Complex 7pjv
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 | 3.10 |
| System mass | 2321.99 kDa |
| Deposition year | 2021 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Escherichia |
| RCSB PDB Entry | 7pjv |
| Reference | Petrychenko Valentyn, Peng Bee-Zen, de A. P. Schwarzer Ana C., Peske Frank, Rodnina Marina V., Fischer Niels. 2021. Structural mechanism of GTPase-powered ribosome-tRNA movement Nature Communications |
| 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 | AM2 |
| Residue | . / 1648 |
| Chain | YN / a |
| Non-redundant | True |
| Interacting RNA chains | HA/a |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | HA/a: rRNA |
| RNA family global | rRNA |
| Volume | 587.90 Å3 |
| Hydrophobicity | 0.161 |
| Hydrophilicity | 1.120 |
| Buriedness | 0.729 |
| Don/acc character | 2.624 |
| SiteScore | 1.021 |
| D Score | 1.012 |
| Kd | — |
| Compound | AM2 |
| Residue | . / 1652 |
| Chain | CO / a |
| Non-redundant | True |
| Interacting RNA chains | HA/a |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | HA/a: rRNA |
| RNA family global | rRNA |
| Volume | 131.03 Å3 |
| Hydrophobicity | 0.157 |
| Hydrophilicity | 1.021 |
| Buriedness | 0.691 |
| Don/acc character | 1.498 |
| SiteScore | 0.768 |
| D Score | 0.533 |
| Kd | — |
| Compound | AM2 |
| Residue | . / 1657 |
| Chain | HO / a |
| Non-redundant | True |
| Interacting RNA chains | HA/a |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | HA/a: rRNA |
| RNA family global | rRNA |
| Volume | 267.20 Å3 |
| Hydrophobicity | 0.041 |
| Hydrophilicity | 1.575 |
| Buriedness | 0.778 |
| Don/acc character | 1.151 |
| SiteScore | 0.723 |
| D Score | 0.570 |
| Kd | — |
| Compound | GDP |
| Residue | . / 801 |
| Chain | RP / x |
| Non-redundant | True |
| Interacting RNA chains | H/A |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | H/A: rRNA |
| RNA family global | rRNA |
| Volume | 428.06 Å3 |
| Hydrophobicity | 0.217 |
| Hydrophilicity | 1.804 |
| Buriedness | 0.819 |
| Don/acc character | 0.706 |
| SiteScore | 1.081 |
| D Score | 0.843 |
| Kd | — |