9KTJ | pdb_00009ktj

Solution NMR structures of ATP-binding DNA aptamer in complex with ATP

PDB DOI: https://doi.org/10.2210/pdb9KTJ/pdb
NAKB: 9KTJ

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

Deposited: 2024-12-02 Released: 2025-08-06
Deposition Author(s): Jiang, Y., Wan, L., Guo, P.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 10
Selection Criteria: structures with the lowest energy

wwPDB Validation 3D Report Full Report

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

Literature

Solution NMR structures of ATP-binding DNA aptamer in complex with ATP

Jiang, Y., Guo, P., Wan, L.

To be published.

Macromolecule Content

Total Structure Weight: 11.1 kDa
Atom Count: 735
Modeled Residue Count: 34
Deposited Residue Count: 34
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (34-MER)	A	34	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP 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]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 10
Selection Criteria: structures with the lowest energy

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-08-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-08-06
Type: Initial release

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.