Complex 8ife
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 | 2.57 |
| System mass | 3828.11 kDa |
| Deposition year | 2023 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Homo |
| RCSB PDB Entry | 8ife |
| 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 | 84G |
| Residue | . / 5101 |
| Chain | CC / 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 | 722.02 Å3 |
| Hydrophobicity | 0.154 |
| Hydrophilicity | 1.405 |
| Buriedness | 0.710 |
| Don/acc character | 1.392 |
| SiteScore | 1.008 |
| D Score | 0.908 |
| Kd | — |
| Compound | 84G |
| Residue | . / 5102 |
| Chain | DC / 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 | 525.82 Å3 |
| Hydrophobicity | 0.071 |
| Hydrophilicity | 1.356 |
| Buriedness | 0.680 |
| Don/acc character | 0.916 |
| SiteScore | 1.073 |
| D Score | 0.822 |
| Kd | — |
| Compound | 84G |
| Residue | . / 5103 |
| Chain | EC / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A, B/1B |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1A: rRNA, B/1B: rRNA |
| RNA family global | rRNA |
| Volume | 399.94 Å3 |
| Hydrophobicity | 0.086 |
| Hydrophilicity | 0.918 |
| Buriedness | 0.615 |
| Don/acc character | 1.600 |
| SiteScore | 1.118 |
| D Score | 1.010 |
| Kd | — |
| Compound | 84G |
| Residue | . / 1901 |
| Chain | DO / 2m |
| Non-redundant | True |
| Interacting RNA chains | UA/2m |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | UA/2m: rRNA |
| RNA family global | rRNA |
| Volume | 362.21 Å3 |
| Hydrophobicity | 0.117 |
| Hydrophilicity | 1.384 |
| Buriedness | 0.650 |
| Don/acc character | 0.913 |
| SiteScore | 1.118 |
| D Score | 0.879 |
| Kd | — |
| Compound | 84G |
| Residue | . / 5104 |
| Chain | FC / 1A |
| Non-redundant | True |
| Interacting RNA chains | C/1C, A/1A |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1A: rRNA, C/1C: rRNA |
| RNA family global | rRNA |
| Volume | 153.66 Å3 |
| Hydrophobicity | 0.020 |
| Hydrophilicity | 1.071 |
| Buriedness | 0.662 |
| Don/acc character | 2.519 |
| SiteScore | 0.670 |
| D Score | 0.596 |
| Kd | — |
| Compound | 84G |
| 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 | 274.06 Å3 |
| Hydrophobicity | 0.127 |
| Hydrophilicity | 1.393 |
| Buriedness | 0.626 |
| Don/acc character | 1.300 |
| SiteScore | 1.101 |
| D Score | 0.861 |
| Kd | — |
| Compound | 84G |
| Residue | . / 5106 |
| Chain | HC / 1A |
| Non-redundant | True |
| Interacting RNA chains | C/1C, A/1A |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1A: rRNA, C/1C: rRNA |
| RNA family global | rRNA |
| Volume | 466.14 Å3 |
| Hydrophobicity | 0.198 |
| Hydrophilicity | 0.985 |
| Buriedness | 0.659 |
| Don/acc character | 1.662 |
| SiteScore | 1.135 |
| D Score | 1.015 |
| Kd | — |
| Compound | 84G |
| Residue | . / 5107 |
| Chain | IC / 1A |
| Non-redundant | True |
| Interacting RNA chains | C/1C, A/1A |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1A: rRNA, C/1C: rRNA |
| RNA family global | rRNA |
| Volume | 697.32 Å3 |
| Hydrophobicity | 0.186 |
| Hydrophilicity | 1.942 |
| Buriedness | 0.800 |
| Don/acc character | 0.926 |
| SiteScore | 1.068 |
| D Score | 0.787 |
| Kd | — |
| Compound | 84G |
| Residue | . / 5108 |
| Chain | JC / 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 | 531.31 Å3 |
| Hydrophobicity | 0.570 |
| Hydrophilicity | 0.810 |
| Buriedness | 0.765 |
| Don/acc character | 1.159 |
| SiteScore | 1.089 |
| D Score | 1.135 |
| Kd | — |
| Compound | 84G |
| 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 | 458.59 Å3 |
| Hydrophobicity | 0.138 |
| Hydrophilicity | 1.036 |
| Buriedness | 0.704 |
| Don/acc character | 0.886 |
| SiteScore | 1.005 |
| D Score | 1.025 |
| Kd | — |
| Compound | 84G |
| Residue | . / 5110 |
| Chain | LC / 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 | 774.15 Å3 |
| Hydrophobicity | 0.121 |
| Hydrophilicity | 1.179 |
| Buriedness | 0.704 |
| Don/acc character | 2.142 |
| SiteScore | 1.154 |
| D Score | 0.978 |
| Kd | — |
| Compound | 84G |
| Residue | . / 5111 |
| Chain | MC / 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 | 433.90 Å3 |
| Hydrophobicity | 0.078 |
| Hydrophilicity | 1.200 |
| Buriedness | 0.796 |
| Don/acc character | 2.716 |
| SiteScore | 0.975 |
| D Score | 0.710 |
| Kd | — |
| Compound | 84G |
| 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 | 560.46 Å3 |
| Hydrophobicity | 0.028 |
| Hydrophilicity | 1.326 |
| Buriedness | 0.650 |
| Don/acc character | 1.354 |
| SiteScore | 1.118 |
| D Score | 0.898 |
| Kd | — |
| Compound | 84G |
| Residue | . / 5113 |
| Chain | OC / 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 | 40.13 Å3 |
| Hydrophobicity | 0.154 |
| Hydrophilicity | 1.041 |
| Buriedness | 0.584 |
| Don/acc character | 4.305 |
| SiteScore | 0.519 |
| D Score | 0.432 |
| Kd | — |
| Compound | 84G |
| Residue | . / 5114 |
| Chain | PC / 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 | - |
| Hydrophobicity | - |
| Hydrophilicity | - |
| Buriedness | - |
| Don/acc character | - |
| SiteScore | - |
| D Score | - |
| Kd | — |
| Compound | 84G |
| Residue | . / 5115 |
| Chain | QC / 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 | 144.75 Å3 |
| Hydrophobicity | 0.000 |
| Hydrophilicity | 1.946 |
| Buriedness | 0.710 |
| Don/acc character | 0.841 |
| SiteScore | 0.865 |
| D Score | 0.356 |
| Kd | — |
| Compound | 84G |
| Residue | . / 5116 |
| Chain | RC / 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 | 456.88 Å3 |
| Hydrophobicity | 0.008 |
| Hydrophilicity | 2.037 |
| Buriedness | 0.811 |
| Don/acc character | 0.983 |
| SiteScore | 1.060 |
| D Score | 0.551 |
| Kd | — |
| Compound | 84G |
| Residue | . / 5117 |
| Chain | SC / 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 | 94.67 Å3 |
| Hydrophobicity | 0.110 |
| Hydrophilicity | 0.922 |
| Buriedness | 0.605 |
| Don/acc character | 2.327 |
| SiteScore | 0.831 |
| D Score | 0.513 |
| Kd | — |
| Compound | 84G |
| Residue | . / 5118 |
| Chain | TC / 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 | 348.49 Å3 |
| Hydrophobicity | 0.036 |
| Hydrophilicity | 1.351 |
| Buriedness | 0.720 |
| Don/acc character | 1.243 |
| SiteScore | 0.820 |
| D Score | 0.682 |
| Kd | — |
| Compound | 84G |
| Residue | . / 5119 |
| Chain | UC / 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 | 233.93 Å3 |
| Hydrophobicity | 0.010 |
| Hydrophilicity | 1.168 |
| Buriedness | 0.670 |
| Don/acc character | 2.497 |
| SiteScore | 0.751 |
| D Score | 0.666 |
| Kd | — |
| Compound | 84G |
| Residue | . / 301 |
| Chain | NN / 2D |
| Non-redundant | True |
| Interacting RNA chains | A/1A, B/1B |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1A: rRNA, B/1B: rRNA |
| RNA family global | rRNA |
| Volume | 103.59 Å3 |
| Hydrophobicity | 0.116 |
| Hydrophilicity | 1.191 |
| Buriedness | 0.636 |
| Don/acc character | 1.147 |
| SiteScore | 0.599 |
| D Score | 0.473 |
| Kd | — |
| Compound | 84G |
| Residue | . / 201 |
| Chain | AO / 2i |
| 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 | 308.70 Å3 |
| Hydrophobicity | 0.508 |
| Hydrophilicity | 1.003 |
| Buriedness | 0.653 |
| Don/acc character | 0.729 |
| SiteScore | 0.840 |
| D Score | 0.828 |
| Kd | — |
| Compound | 84G |
| Residue | . / 1902 |
| 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 | 569.04 Å3 |
| Hydrophobicity | 0.166 |
| Hydrophilicity | 1.098 |
| Buriedness | 0.691 |
| Don/acc character | 2.358 |
| SiteScore | 0.995 |
| D Score | 0.997 |
| Kd | — |