Complex 8k2d
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 | 3.20 |
| System mass | 3327.24 kDa |
| Deposition year | 2023 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Saccharomyces |
| RCSB PDB Entry | 8k2d |
| 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 | GDP |
| Residue | . / 902 |
| Chain | ZC / CD |
| Non-redundant | True |
| Interacting RNA chains | B/C1 |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | B/C1: rRNA |
| RNA family global | rRNA |
| Volume | 451.73 Å3 |
| Hydrophobicity | 0.195 |
| Hydrophilicity | 1.757 |
| Buriedness | 0.744 |
| Don/acc character | 0.920 |
| SiteScore | 1.031 |
| D Score | 0.814 |
| Kd | — |
| Compound | T1C |
| Residue | . / 3401 |
| Chain | HC / C1 |
| Non-redundant | True |
| Interacting RNA chains | B/C1, A/C2 |
| RNA environment detailled | other |
| RNA environment global | RNA/Other |
| RNA family chains | A/C2: rRNA, B/C1: rRNA |
| RNA family global | rRNA |
| Volume | 388.96 Å3 |
| Hydrophobicity | 0.251 |
| Hydrophilicity | 1.078 |
| Buriedness | 0.653 |
| Don/acc character | 2.776 |
| SiteScore | 1.120 |
| D Score | 0.980 |
| Kd | — |
| Compound | T1C |
| Residue | . / 3402 |
| Chain | IC / C1 |
| Non-redundant | True |
| Interacting RNA chains | B/C1 |
| RNA environment detailled | other |
| RNA environment global | RNA/Other |
| RNA family chains | B/C1: rRNA |
| RNA family global | rRNA |
| Volume | 459.62 Å3 |
| Hydrophobicity | 0.180 |
| Hydrophilicity | 1.256 |
| Buriedness | 0.718 |
| Don/acc character | 2.703 |
| SiteScore | 1.163 |
| D Score | 0.961 |
| Kd | — |
| Compound | T1C |
| Residue | . / 3403 |
| Chain | JC / C1 |
| Non-redundant | True |
| Interacting RNA chains | B/C1 |
| RNA environment detailled | other |
| RNA environment global | RNA/Other |
| RNA family chains | B/C1: rRNA |
| RNA family global | rRNA |
| Volume | 779.30 Å3 |
| Hydrophobicity | 0.278 |
| Hydrophilicity | 1.152 |
| Buriedness | 0.721 |
| Don/acc character | 1.798 |
| SiteScore | 1.166 |
| D Score | 0.997 |
| Kd | — |
| Compound | T1C |
| Residue | . / 3404 |
| Chain | KC / C1 |
| Non-redundant | True |
| Interacting RNA chains | B/C1, D/C3 |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | B/C1: rRNA, D/C3: rRNA |
| RNA family global | rRNA |
| Volume | 724.42 Å3 |
| Hydrophobicity | 0.327 |
| Hydrophilicity | 1.067 |
| Buriedness | 0.664 |
| Don/acc character | 1.123 |
| SiteScore | 0.977 |
| D Score | 0.991 |
| Kd | — |
| Compound | T1C |
| Residue | . / 3405 |
| Chain | LC / C1 |
| Non-redundant | True |
| Interacting RNA chains | B/C1 |
| RNA environment detailled | ion, other |
| RNA environment global | RNA/Other |
| RNA family chains | B/C1: rRNA |
| RNA family global | rRNA |
| Volume | 692.52 Å3 |
| Hydrophobicity | 0.195 |
| Hydrophilicity | 1.118 |
| Buriedness | 0.659 |
| Don/acc character | 0.979 |
| SiteScore | 0.974 |
| D Score | 0.971 |
| Kd | — |
| Compound | T1C |
| Residue | . / 3406 |
| Chain | MC / C1 |
| Non-redundant | True |
| Interacting RNA chains | B/C1 |
| RNA environment detailled | ion, other |
| RNA environment global | RNA/Other |
| RNA family chains | B/C1: rRNA |
| RNA family global | rRNA |
| Volume | 351.23 Å3 |
| Hydrophobicity | 0.058 |
| Hydrophilicity | 1.679 |
| Buriedness | 0.656 |
| Don/acc character | 0.943 |
| SiteScore | 0.823 |
| D Score | 0.786 |
| Kd | — |