A holo binding site is matched to an apo structure with ≥90% local (BLAST) sequence identity and ≥90% alignment coverage. The corresponding pocket is unoccupied in the apo structure.
Local identity scores the BLAST-aligned region only; global identity scores the entire declared (SEQRES) sequence, so terminal overhangs and gaps count against the match. The ? beside the Global identity facet gives the full definition of both.
The gallery opens on the full release: both identity facets start on the whole span present in the data, so nothing is hidden until you narrow one, and Reset filters puts them back.
The range you browse in follows you into a pair page's Apo state list, which can be reopened there to every curated alternative for that pocket.
| Local identity | the upstream BLAST pident — a local
(Smith–Waterman-type) alignment, found by blastn's seed-and-extend heuristic rather
than a full dynamic-programming matrix — measured only inside the aligned
region. A mismatch near an end is simply trimmed out of that region, so this can read
100 % even when the ends differ. Every served pair is curated to ≥90 % identity over
≥90 % mutual coverage, which is why this facet starts at 90. |
| Global identity | a Needleman–Wunsch alignment over the full declared (SEQRES) sequences, where every mismatch and every gap column counts, terminal overhangs included. Unmodelled (disordered) residues do not penalise it, because it reads the declared sequence rather than the coordinates. |
Where a pocket spans more than one RNA chain, the value published here is the ligand’s own (auth) chain’s — the chain the PDB entry assigns the ligand to. Every chain’s own number is shown on the pair page beside that chain’s alignment.
| single-chain (RNA) | the binding site lies on one RNA chain. |
| multi-chain (RNA) | the binding site spans two or more RNA chains — a duplex, a kissing loop, or a ligand bound at a strand interface. The pair page then draws one alignment and one displacement panel per chain. |
| multiple holo copies | the crystal contains 2+ crystallographic copies of the same pocket (same ligand, same apo, different chain). They are collapsed into one card, badged “N holo copies”; the pair page’s Holo copy dropdown switches between them. |
| multiple apo copies | the apo crystal contains 2+ copies of the same RNA. The pair page’s Apo copy dropdown picks which one to superpose — useful when one copy is more completely modelled than another. |
| multiple apo states | the pocket has alternative ligand-free apo structures from other PDB entries, not just the default one. Badged “+N apo states” on the card; each alternative also gets its own row in the table and the download. |
“Copies” are the same deposited structure seen more than once; “states” are different PDB entries of the same RNA without the ligand.