23KA | pdb_000023ka

pre-miR-6074 internal loop in complex with amiloride (Form 2)

PDB DOI: https://doi.org/10.2210/pdb23KA/pdb
NAKB: 23KA

Classification: RNA
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2026-02-09 Released: 2026-05-06
Deposition Author(s): Kondo, J., Okada, M., Tsuzuki, K., Onizuka, K., Nagasawa, R., Miyashita, E., Komatsu, K.R., Saito, H., Nagatsugi, F.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free:
0.219 (Depositor), 0.221 (DCC)
R-Value Work:
0.182 (Depositor), 0.182 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

RNA-binding Landscape of Amiloride: Large-scale Profiling and Structural Basis of U-U Mismatch Recognition

Tsuzuki, K., Onizuka, K., Okada, M., Nagasawa, R., Miyashita, E., Komatsu, K.R., Saito, H., Kondo, J., Nagatsugi, F.

(2025) RSC Chem Biol

DOI: https://doi.org/10.1039/D6CB00055J

Macromolecule Content

Total Structure Weight: 34.75 kDa
Atom Count: 2,333
Modeled Residue Count: 105
Deposited Residue Count: 105
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
RNA (35-MER)	A, B, C	35	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMR (Subject of Investigation/LOI) Query on AMR Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain I [auth C] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain I [auth C] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B], I [auth C]	3,5-DIAMINO-N-(AMINOIMINOMETHYL)-6-CHLOROPYRAZINECARBOXAMIDE C₆ H₈ Cl N₇ O XSDQTOBWRPYKKA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain I [auth C] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain I [auth C]
CAD Query on CAD Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	CACODYLIC ACID C₂ H₇ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], J [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C]