Complex 2vqe
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 | 2.50 |
| System mass | 799.28 kDa |
| Deposition year | 2008 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Thermus |
| RCSB PDB Entry | 2vqe |
| Reference | Kurata Shinya, Weixlbaumer Albert, Ohtsuki Takashi, Shimazaki Tomomi, Wada Takeshi, Kirino Yohei, Takai Kazuyuki, Watanabe Kimitsuna, Ramakrishnan V., Suzuki Tsutomu. 2008. Modified Uridines with C5-methylene Substituents at the First Position of the tRNA Anticodon Stabilize U·G Wobble Pairing during Decoding Journal of Biological Chemistry |
| Equivalence Class |
NR_all_65795.87
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 | PAR |
| Residue | . / 1854 |
| Chain | QJ / A |
| Non-redundant | True |
| Interacting RNA chains | A/A |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/A: rRNA |
| RNA family global | rRNA |
| Volume | 126.91 Å3 |
| Hydrophobicity | 0.078 |
| Hydrophilicity | 0.926 |
| Buriedness | 0.616 |
| Don/acc character | 3.421 |
| SiteScore | 0.703 |
| D Score | 0.647 |
| Kd | — |