Complex 4v8a
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 | 3.20 |
| System mass | 4328.29 kDa |
| Deposition year | 2011 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Thermus |
| RCSB PDB Entry | 4v8a |
| Reference | Bulkley David, Johnson Francis, Steitz Thomas A.. 2012. The Antibiotic Thermorubin Inhibits Protein Synthesis by Binding to Inter-Subunit Bridge B2a of the Ribosome Journal of Molecular Biology |
| Equivalence Class |
NR_all_65795.87,
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 | T8B |
| Residue | . / 3001 |
| Chain | YC / AA |
| Non-redundant | True |
| Interacting RNA chains | DC/DA, A/AA |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/AA: rRNA, DC/DA: rRNA |
| RNA family global | rRNA |
| Volume | 294.64 Å3 |
| Hydrophobicity | 0.185 |
| Hydrophilicity | 1.567 |
| Buriedness | 0.660 |
| Don/acc character | 0.811 |
| SiteScore | 1.125 |
| D Score | 0.825 |
| Kd | — |
| Compound | T8B |
| Residue | . / 3001 |
| Chain | BD / BA |
| Non-redundant | True |
| Interacting RNA chains | EA/BA, IB/CA |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | EA/BA: rRNA, IB/CA: rRNA |
| RNA family global | rRNA |
| Volume | 309.04 Å3 |
| Hydrophobicity | 0.135 |
| Hydrophilicity | 1.373 |
| Buriedness | 0.618 |
| Don/acc character | 0.852 |
| SiteScore | 1.097 |
| D Score | 0.863 |
| Kd | — |