9HIO | pdb_00009hio

RKEC1 DNA aptamer bound to dopamine

PDB DOI: https://doi.org/10.2210/pdb9HIO/pdb
NAKB: 9HIO
BMRB: 52690
BMRB: 52689

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

Deposited: 2024-11-26 Released: 2025-12-10
Deposition Author(s): Largy, E., Kaiyum, Y.A., Chao, E.H.P., Vialet, B., Johnson, P.E., Mackereth, C.D.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 15
Selection Criteria: structures with the lowest energy

wwPDB Validation 3D Report Full Report

Validation slider image for 9HIO

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

Literature

Unconventional DNA architecture in a dopamine–bound aptamer complex

Chao, E.H.P., Largy, E., Kaiyum, Y.A., Nguyen, M.D., Vialet, B., Dauphin-Ducharme, P., Johnson, P.E., Mackereth, C.D.

(2025) bioRxiv

DOI: https://doi.org/10.1101/2025.11.27.690961

Macromolecule Content

Total Structure Weight: 8.59 kDa
Atom Count: 571
Modeled Residue Count: 27
Deposited Residue Count: 27
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 1
RKEC1 DNA (27-MER)	A	27	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LDP (Subject of Investigation/LOI) Query on LDP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	L-DOPAMINE C₈ H₁₁ N O₂ VYFYYTLLBUKUHU-UHFFFAOYSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 15
Selection Criteria: structures with the lowest energy

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-10

Deposition Author(s):

Mackereth, C.D.

Funding Organization	Location	Grant Number
Other government	Canada	France Canada Research Fund

Revision History (Full details and data files)

Version 1.0: 2025-12-10
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.