// Golden target · RNA pipeline, evidence layer
FMN riboswitch (5C45)
54 nt · predicted structure regenerated live for this page (same single-sequence RhoFold + ANM ensemble + fpocket + ranker pipeline as every worked example on this site).
// Sequence
// Findings
Family, precedent, and provenance
Family classification
returned dataFMN (RF00050) — FMN riboswitch aptamer (RFN element)
E=4.60e-9 · bit score 41.3 · passes full-length threshold: no
hit is statistically significant (E=4.6e-09) but scores below the family's own curated full-length gathering threshold (bit_score=41.3 < GA=66.2) — consistent with a partial/sub-domain match rather than a full-length family member
Known ligand precedent
returned data19 HARIBOSS-curated · 19 broader RCSB structures
- 2YIE — FMN, GZ7
- 2YIF — FMN, GZ7
- 6DN1 — FMN, GZ7
- 3F2Q — FMN
- 3F2T — FMN
Conservation
returned data146 seed sequences · mean pairwise identity 61.5%
Similar known RNAs
returned data- 3F4E — 100.0% identity · 51B, 6YG, DKM, FMN, GZ4, GZG, RBF, RS3
- 2YIE — 94.4% identity · FMN, GZ7
- 2YIF — 46.5% identity · FMN, GZ7
- 3F4G — 46.4% identity · 51B, 6YG, DKM, FMN, GZ4, GZG, RBF, RS3
- 3F2Q — 21.4% identity · FMN
Structure-based: not applicable. Foldseek does not support nucleic-acid structures — its 3Di structural alphabet is protein-specific. Confirmed by testing against the FMN riboswitch golden target (PDB 5C45): querying with an all-RNA structure produces no queryable representation in Foldseek's own database, not merely zero hits. This is a permanent tool limitation for this phase, not a missing computation.
Interaction fingerprints (Evidence Integration Layer)
returned dataRepresentative complex: 2YIE (FMN, 2.94 Å)
| Residue (PDB) | Residue (pipeline) | Interaction | Partner |
|---|---|---|---|
| 48 | 48 | hydrogen bond | A48 (hydrogen bond) with ligand FMN |
| 84 | ? | hydrogen bond | G84 (hydrogen bond) with ligand FMN |
| 99 | ? | hydrogen bond | A99 (hydrogen bond) with ligand FMN |
| 48 | 48 | hydrogen bond | A48 (hydrogen bond) with ligand FMN |
| 99 | ? | hydrogen bond | A99 (hydrogen bond) with ligand FMN |
| 11 | 11 | hydrogen bond | G11 (hydrogen bond) with ligand FMN |
| 10 | 10 | hydrogen bond | G10 (hydrogen bond) with ligand FMN |
| 62 | ? | hydrogen bond | G62 (hydrogen bond) with ligand FMN |
| 62 | ? | hydrogen bond | G62 (hydrogen bond) with ligand FMN |
| 32 | 32 | hydrogen bond | G32 (hydrogen bond) with ligand FMN |
| 84 | ? | hydrogen bond | G84 (hydrogen bond) with ligand FMN |
| 10 | 10 | hydrogen bond | G10 (hydrogen bond) with ligand FMN |
| 11 | 11 | hydrogen bond | G11 (hydrogen bond) with ligand FMN |
| 85 | ? | pi stacking | A85 (pi stacking) with ligand FMN |
| 85 | ? | pi stacking | A85 (pi stacking) with ligand FMN |
| 85 | ? | pi stacking | A85 (pi stacking) with ligand FMN |
| 85 | ? | pi stacking | A85 (pi stacking) with ligand FMN |
| 48 | 48 | pi stacking | A48 (pi stacking) with ligand FMN |
Representative complex: 3F4E (51B, 3.05 Å)
ligand 51B not found as an analyzable PLIP binding site in this structure
1/2 representative structure(s) produced interaction data
Structural analysis — ranked pocket clusters
returned data| Rank | Persistence | Residues |
|---|---|---|
| #1 | 1 | 9, 10, 11, 31, 32, 33, 34, 35, 41, 42 |
| #2 | 0.4 | 10, 11, 12, 29, 30, 31 |
| #3 | 0.4 | 18, 19, 21, 22, 24 |
Pocket residues overlapping known interaction sites
- Pocket 1: residues 10, 11, 32 (3 of 10 pocket residues match a known interaction site)
- Pocket 2: residues 10, 11 (2 of 6 pocket residues match a known interaction site)
- Pocket 3: no overlap with known interaction sites (5 checked)
// Limitations & data provenance
Auto-populated from each section’s own status — not hand-maintained.