Complex 4v5y
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 | 4.45 |
| System mass | 4339.77 kDa |
| Deposition year | 2007 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Escherichia |
| RCSB PDB Entry | 4v5y |
| Reference | Borovinskaya Maria A, Pai Raj D, Zhang Wen, Schuwirth Barbara S, Holton James M, Hirokawa Go, Kaji Hideko, Kaji Akira, Cate Jamie H Doudna. 2007. Structural basis for aminoglycoside inhibition of bacterial ribosome recycling Nature Structural & Molecular Biology |
| 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 | PAR |
| Residue | . / 1661 |
| Chain | KF / AA |
| Non-redundant | False |
| Interacting RNA chains | A/AA |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/AA: rRNA |
| RNA family global | rRNA |
| Volume | 151.95 Å3 |
| Hydrophobicity | 0.065 |
| Hydrophilicity | 1.025 |
| Buriedness | 0.630 |
| Don/acc character | 2.842 |
| SiteScore | 0.933 |
| D Score | 0.760 |
| Kd | — |
| Compound | PAR |
| Residue | . / 3111 |
| Chain | RJ / BB |
| Non-redundant | True |
| Interacting RNA chains | A/AA, W/BB |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | A/AA: rRNA, W/BB: rRNA |
| RNA family global | rRNA |
| Volume | 204.09 Å3 |
| Hydrophobicity | 0.219 |
| Hydrophilicity | 0.752 |
| Buriedness | 0.653 |
| Don/acc character | 2.662 |
| SiteScore | 0.818 |
| D Score | 0.635 |
| Kd | — |
| Compound | PAR |
| Residue | . / 1662 |
| Chain | CM / CA |
| Non-redundant | True |
| Interacting RNA chains | BB/CA |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | BB/CA: rRNA |
| RNA family global | rRNA |
| Volume | 345.06 Å3 |
| Hydrophobicity | 0.086 |
| Hydrophilicity | 1.004 |
| Buriedness | 0.633 |
| Don/acc character | 2.257 |
| SiteScore | 1.041 |
| D Score | 0.899 |
| Kd | — |
| Compound | PAR |
| Residue | . / 3112 |
| Chain | LQ / DB |
| Non-redundant | True |
| Interacting RNA chains | BB/CA, XB/DB |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | BB/CA: rRNA, XB/DB: rRNA |
| RNA family global | rRNA |
| Volume | 178.02 Å3 |
| Hydrophobicity | 0.248 |
| Hydrophilicity | 0.766 |
| Buriedness | 0.691 |
| Don/acc character | 1.711 |
| SiteScore | 0.816 |
| D Score | 0.615 |
| Kd | — |