| RMSD | C3′ atoms after superposition. Global: the binding-site RNA chains; pocket: the residues within 8 Å of the ligand (Help explains the fit). |
| TM-score | US-align, ligand’s host chain, normalised by the holo length. |
| Radius of gyration | The same C3′ atoms as the global RMSD (binding-site chains, residues modelled in both structures). |
| Sequence identity | Local: BLAST+, aligned region. Global: Needleman–Wunsch, declared (SEQRES) sequences. Binding site on several chains: the ligand’s own chain. |
| Base pairs, motifs | x3dna-dssr. Base pairs: the binding-site chains; motifs: the ligand’s host chain. |
| Binding site | RNA residues within 8 Å of the ligand, all chains; H-bonds from x3dna-dssr (PLIP where DSSR cannot read the ligand). |
| RNA length | Modelled nucleotides of the ligand’s host chain. |
| Functional type | NAKB functional class of the host chain. The chart shows its group; the Database facet opens each group into its classes. Unannotated = no NAKB functional class. |
in the holo structure only
in the apo structure only
in both structures
Click a bar to open them in the Database.
Pairs whose two bases sit on different chains, such as the aminoglycoside A-site duplexes, are counted too. The pair page draws them as a two-strand ladder (“chains X ⇄ Y · inter-strand” in the Base-pair rewiring chain menu).
Base pairs from x3dna-dssr; canonical = DSSR pair name WC or Wobble. Apo and holo positions are matched by a Needleman–Wunsch alignment of each chain’s sequence (the declared SEQRES where available). This compares two experimental end states, not a binding pathway.