Complex 5wdt
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 | Electron Microscopy |
| Experimental resolution | 3.00 |
| System mass | 2308.00 kDa |
| Deposition year | 2017 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Escherichia |
| RCSB PDB Entry | 5wdt |
| Reference | Fislage Marcus, Zhang Jingji, Brown Zuben Patrick, Mandava Chandra Sekhar, Sanyal Suparna, Ehrenberg Måns, Frank Joachim. 2018. Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-TuH84A Nucleic Acids Research |
| Equivalence Class |
NR_all_35542.167,
NR_all_83717.187,
NR_all_19951.102
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 | FME |
| Residue | . / 3001 |
| Chain | HB / A |
| Non-redundant | True |
| Interacting RNA chains | A/A, CB/v |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/A: rRNA, CB/v: tRNA |
| RNA family global | multiple |
| Volume | 591.68 Å3 |
| Hydrophobicity | 0.063 |
| Hydrophilicity | 2.064 |
| Buriedness | 0.761 |
| Don/acc character | 0.746 |
| SiteScore | 1.192 |
| D Score | 0.724 |
| Kd | — |
| Compound | GNP |
| Residue | . / 402 |
| Chain | QWB / z |
| Non-redundant | True |
| Interacting RNA chains | A/A |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | A/A: rRNA |
| RNA family global | rRNA |
| Volume | 614.31 Å3 |
| Hydrophobicity | 0.214 |
| Hydrophilicity | 1.840 |
| Buriedness | 0.791 |
| Don/acc character | 0.619 |
| SiteScore | 1.062 |
| D Score | 0.815 |
| Kd | — |
| Compound | PHE |
| Residue | . / 401 |
| Chain | PWB / z |
| Non-redundant | True |
| Interacting RNA chains | FB/y |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | FB/y: tRNA |
| RNA family global | tRNA |
| Volume | 454.82 Å3 |
| Hydrophobicity | 0.144 |
| Hydrophilicity | 1.433 |
| Buriedness | 0.881 |
| Don/acc character | 0.895 |
| SiteScore | 1.122 |
| D Score | 1.002 |
| Kd | — |