Complex 5vp2
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 | 2.80 |
| System mass | 4571.58 kDa |
| Deposition year | 2017 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Thermus |
| RCSB PDB Entry | 5vp2 |
| Reference | Osterman Ilya A., Khabibullina Nelli F., Komarova Ekaterina S., Kasatsky Pavel, Kartsev Victor G., Bogdanov Alexey A., Dontsova Olga A., Konevega Andrey L., Sergiev Petr V., Polikanov Yury S.. 2017. Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state Nucleic Acids Research |
| Equivalence Class |
NR_all_97519.80
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 | M2D |
| Residue | . / 4118 |
| Chain | HUA / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | 955.60 Å3 |
| Hydrophobicity | 0.441 |
| Hydrophilicity | 1.765 |
| Buriedness | 0.802 |
| Don/acc character | 0.534 |
| SiteScore | 1.220 |
| D Score | 0.846 |
| Kd | — |
| Compound | M2D |
| Residue | . / 3864 |
| Chain | XTC / 2A |
| Non-redundant | True |
| Interacting RNA chains | EB/2A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | EB/2A: rRNA |
| RNA family global | rRNA |
| Volume | 654.79 Å3 |
| Hydrophobicity | 0.917 |
| Hydrophilicity | 1.209 |
| Buriedness | 0.807 |
| Don/acc character | 0.674 |
| SiteScore | 1.223 |
| D Score | 1.030 |
| Kd | — |