About · SMARTFlexDB

How SMARTFlexDB is built

Each entry pairs one ligand-bound (holo) RNA structure with one ligand-free (apo) structure of the same RNA, so you can see how the RNA changes shape when a small molecule binds. Below: an example entry, the selection rules, where each value comes from, and the license.

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Example · the adenine riboswitch

The Vibrio vulnificus adenine riboswitch aptamer bound to adenine (5SWE) and ligand-free (5E54). Both come from one XFEL study in which adenine was mixed into ligand-free crystals and the RNA switched to its bound form inside the crystal (Stagno et al., Nature 2017).

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How entries are selected

A holo and an apo structure form an entry only if all of these hold:

A real ligand. The holo structure binds a small molecule that contains carbon, whose elements are all among C, H, N, O, P, S, F, Cl, Br, B, Si, Se and Co, and that is neither water, part of an RNA chain, nor the RNA's own 5′-end group. There is no size limit and no exclusion list, so buffer molecules such as glycerol or HEPES can be ligands.
A ligand-free apo. The apo structure contains no such molecule anywhere; water and ions may be present.
RNA only. Neither structure contains a protein or DNA chain.
The same RNA. Every RNA chain of the binding site (residues with any atom within 8 Å of the ligand) has its own apo chain with ≥90% identity over ≥90% of both chains (BLASTN).
The same pocket. Every binding-site residue has the same base in the apo, and the apo models at least part of the site.
The same assembly. Both have the same number of RNA strands in their author-defined biological assembly, and the apo carries no extra RNA molecule the holo lacks. For introns, both or neither carry a bound RNA partner such as the exon.

What the pair page shows, and where it comes from

Tags: deposited metadata read as is from the PDB entry or NAKB · tool-derived computed by a published tool (x3dna-dssr, US-align, PLIP, RDKit) · geometry-derived computed here from the deposited coordinates and sequences (gemmi, NumPy, Biopython).

Feature	What you see	How it is made
Basic Information	Overview numbers (next rows), each structure's PDB details, ligand properties	RCSB Data API (read live) and Chemical Component Dictionary; RDKit for ligand properties deposited metadatatool-derived
Global / pocket RMSD	apo→holo C3′ RMSD over all binding-site chains (global) or over the residues within 8 Å of the ligand (pocket)	after the superposition below geometry-derived
TM-score	fold similarity of the ligand's host chain, normalised by the holo length. Under ~30 nt it tracks chain length, so a low value there does not mean a different fold	US-align tool-derived
Radius of gyration	size of the fitted chains, apo → holo, over the residues modelled in both	C3′ atoms, NumPy geometry-derived
Ligand burial	share of the ligand surface covered by RNA in the holo complex	Shrake–Rupley surface area, Biopython geometry-derived
Functional type	the most specific functional class of the host chain; Unannotated when NAKB gives none	NAKB deposited metadata
Sequence alignment	apo and holo lined up residue by residue; faded letters are declared but not modelled	Needleman–Wunsch on the declared (SEQRES) sequences geometry-derived
Per-residue displacement	how far each nucleotide's C3′ atom moved; one chart per binding-site chain, all in the same frame	distance after the superposition below geometry-derived
3D superposition + morph	the apo overlaid on the holo, and the morph from apo to holo (an entry without a morph says so)	one rigid Kabsch fit on the paired C3′ atoms of all binding-site chains (residues paired by sequence, one apo chain per holo chain). The morph is a straight-line interpolation for display, not a simulation geometry-derived
Secondary structure (2D)	apo and holo base pairing; click a base to find it in 3D · what DSSR extracts ↓	x3dna-dssr tool-derived
Conformational dashboard	one cell per holo nucleotide: displacement colour, binding-site marker, motif band	displacement + x3dna-dssr motifs geometry-derivedtool-derived
Base-pair rewiring	base pairs formed, disrupted or unchanged on binding	x3dna-dssr pairs of both structures, matched through the sequence alignment tool-derived
Ligand interactions (3D) · Interaction data	H-bonds, π-stacking, halogen bonds, ligand–metal coordination and residue distances; tables of base pairs, interactions, H-bonds, rewiring and motifs	H-bonds: x3dna-dssr (PLIP when DSSR cannot read the ligand). π-stacking, halogen bonds, metal coordination: PLIP. Distances: gemmi tool-derivedgeometry-derived

What x3dna-dssr extracts

x3dna-dssr reads the coordinates of each apo and holo structure (nothing is predicted from sequence) and reports:

2D layout

the sequence and dot-bracket of each chain → the Secondary structure (2D) diagram.

Base pairs

every pair, canonical and non-canonical, with its Leontis–Westhof and Saenger class → the Base pairing table and Base-pair rewiring.

Structural motifs

stems, hairpin, internal and bulge loops, junctions and single strands → the Structural motifs table and the motif colouring.

Reading the Leontis–Westhof code (cWW, tHS, …)

Each base has three edges: Watson–Crick, Hoogsteen and Sugar. A pair is named by its glycosidic orientation (cis or trans) and the two edges in contact, giving 12 families. cWW is the standard A–U, G–C or G–U pair; tHS is a common non-canonical pair. Non-canonical pairs, which dot-bracket cannot show, still appear in the Base pairing table.

Contact & feedback

Questions, corrections, bug reports, or an apo–holo pair we missed? Email yanjun.li@ufl.edu and jiang.shiyu@ufl.edu; we respond to data corrections promptly. To analyse your own apo and holo structures, use Query.