Complex 8dh5
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 | 2.85 |
| System mass | 446.13 kDa |
| Deposition year | 2022 |
| Molecule type | RNA/DNA/Protein |
| # RNA entities | 1 |
| Organism | N/A |
| RCSB PDB Entry | 8dh5 |
| Reference | Oh Juntaek, Kimoto Michiko, Xu Haoqing, Chong Jenny, Hirao Ichiro, Wang Dong. 2023. Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase Nature Communications |
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 | ATP |
| Residue | . / 901 |
| Chain | Q / B |
| Non-redundant | True |
| Interacting RNA chains | C/C |
| RNA environment detailled | DNA, protein, ion |
| RNA environment global | RNA/DNA/Protein |
| RNA family chains | C/C: synthetic construct |
| RNA family global | synthetic construct |
| Volume | 401.65 Å3 |
| Hydrophobicity | 0.435 |
| Hydrophilicity | 1.157 |
| Buriedness | 0.824 |
| Don/acc character | 0.633 |
| SiteScore | 1.084 |
| D Score | 1.057 |
| Kd | — |
| Compound | ATP |
| Residue | . / 901 |
| Chain | S / E |
| Non-redundant | True |
| Interacting RNA chains | G/G |
| RNA environment detailled | DNA, protein, ion |
| RNA environment global | RNA/DNA/Protein |
| RNA family chains | G/G: synthetic construct |
| RNA family global | synthetic construct |
| Volume | 539.20 Å3 |
| Hydrophobicity | 0.484 |
| Hydrophilicity | 1.173 |
| Buriedness | 0.809 |
| Don/acc character | 0.674 |
| SiteScore | 1.074 |
| D Score | 1.043 |
| Kd | — |
| Compound | ATP |
| Residue | . / 901 |
| Chain | U / I |
| Non-redundant | True |
| Interacting RNA chains | K/K |
| RNA environment detailled | DNA, protein |
| RNA environment global | RNA/DNA/Protein |
| RNA family chains | K/K: synthetic construct |
| RNA family global | synthetic construct |
| Volume | 464.42 Å3 |
| Hydrophobicity | 0.451 |
| Hydrophilicity | 1.244 |
| Buriedness | 0.819 |
| Don/acc character | 0.850 |
| SiteScore | 1.081 |
| D Score | 1.026 |
| Kd | — |
| Compound | ATP |
| Residue | . / 901 |
| Chain | V / M |
| Non-redundant | True |
| Interacting RNA chains | O/O |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | O/O: synthetic construct |
| RNA family global | synthetic construct |
| Volume | 683.26 Å3 |
| Hydrophobicity | 0.682 |
| Hydrophilicity | 1.040 |
| Buriedness | 0.813 |
| Don/acc character | 0.820 |
| SiteScore | 1.077 |
| D Score | 1.089 |
| Kd | — |