Complex 7yse
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 | X-ray |
| Experimental resolution | 2.91 |
| System mass | 275.55 kDa |
| Deposition year | 2022 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Escherichia |
| RCSB PDB Entry | 7yse |
| Reference | Han Lu, Luo Zhiteng, Ju Yingchen, Chen Bingyi, Zou Taotao, Wang Junjian, Xu Jun, Gu Qiong, Yang Xiang-Lei, Schimmel Paul, Zhou Huihao. 2023. The binding mode of orphan glycyl-tRNA synthetase with tRNA supports the synthetase classification and reveals large domain movements Science Advances |
| Equivalence Class |
NR_all_05887.9
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 | JPO |
| Residue | . / 401 |
| Chain | G / A |
| Non-redundant | True |
| Interacting RNA chains | E/E |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | E/E: tRNA |
| RNA family global | tRNA |
| Volume | 354.32 Å3 |
| Hydrophobicity | 1.328 |
| Hydrophilicity | 1.243 |
| Buriedness | 0.837 |
| Don/acc character | 0.549 |
| SiteScore | 1.093 |
| D Score | 1.037 |
| Kd | — |
| Compound | JPO |
| Residue | . / 401 |
| Chain | I / B |
| Non-redundant | True |
| Interacting RNA chains | F/F |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | F/F: tRNA |
| RNA family global | tRNA |
| Volume | 348.49 Å3 |
| Hydrophobicity | 0.981 |
| Hydrophilicity | 1.119 |
| Buriedness | 0.821 |
| Don/acc character | 0.416 |
| SiteScore | 1.082 |
| D Score | 1.068 |
| Kd | — |