Complex 7uqb
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 | 2620.53 kDa |
| Deposition year | 2022 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Saccharomyces |
| RCSB PDB Entry | 7uqb |
| 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 | . / 3401 |
| Chain | IB / 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 | 607.45 Å3 |
| Hydrophobicity | 0.181 |
| Hydrophilicity | 1.111 |
| Buriedness | 0.731 |
| Don/acc character | 1.273 |
| SiteScore | 1.172 |
| D Score | 1.016 |
| Kd | — |
| Compound | B3P |
| Residue | . / 3402 |
| Chain | JB / 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 | 667.48 Å3 |
| Hydrophobicity | 0.010 |
| Hydrophilicity | 1.525 |
| Buriedness | 0.753 |
| Don/acc character | 1.115 |
| SiteScore | 1.037 |
| D Score | 0.895 |
| Kd | — |
| Compound | B3P |
| Residue | . / 3403 |
| Chain | KB / 1 |
| 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 | 441.44 Å3 |
| Hydrophobicity | 0.400 |
| Hydrophilicity | 1.406 |
| Buriedness | 0.825 |
| Don/acc character | 0.772 |
| SiteScore | 0.965 |
| D Score | 0.823 |
| Kd | — |
| Compound | GDP |
| Residue | . / 801 |
| Chain | RE / 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 | 794.05 Å3 |
| Hydrophobicity | 0.371 |
| Hydrophilicity | 1.392 |
| Buriedness | 0.830 |
| Don/acc character | 0.836 |
| SiteScore | 1.088 |
| D Score | 0.984 |
| Kd | — |