Complex 8qyx
System information
| Experimental technique | Electron Microscopy |
| Experimental resolution | 1.78 |
| System mass | 2564.90 kDa |
| Deposition year | 2023 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Homo |
| RCSB PDB Entry | 8qyx |
| Reference | Wiechert Franziska, Unbehaun Anett, Sprink Thiemo, Seibel Helena, Bürger Jörg, Loerke Justus, Mielke Thorsten, Diebolder Christoph A, Schacherl Magdalena, Spahn Christian M T. . Visualizing the modification landscape of the human 60S ribosomal subunit at close to atomic resolution Nucleic Acids Research |
| Equivalence Class |
NR_all_65061.63
BGSU version: 4.49 |
| Compound | ATP |
| Residue | . / 5418 |
| Chain | XB / A2 |
| Non-redundant | True |
| Interacting RNA chains | KA/A2 |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | KA/A2: rRNA |
| RNA family global | rRNA |
| Volume | 506.61 Å3 |
| Hydrophobicity | 0.441 |
| Hydrophilicity | 1.099 |
| Buriedness | 0.767 |
| Don/acc character | 1.035 |
| SiteScore | 1.046 |
| D Score | 1.042 |
| Kd | — |
| Compound | SPM |
| Residue | . / 5413 |
| Chain | SB / A2 |
| Non-redundant | True |
| Interacting RNA chains | KA/A2 |
| RNA environment detailled | protein, ion, other |
| RNA environment global | RNA/Other |
| RNA family chains | KA/A2: rRNA |
| RNA family global | rRNA |
| Volume | 468.20 Å3 |
| Hydrophobicity | 0.207 |
| Hydrophilicity | 1.447 |
| Buriedness | 0.692 |
| Don/acc character | 1.336 |
| SiteScore | 1.146 |
| D Score | 0.883 |
| Kd | — |
| Compound | SPM |
| Residue | . / 5414 |
| Chain | TB / A2 |
| Non-redundant | True |
| Interacting RNA chains | KA/A2 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | KA/A2: rRNA |
| RNA family global | rRNA |
| Volume | 686.00 Å3 |
| Hydrophobicity | 0.364 |
| Hydrophilicity | 1.276 |
| Buriedness | 0.848 |
| Don/acc character | 1.128 |
| SiteScore | 1.100 |
| D Score | 1.033 |
| Kd | — |
| Compound | SPM |
| Residue | . / 5415 |
| Chain | UB / A2 |
| Non-redundant | True |
| Interacting RNA chains | KA/A2 |
| RNA environment detailled | protein, ion, other |
| RNA environment global | RNA/Other |
| RNA family chains | KA/A2: rRNA |
| RNA family global | rRNA |
| Volume | 634.21 Å3 |
| Hydrophobicity | 0.133 |
| Hydrophilicity | 1.907 |
| Buriedness | 0.867 |
| Don/acc character | 0.900 |
| SiteScore | 1.113 |
| D Score | 0.838 |
| Kd | — |
| Compound | SPM |
| Residue | . / 5416 |
| Chain | VB / A2 |
| Non-redundant | True |
| Interacting RNA chains | KA/A2 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | KA/A2: rRNA |
| RNA family global | rRNA |
| Volume | 378.33 Å3 |
| Hydrophobicity | 0.368 |
| Hydrophilicity | 1.048 |
| Buriedness | 0.793 |
| Don/acc character | 3.368 |
| SiteScore | 0.908 |
| D Score | 0.682 |
| Kd | — |
| Compound | SPM |
| Residue | . / 5417 |
| Chain | WB / A2 |
| Non-redundant | True |
| Interacting RNA chains | KA/A2 |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | KA/A2: rRNA |
| RNA family global | rRNA |
| Volume | 663.71 Å3 |
| Hydrophobicity | 0.154 |
| Hydrophilicity | 1.115 |
| Buriedness | 0.674 |
| Don/acc character | 1.720 |
| SiteScore | 1.134 |
| D Score | 0.981 |
| Kd | — |