Complex 5ibb
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 | 2.96 |
| System mass | 4568.55 kDa |
| Deposition year | 2016 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Thermus |
| RCSB PDB Entry | 5ibb |
| Reference | Rozov Alexey, Westhof Eric, Yusupov Marat, Yusupova Gulnara. 2016. The ribosome prohibits the G•U wobble geometry at the first position of the codon–anticodon helix Nucleic Acids Research |
| Equivalence Class |
NR_all_65795.87,
NR_all_42622.80,
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 | SPE |
| Residue | . / 1733 |
| Chain | UKA / 1G |
| Non-redundant | True |
| Interacting RNA chains | DB/1G |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | DB/1G: rRNA |
| RNA family global | rRNA |
| Volume | - |
| Hydrophobicity | - |
| Hydrophilicity | - |
| Buriedness | - |
| Don/acc character | - |
| SiteScore | - |
| D Score | - |
| Kd | — |
| Compound | SPE |
| Residue | . / 3446 |
| Chain | KCB / 14 |
| Non-redundant | True |
| Interacting RNA chains | CC/14 |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | CC/14: rRNA |
| RNA family global | rRNA |
| Volume | 607.11 Å3 |
| Hydrophobicity | 0.081 |
| Hydrophilicity | 1.879 |
| Buriedness | 0.779 |
| Don/acc character | 1.260 |
| SiteScore | 1.204 |
| D Score | 0.795 |
| Kd | — |
| Compound | SPE |
| Residue | . / 208 |
| Chain | TCB / 1J |
| Non-redundant | True |
| Interacting RNA chains | CC/14, DC/1J |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | CC/14: rRNA, DC/1J: rRNA |
| RNA family global | rRNA |
| Volume | 281.95 Å3 |
| Hydrophobicity | 0.044 |
| Hydrophilicity | 2.129 |
| Buriedness | 0.711 |
| Don/acc character | 0.691 |
| SiteScore | 1.094 |
| D Score | 0.589 |
| Kd | — |