Complex 8ifc
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 | 2.90 |
| System mass | 2212.47 kDa |
| Deposition year | 2023 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Escherichia |
| RCSB PDB Entry | 8ifc |
| 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_35542.167,
NR_all_83717.187,
NR_all_56726.172
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 | . / 1791 |
| Chain | LI / A |
| Non-redundant | True |
| Interacting RNA chains | CB/7, A/A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/A: rRNA, CB/7: mRNA |
| RNA family global | multiple |
| Volume | 270.63 Å3 |
| Hydrophobicity | 0.057 |
| Hydrophilicity | 0.983 |
| Buriedness | 0.690 |
| Don/acc character | 1.553 |
| SiteScore | 0.836 |
| D Score | 0.816 |
| Kd | — |
| Compound | 84G |
| Residue | . / 1792 |
| Chain | MI / A |
| Non-redundant | True |
| Interacting RNA chains | A/A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/A: rRNA |
| RNA family global | rRNA |
| Volume | 194.14 Å3 |
| Hydrophobicity | 0.222 |
| Hydrophilicity | 1.208 |
| Buriedness | 0.723 |
| Don/acc character | 1.370 |
| SiteScore | 0.998 |
| D Score | 0.528 |
| Kd | — |
| Compound | 84G |
| Residue | . / 1793 |
| Chain | NI / A |
| Non-redundant | False |
| Interacting RNA chains | A/A |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/A: rRNA |
| RNA family global | rRNA |
| Volume | 377.64 Å3 |
| Hydrophobicity | 0.170 |
| Hydrophilicity | 1.541 |
| Buriedness | 0.818 |
| Don/acc character | 1.074 |
| SiteScore | 0.943 |
| D Score | 0.752 |
| Kd | — |
| Compound | 84G |
| Residue | . / 6249 |
| Chain | US / a |
| Non-redundant | True |
| Interacting RNA chains | BB/6, V/a |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | V/a: rRNA, BB/6: tRNA |
| RNA family global | multiple |
| Volume | 586.87 Å3 |
| Hydrophobicity | 0.073 |
| Hydrophilicity | 0.986 |
| Buriedness | 0.680 |
| Don/acc character | 1.754 |
| SiteScore | 1.123 |
| D Score | 0.993 |
| Kd | — |
| Compound | 84G |
| Residue | . / 6250 |
| Chain | VS / a |
| Non-redundant | True |
| Interacting RNA chains | V/a |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | V/a: rRNA |
| RNA family global | rRNA |
| Volume | 253.48 Å3 |
| Hydrophobicity | 0.258 |
| Hydrophilicity | 1.007 |
| Buriedness | 0.758 |
| Don/acc character | 1.876 |
| SiteScore | 0.815 |
| D Score | 0.577 |
| Kd | — |
| Compound | 84G |
| Residue | . / 6251 |
| Chain | WS / a |
| Non-redundant | True |
| Interacting RNA chains | V/a |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | V/a: rRNA |
| RNA family global | rRNA |
| Volume | 473.00 Å3 |
| Hydrophobicity | 0.104 |
| Hydrophilicity | 1.150 |
| Buriedness | 0.693 |
| Don/acc character | 0.896 |
| SiteScore | 1.147 |
| D Score | 0.981 |
| Kd | — |
| Compound | 84G |
| Residue | . / 6252 |
| Chain | XS / a |
| Non-redundant | True |
| Interacting RNA chains | V/a |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | V/a: rRNA |
| RNA family global | rRNA |
| Volume | 74.09 Å3 |
| Hydrophobicity | 0.255 |
| Hydrophilicity | 0.822 |
| Buriedness | 0.596 |
| Don/acc character | 2.029 |
| SiteScore | 0.585 |
| D Score | 0.339 |
| Kd | — |
| Compound | 84G |
| Residue | . / 6253 |
| Chain | YS / a |
| Non-redundant | True |
| Interacting RNA chains | V/a |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | V/a: rRNA |
| RNA family global | rRNA |
| Volume | 187.96 Å3 |
| Hydrophobicity | 0.071 |
| Hydrophilicity | 0.870 |
| Buriedness | 0.689 |
| Don/acc character | 2.915 |
| SiteScore | 0.764 |
| D Score | 0.540 |
| Kd | — |
| Compound | 84G |
| Residue | . / 6254 |
| Chain | ZS / a |
| Non-redundant | True |
| Interacting RNA chains | V/a |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | V/a: rRNA |
| RNA family global | rRNA |
| Volume | 292.24 Å3 |
| Hydrophobicity | 0.006 |
| Hydrophilicity | 1.063 |
| Buriedness | 0.675 |
| Don/acc character | 1.764 |
| SiteScore | 0.882 |
| D Score | 0.675 |
| Kd | — |
| Compound | 84G |
| Residue | . / 6255 |
| Chain | AT / a |
| Non-redundant | True |
| Interacting RNA chains | V/a |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | V/a: rRNA |
| RNA family global | rRNA |
| Volume | 306.99 Å3 |
| Hydrophobicity | 0.093 |
| Hydrophilicity | 1.169 |
| Buriedness | 0.751 |
| Don/acc character | 1.986 |
| SiteScore | 0.904 |
| D Score | 0.649 |
| Kd | — |
| Compound | SPM |
| Residue | . / 6204 |
| Chain | BR / a |
| Non-redundant | True |
| Interacting RNA chains | V/a |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | V/a: rRNA |
| RNA family global | rRNA |
| Volume | 300.13 Å3 |
| Hydrophobicity | 0.172 |
| Hydrophilicity | 1.187 |
| Buriedness | 0.742 |
| Don/acc character | 1.012 |
| SiteScore | 1.037 |
| D Score | 0.816 |
| Kd | — |