Complex 7v08
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 | 2.36 |
| System mass | 2673.43 kDa |
| Deposition year | 2022 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Saccharomyces |
| RCSB PDB Entry | 7v08 |
| Reference | Sekulski Kamil, Cruz Victor Emmanuel, Weirich Christine S., Erzberger Jan P.. 2023. rRNA methylation by Spb1 regulates the GTPase activity of Nog2 during 60S ribosomal subunit assembly Nature Communications |
| Equivalence Class |
NR_all_90506.85
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 | B3P |
| Residue | . / 3475 |
| Chain | EE / 1 |
| Non-redundant | True |
| Interacting RNA chains | B/1 |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | B/1: rRNA |
| RNA family global | rRNA |
| Volume | 696.63 Å3 |
| Hydrophobicity | 0.138 |
| Hydrophilicity | 1.183 |
| Buriedness | 0.756 |
| Don/acc character | 1.237 |
| SiteScore | 1.189 |
| D Score | 1.008 |
| Kd | — |
| Compound | B3P |
| Residue | . / 3476 |
| Chain | FE / 1 |
| Non-redundant | True |
| Interacting RNA chains | B/1 |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | B/1: rRNA |
| RNA family global | rRNA |
| Volume | 726.82 Å3 |
| Hydrophobicity | 0.056 |
| Hydrophilicity | 1.693 |
| Buriedness | 0.768 |
| Don/acc character | 1.046 |
| SiteScore | 1.047 |
| D Score | 0.849 |
| Kd | — |
| Compound | B3P |
| Residue | . / 3601 |
| Chain | VE / z |
| Non-redundant | True |
| Interacting RNA chains | B/1 |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | B/1: rRNA |
| RNA family global | rRNA |
| Volume | 761.46 Å3 |
| Hydrophobicity | 0.332 |
| Hydrophilicity | 1.210 |
| Buriedness | 0.761 |
| Don/acc character | 1.401 |
| SiteScore | 1.042 |
| D Score | 1.002 |
| Kd | — |
| Compound | GDP |
| Residue | . / 501 |
| Chain | QE / m |
| Non-redundant | True |
| Interacting RNA chains | B/1 |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | B/1: rRNA |
| RNA family global | rRNA |
| Volume | 693.20 Å3 |
| Hydrophobicity | 0.338 |
| Hydrophilicity | 1.428 |
| Buriedness | 0.843 |
| Don/acc character | 0.732 |
| SiteScore | 1.097 |
| D Score | 0.980 |
| Kd | — |