |
| Compound | T1C |
| Residue | . / 3401 |
| Chain | WF / C1 |
| Non-redundant | True |
| Interacting RNA chains | D/C1 |
| RNA environment detailled | other |
| RNA environment global | RNA/Other |
| RNA family chains | D/C1: rRNA |
| RNA family global | rRNA |
| Volume | 188.99 Å3 |
| Hydrophobicity | 0.028 |
| Hydrophilicity | 1.455 |
| Buriedness | 0.671 |
| Don/acc character | 1.569 |
| SiteScore | 0.976 |
| D Score | 0.668 |
| Kd | — |
| Compound | T1C |
| Residue | . / 3402 |
| Chain | XF / C1 |
| Non-redundant | True |
| Interacting RNA chains | D/C1 |
| RNA environment detailled | protein, other |
| RNA environment global | RNA/Other |
| RNA family chains | D/C1: rRNA |
| RNA family global | rRNA |
| Volume | 408.17 Å3 |
| Hydrophobicity | 0.055 |
| Hydrophilicity | 1.453 |
| Buriedness | 0.706 |
| Don/acc character | 1.270 |
| SiteScore | 1.155 |
| D Score | 0.890 |
| Kd | — |
| Compound | T1C |
| Residue | . / 3403 |
| Chain | YF / C1 |
| Non-redundant | True |
| Interacting RNA chains | D/C1, F/C3 |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | D/C1: rRNA, F/C3: rRNA |
| RNA family global | rRNA |
| Volume | 325.16 Å3 |
| Hydrophobicity | 0.296 |
| Hydrophilicity | 1.111 |
| Buriedness | 0.710 |
| Don/acc character | 2.009 |
| SiteScore | 0.788 |
| D Score | 0.722 |
| Kd | — |
| Compound | T1C |
| Residue | . / 3404 |
| Chain | ZF / C1 |
| Non-redundant | True |
| Interacting RNA chains | D/C1 |
| RNA environment detailled | ion, other |
| RNA environment global | RNA/Other |
| RNA family chains | D/C1: rRNA |
| RNA family global | rRNA |
| Volume | 558.40 Å3 |
| Hydrophobicity | 0.149 |
| Hydrophilicity | 1.383 |
| Buriedness | 0.668 |
| Don/acc character | 0.912 |
| SiteScore | 0.980 |
| D Score | 0.890 |
| Kd | — |
| Compound | T1C |
| Residue | . / 3405 |
| Chain | AG / C1 |
| Non-redundant | True |
| Interacting RNA chains | D/C1 |
| RNA environment detailled | ion, other |
| RNA environment global | RNA/Other |
| RNA family chains | D/C1: rRNA |
| RNA family global | rRNA |
| Volume | 373.18 Å3 |
| Hydrophobicity | 0.064 |
| Hydrophilicity | 1.505 |
| Buriedness | 0.655 |
| Don/acc character | 1.060 |
| SiteScore | 0.729 |
| D Score | 0.842 |
| Kd | — |