Complex 8ifd
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 | 2.59 |
| System mass | 3825.79 kDa |
| Deposition year | 2023 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Homo |
| RCSB PDB Entry | 8ifd |
| Reference | Tomono Junta, Asano Kosuke, Chiashi Takuma, Suzuki Masato, Igarashi Masayuki, Takahashi Yoshiaki, Tanaka Yoshikazu, Yokoyama Takeshi. 2024. Direct visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside The Journal of Biochemistry |
| Equivalence Class |
NR_all_65061.63,
NR_all_46995.72,
NR_all_52752.59
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 | 84D |
| Residue | . / 5101 |
| Chain | CC / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | 238.73 Å3 |
| Hydrophobicity | 0.115 |
| Hydrophilicity | 1.074 |
| Buriedness | 0.668 |
| Don/acc character | 1.597 |
| SiteScore | 0.969 |
| D Score | 0.785 |
| Kd | — |
| Compound | 84D |
| Residue | . / 5102 |
| Chain | DC / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | 208.89 Å3 |
| Hydrophobicity | 0.491 |
| Hydrophilicity | 0.916 |
| Buriedness | 0.808 |
| Don/acc character | 1.745 |
| SiteScore | 0.817 |
| D Score | 0.766 |
| Kd | — |
| Compound | 84D |
| Residue | . / 5103 |
| Chain | EC / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | 201.68 Å3 |
| Hydrophobicity | 0.152 |
| Hydrophilicity | 1.045 |
| Buriedness | 0.620 |
| Don/acc character | 1.531 |
| SiteScore | 0.873 |
| D Score | 0.683 |
| Kd | — |
| Compound | 84D |
| Residue | . / 5104 |
| Chain | FC / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | 569.04 Å3 |
| Hydrophobicity | 0.019 |
| Hydrophilicity | 1.794 |
| Buriedness | 0.812 |
| Don/acc character | 1.134 |
| SiteScore | 1.080 |
| D Score | 0.654 |
| Kd | — |
| Compound | 84D |
| Residue | . / 5105 |
| Chain | GC / 1A |
| 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 | 548.11 Å3 |
| Hydrophobicity | 0.140 |
| Hydrophilicity | 1.304 |
| Buriedness | 0.684 |
| Don/acc character | 1.508 |
| SiteScore | 1.141 |
| D Score | 0.925 |
| Kd | — |
| Compound | 84D |
| Residue | . / 5106 |
| Chain | HC / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A, C/1C |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1A: rRNA, C/1C: rRNA |
| RNA family global | rRNA |
| Volume | 451.39 Å3 |
| Hydrophobicity | 0.174 |
| Hydrophilicity | 1.306 |
| Buriedness | 0.822 |
| Don/acc character | 1.423 |
| SiteScore | 1.026 |
| D Score | 0.934 |
| Kd | — |
| Compound | 84D |
| Residue | . / 5107 |
| Chain | IC / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | 773.12 Å3 |
| Hydrophobicity | 0.259 |
| Hydrophilicity | 1.068 |
| Buriedness | 0.730 |
| Don/acc character | 3.037 |
| SiteScore | 1.171 |
| D Score | 1.030 |
| Kd | — |
| Compound | 84D |
| Residue | . / 5108 |
| Chain | JC / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | 441.10 Å3 |
| Hydrophobicity | 0.108 |
| Hydrophilicity | 1.050 |
| Buriedness | 0.711 |
| Don/acc character | 1.441 |
| SiteScore | 0.898 |
| D Score | 0.882 |
| Kd | — |
| Compound | 84D |
| Residue | . / 5109 |
| Chain | KC / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | 249.70 Å3 |
| Hydrophobicity | 0.010 |
| Hydrophilicity | 2.325 |
| Buriedness | 0.770 |
| Don/acc character | 0.389 |
| SiteScore | 0.962 |
| D Score | 0.341 |
| Kd | — |
| Compound | 84D |
| Residue | . / 5110 |
| Chain | LC / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | 624.95 Å3 |
| Hydrophobicity | 0.058 |
| Hydrophilicity | 1.860 |
| Buriedness | 0.780 |
| Don/acc character | 1.022 |
| SiteScore | 1.186 |
| D Score | 0.778 |
| Kd | — |
| Compound | 84D |
| Residue | . / 5111 |
| Chain | MC / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | 780.33 Å3 |
| Hydrophobicity | 0.105 |
| Hydrophilicity | 1.603 |
| Buriedness | 0.753 |
| Don/acc character | 0.989 |
| SiteScore | 1.187 |
| D Score | 0.869 |
| Kd | — |
| Compound | 84D |
| Residue | . / 5112 |
| Chain | NC / 1A |
| 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 | 84D |
| Residue | . / 5113 |
| Chain | OC / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A, B/1B |
| RNA environment detailled | ion, other |
| RNA environment global | RNA/Other |
| RNA family chains | A/1A: rRNA, B/1B: rRNA |
| RNA family global | rRNA |
| Volume | 649.99 Å3 |
| Hydrophobicity | 0.149 |
| Hydrophilicity | 1.234 |
| Buriedness | 0.733 |
| Don/acc character | 1.151 |
| SiteScore | 1.173 |
| D Score | 0.978 |
| Kd | — |
| Compound | 84D |
| Residue | . / 5114 |
| Chain | PC / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A, UA/2m |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1A: rRNA, UA/2m: rRNA |
| RNA family global | rRNA |
| Volume | 278.17 Å3 |
| Hydrophobicity | 0.042 |
| Hydrophilicity | 1.228 |
| Buriedness | 0.738 |
| Don/acc character | 1.177 |
| SiteScore | 0.671 |
| D Score | 0.637 |
| Kd | — |
| Compound | 84D |
| Residue | . / 5115 |
| Chain | QC / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A, B/1B |
| RNA environment detailled | protein, other |
| RNA environment global | RNA/Other |
| RNA family chains | A/1A: rRNA, B/1B: rRNA |
| RNA family global | rRNA |
| Volume | 147.83 Å3 |
| Hydrophobicity | 0.189 |
| Hydrophilicity | 0.959 |
| Buriedness | 0.759 |
| Don/acc character | 3.236 |
| SiteScore | 0.884 |
| D Score | 0.519 |
| Kd | — |
| Compound | 84D |
| Residue | . / 5116 |
| Chain | RC / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | 225.69 Å3 |
| Hydrophobicity | 0.161 |
| Hydrophilicity | 1.175 |
| Buriedness | 0.733 |
| Don/acc character | 2.305 |
| SiteScore | 0.776 |
| D Score | 0.488 |
| Kd | — |
| Compound | 84D |
| Residue | . / 5117 |
| Chain | SC / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | protein, other |
| RNA environment global | RNA/Other |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | 261.71 Å3 |
| Hydrophobicity | 0.263 |
| Hydrophilicity | 1.203 |
| Buriedness | 0.771 |
| Don/acc character | 1.123 |
| SiteScore | 0.697 |
| D Score | 0.559 |
| Kd | — |
| Compound | 84D |
| Residue | . / 5118 |
| Chain | TC / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | protein, other |
| RNA environment global | RNA/Other |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | 208.89 Å3 |
| Hydrophobicity | 0.204 |
| Hydrophilicity | 1.025 |
| Buriedness | 0.794 |
| Don/acc character | 1.618 |
| SiteScore | 0.627 |
| D Score | 0.518 |
| Kd | — |
| Compound | 84D |
| Residue | . / 5119 |
| Chain | UC / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | 287.09 Å3 |
| Hydrophobicity | 0.063 |
| Hydrophilicity | 1.133 |
| Buriedness | 0.657 |
| Don/acc character | 1.765 |
| SiteScore | 1.119 |
| D Score | 0.960 |
| Kd | — |
| Compound | 84D |
| Residue | . / 5120 |
| Chain | VC / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | 678.80 Å3 |
| Hydrophobicity | 0.148 |
| Hydrophilicity | 0.936 |
| Buriedness | 0.713 |
| Don/acc character | 2.160 |
| SiteScore | 1.131 |
| D Score | 1.000 |
| Kd | — |
| Compound | 84D |
| Residue | . / 5121 |
| Chain | WC / 1A |
| 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 | 329.62 Å3 |
| Hydrophobicity | 0.100 |
| Hydrophilicity | 1.474 |
| Buriedness | 0.758 |
| Don/acc character | 1.124 |
| SiteScore | 0.865 |
| D Score | 0.690 |
| Kd | — |
| Compound | 84D |
| Residue | . / 1901 |
| Chain | CO / 2m |
| Non-redundant | True |
| Interacting RNA chains | UA/2m |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | UA/2m: rRNA |
| RNA family global | rRNA |
| Volume | 146.46 Å3 |
| Hydrophobicity | 0.102 |
| Hydrophilicity | 0.955 |
| Buriedness | 0.668 |
| Don/acc character | 2.285 |
| SiteScore | 0.697 |
| D Score | 0.453 |
| Kd | — |
| Compound | 84D |
| Residue | . / 1902 |
| Chain | DO / 2m |
| Non-redundant | True |
| Interacting RNA chains | UA/2m |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | UA/2m: rRNA |
| RNA family global | rRNA |
| Volume | 306.64 Å3 |
| Hydrophobicity | 0.260 |
| Hydrophilicity | 0.893 |
| Buriedness | 0.604 |
| Don/acc character | 1.432 |
| SiteScore | 1.115 |
| D Score | 1.011 |
| Kd | — |
| Compound | 84D |
| Residue | . / 1903 |
| Chain | EO / 2m |
| Non-redundant | True |
| Interacting RNA chains | UA/2m |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | UA/2m: rRNA |
| RNA family global | rRNA |
| Volume | 732.31 Å3 |
| Hydrophobicity | 0.038 |
| Hydrophilicity | 1.081 |
| Buriedness | 0.724 |
| Don/acc character | 2.335 |
| SiteScore | 0.902 |
| D Score | 0.874 |
| Kd | — |