Local identity vs Global identity
Both compare the holo RNA with the apo RNA of an entry; they differ in which part of the
sequence is scored.
| Local identity | BLAST identity over the aligned region only, so differences at the
chain ends are not counted. Every entry has ≥90 % local identity over ≥90 % coverage,
which is why this filter starts at 90. |
| Global identity | Identity over the full declared (SEQRES) sequences aligned end to
end: every mismatch and gap counts, including terminal overhangs. Residues missing from the coordinates
do not lower it. |
For a binding pocket that spans several RNA chains, the value shown is that of the chain the
ligand is assigned to; the pair page shows each chain’s own value. Both filters apply to the
Entry view.
Functional type
From the Nucleic Acid
Knowledgebase (NAKB): the most specific functional class NAKB gives to the RNA chain the ligand binds.
The 23 classes are grouped under 9 categories, the first level of NAKB’s function hierarchy
(e.g. Riboswitch › Purine-compound riboswitch).
Unannotated: NAKB gives this RNA no functional class. NAKB’s structural terms
(e.g. A-form duplex) describe geometry, not function, and are not used.
Composition
Ticking several boxes keeps only the cards that satisfy all of them.
| single-chain | The binding site lies on one RNA chain. |
| multi-chain | The binding site spans two or more RNA chains, e.g. a duplex or a
ligand at a strand interface. The pair page shows one alignment and one displacement panel per
chain. |
| multiple binding pockets | The holo structure has two or more binding pockets
— separate ligand sites, possibly with different ligands. They share one card; the pair
page’s Binding Pocket menu switches between them, and each keeps its own
measurements. |
Pocket motif
The secondary-structure elements the binding site lies in, from x3dna-DSSR’s motif
annotation of the holo structure: the nucleotides within 8 Å of the ligand on the RNA chain it
binds. A binding site usually touches several motifs and is counted under each, so the counts do not add
up to the number of cards.
Junction opens into subtypes (3-way, 4-way, …). A binding site can sit at more
than one junction, so the subtypes can add up to more than the junction row.