Complex 9pbe
System information
| Experimental technique | Electron Microscopy |
| Experimental resolution | 2.19 |
| System mass | 3693.59 kDa |
| Deposition year | 2025 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Homo |
| RCSB PDB Entry | 9pbe |
| Reference | Zheng Wei, Zhang Yuekang, Wang Jimin, Wang Shuhui, Chai Pengxin, Bailey Elizabeth J., Zhu Chenghao, Guo Wangbiao, Devarkar Swapnil C., Wu Shenping, Lin Jianfeng, Zhang Kai, Liu Jun, Lomakin Ivan B., Xiong Yong. . Visualizing the translation landscape in human cells at high resolution Nature Communications |
| Equivalence Class |
NR_all_46995.72,
NR_all_65061.63
BGSU version: 4.49 |
| Compound | SPM |
| Residue | . / 5259 |
| Chain | II / L5 |
| Non-redundant | True |
| Interacting RNA chains | C/L5 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | C/L5: rRNA |
| RNA family global | rRNA |
| Volume | 345.74 Å3 |
| Hydrophobicity | 0.400 |
| Hydrophilicity | 0.930 |
| Buriedness | 0.672 |
| Don/acc character | 1.535 |
| SiteScore | 1.154 |
| D Score | 1.040 |
| Kd | — |
| Compound | SPM |
| Residue | . / 5263 |
| Chain | MI / L5 |
| Non-redundant | True |
| Interacting RNA chains | C/L5 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | C/L5: rRNA |
| RNA family global | rRNA |
| Volume | - |
| Hydrophobicity | - |
| Hydrophilicity | - |
| Buriedness | - |
| Don/acc character | - |
| SiteScore | - |
| D Score | - |
| Kd | — |
| Compound | SPM |
| Residue | . / 5264 |
| Chain | NI / L5 |
| Non-redundant | True |
| Interacting RNA chains | C/L5 |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | C/L5: rRNA |
| RNA family global | rRNA |
| Volume | - |
| Hydrophobicity | - |
| Hydrophilicity | - |
| Buriedness | - |
| Don/acc character | - |
| SiteScore | - |
| D Score | - |
| Kd | — |
| Compound | SPM |
| Residue | . / 5267 |
| Chain | QI / L5 |
| Non-redundant | True |
| Interacting RNA chains | C/L5 |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | C/L5: rRNA |
| RNA family global | rRNA |
| Volume | 872.25 Å3 |
| Hydrophobicity | 0.113 |
| Hydrophilicity | 1.832 |
| Buriedness | 0.835 |
| Don/acc character | 1.176 |
| SiteScore | 1.091 |
| D Score | 0.844 |
| Kd | — |
| Compound | SPM |
| Residue | . / 5288 |
| Chain | LJ / L5 |
| Non-redundant | True |
| Interacting RNA chains | C/L5 |
| RNA environment detailled | protein, ion, other |
| RNA environment global | RNA/Other |
| RNA family chains | C/L5: rRNA |
| RNA family global | rRNA |
| Volume | 351.23 Å3 |
| Hydrophobicity | 0.087 |
| Hydrophilicity | 1.777 |
| Buriedness | 0.836 |
| Don/acc character | 0.767 |
| SiteScore | 0.761 |
| D Score | 0.437 |
| Kd | — |
| Compound | SPM |
| Residue | . / 5291 |
| Chain | OJ / L5 |
| Non-redundant | True |
| Interacting RNA chains | C/L5 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | C/L5: rRNA |
| RNA family global | rRNA |
| Volume | 1457.06 Å3 |
| Hydrophobicity | 0.092 |
| Hydrophilicity | 1.460 |
| Buriedness | 0.789 |
| Don/acc character | 1.449 |
| SiteScore | 1.061 |
| D Score | 0.938 |
| Kd | — |
| Compound | SPM |
| Residue | . / 5292 |
| Chain | PJ / L5 |
| Non-redundant | True |
| Interacting RNA chains | C/L5 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | C/L5: rRNA |
| RNA family global | rRNA |
| Volume | 625.98 Å3 |
| Hydrophobicity | 0.240 |
| Hydrophilicity | 1.222 |
| Buriedness | 0.772 |
| Don/acc character | 1.196 |
| SiteScore | 1.049 |
| D Score | 1.005 |
| Kd | — |
| Compound | SPM |
| Residue | . / 1929 |
| Chain | QO / S2 |
| Non-redundant | True |
| Interacting RNA chains | YA/S2 |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | YA/S2: rRNA |
| RNA family global | rRNA |
| Volume | 783.41 Å3 |
| Hydrophobicity | 0.222 |
| Hydrophilicity | 1.199 |
| Buriedness | 0.782 |
| Don/acc character | 1.766 |
| SiteScore | 1.206 |
| D Score | 1.018 |
| Kd | — |