Complex 8ifb
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 | 2.43 |
| System mass | 2211.28 kDa |
| Deposition year | 2023 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Escherichia |
| RCSB PDB Entry | 8ifb |
| 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_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 | 84D |
| Residue | . / 1738 |
| Chain | KG / A |
| Non-redundant | True |
| 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 | 237.70 Å3 |
| Hydrophobicity | 0.127 |
| Hydrophilicity | 0.984 |
| Buriedness | 0.685 |
| Don/acc character | 3.187 |
| SiteScore | 0.837 |
| D Score | 0.818 |
| Kd | — |
| Compound | 84D |
| Residue | . / 1739 |
| Chain | LG / A |
| Non-redundant | True |
| 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 | 514.50 Å3 |
| Hydrophobicity | 0.035 |
| Hydrophilicity | 0.678 |
| Buriedness | 0.511 |
| Don/acc character | 3.118 |
| SiteScore | 1.095 |
| D Score | 1.026 |
| Kd | — |
| Compound | 84D |
| Residue | . / 1740 |
| Chain | MG / A |
| Non-redundant | True |
| Interacting RNA chains | A/A |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | A/A: rRNA |
| RNA family global | rRNA |
| Volume | - |
| Hydrophobicity | - |
| Hydrophilicity | - |
| Buriedness | - |
| Don/acc character | - |
| SiteScore | - |
| D Score | - |
| Kd | — |
| Compound | 84D |
| Residue | . / 1741 |
| Chain | NG / A |
| Non-redundant | True |
| Interacting RNA chains | A/A |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | A/A: rRNA |
| RNA family global | rRNA |
| Volume | 564.24 Å3 |
| Hydrophobicity | 0.030 |
| Hydrophilicity | 1.302 |
| Buriedness | 0.780 |
| Don/acc character | 1.081 |
| SiteScore | 1.094 |
| D Score | 0.983 |
| Kd | — |
| Compound | 84D |
| Residue | . / 1742 |
| Chain | OG / A |
| Non-redundant | True |
| Interacting RNA chains | A/A |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | A/A: rRNA |
| RNA family global | rRNA |
| Volume | 573.15 Å3 |
| Hydrophobicity | 0.165 |
| Hydrophilicity | 1.289 |
| Buriedness | 0.775 |
| Don/acc character | 1.849 |
| SiteScore | 1.201 |
| D Score | 0.985 |
| Kd | — |
| Compound | 84D |
| Residue | . / 3255 |
| Chain | RQ / a |
| Non-redundant | True |
| Interacting RNA chains | A/A, V/a |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/A: rRNA, V/a: rRNA |
| RNA family global | rRNA |
| Volume | 218.83 Å3 |
| Hydrophobicity | 0.445 |
| Hydrophilicity | 1.052 |
| Buriedness | 0.715 |
| Don/acc character | 2.312 |
| SiteScore | 1.092 |
| D Score | 0.937 |
| Kd | — |
| Compound | 84D |
| Residue | . / 3256 |
| Chain | SQ / 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 | 88.15 Å3 |
| Hydrophobicity | 0.000 |
| Hydrophilicity | 0.892 |
| Buriedness | 0.651 |
| Don/acc character | 4.494 |
| SiteScore | 0.594 |
| D Score | 0.330 |
| Kd | — |
| Compound | 84D |
| Residue | . / 3257 |
| Chain | TQ / 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 | 259.31 Å3 |
| Hydrophobicity | 0.012 |
| Hydrophilicity | 1.424 |
| Buriedness | 0.700 |
| Don/acc character | 0.979 |
| SiteScore | 0.921 |
| D Score | 0.600 |
| Kd | — |
| Compound | 84D |
| Residue | . / 3258 |
| Chain | UQ / 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 | 536.11 Å3 |
| Hydrophobicity | 0.143 |
| Hydrophilicity | 0.948 |
| Buriedness | 0.700 |
| Don/acc character | 3.214 |
| SiteScore | 1.075 |
| D Score | 0.930 |
| Kd | — |
| Compound | 84D |
| Residue | . / 3259 |
| Chain | VQ / a |
| Non-redundant | True |
| Interacting RNA chains | V/a |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | V/a: rRNA |
| RNA family global | rRNA |
| Volume | 555.66 Å3 |
| Hydrophobicity | 0.185 |
| Hydrophilicity | 1.159 |
| Buriedness | 0.769 |
| Don/acc character | 1.176 |
| SiteScore | 1.171 |
| D Score | 0.990 |
| Kd | — |
| Compound | 84D |
| Residue | . / 3260 |
| Chain | WQ / 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 | 649.30 Å3 |
| Hydrophobicity | 0.087 |
| Hydrophilicity | 1.301 |
| Buriedness | 0.730 |
| Don/acc character | 1.114 |
| SiteScore | 1.171 |
| D Score | 0.954 |
| Kd | — |
| Compound | 84D |
| Residue | . / 3261 |
| Chain | XQ / 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 | 380.73 Å3 |
| Hydrophobicity | 0.102 |
| Hydrophilicity | 1.020 |
| Buriedness | 0.666 |
| Don/acc character | 1.599 |
| SiteScore | 0.934 |
| D Score | 0.752 |
| Kd | — |
| Compound | 84D |
| Residue | . / 3262 |
| Chain | YQ / 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 | 752.20 Å3 |
| Hydrophobicity | 0.061 |
| Hydrophilicity | 1.172 |
| Buriedness | 0.670 |
| Don/acc character | 1.513 |
| SiteScore | 1.131 |
| D Score | 0.960 |
| Kd | — |
| Compound | SPM |
| Residue | . / 3180 |
| Chain | UN / 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 | 323.45 Å3 |
| Hydrophobicity | 0.299 |
| Hydrophilicity | 1.125 |
| Buriedness | 0.755 |
| Don/acc character | 1.161 |
| SiteScore | 1.028 |
| D Score | 0.821 |
| Kd | — |