Complex 3k0j
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 | 3.10 |
| System mass | 101.40 kDa |
| Deposition year | 2009 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Escherichia |
| RCSB PDB Entry | 3k0j |
| Reference | Kulshina Nadia, Edwards Thomas E., Ferré-D'Amaré Adrian R.. 2010. Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch RNA |
| Equivalence Class |
NR_all_19099.3
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 | TPP |
| Residue | . / 601 |
| Chain | G / E |
| Non-redundant | False |
| Interacting RNA chains | E/E |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | E/E: riboswitch |
| RNA family global | riboswitch |
| Volume | 762.15 Å3 |
| Hydrophobicity | 0.262 |
| Hydrophilicity | 1.204 |
| Buriedness | 0.741 |
| Don/acc character | 1.591 |
| SiteScore | 1.179 |
| D Score | 0.992 |
| Kd | — |
| Compound | TPP |
| Residue | . / 602 |
| Chain | N / F |
| Non-redundant | False |
| Interacting RNA chains | F/F |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | F/F: riboswitch |
| RNA family global | riboswitch |
| Volume | 688.40 Å3 |
| Hydrophobicity | 0.225 |
| Hydrophilicity | 1.104 |
| Buriedness | 0.721 |
| Don/acc character | 1.033 |
| SiteScore | 1.166 |
| D Score | 1.013 |
| Kd | — |