9K8N | pdb_00009k8n

Solution structure of a short zinc-dependent DNAzyme minGAA

PDB DOI: https://doi.org/10.2210/pdb9K8N/pdb
NAKB: 9K8N

Classification: DNA-RNA HYBRID
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2024-10-24 Released: 2025-10-29
Deposition Author(s): Yamasaki, K., Yamasaki, T., Takeuchi, K.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 20
Selection Criteria: structures with the least restraint violations

wwPDB Validation 3D Report Full Report

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

Literature

A minimal Zn2+-dependent RNA-cleaving DNAzyme and its B-DNA-like crystal and solution structures

Yamasaki, K., Inomata, R., Yamasaki, T., Kubota, T., Miyashita, N., Takeuchi, K., Miyagishi, M.

To be published.

Macromolecule Content

Total Structure Weight: 8.16 kDa
Atom Count: 539
Modeled Residue Count: 26
Deposited Residue Count: 26
Unique hybrid chains: 1

Macromolecules

Find similar nucleic acids by: | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNAzyme minGAA	A	26	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN 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]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 20
Selection Criteria: structures with the least restraint violations

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-10-29
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.