9US0 | pdb_00009us0

Crystal structure of Ade1304 DNA aptamer (Ade1304b) bound to AMP

PDB DOI: https://doi.org/10.2210/pdb9US0/pdb

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

Deposited: 2025-04-30 Released: 2026-11-11
Deposition Author(s): Chen, X., Luo, Y., Ren, Y., Huang, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.274 (Depositor), 0.272 (DCC)
R-Value Work:
0.217 (Depositor), 0.214 (DCC)
R-Value Observed:
0.220 (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

Crystal structure of adenosine and ATP-binding DNA aptamer

Chen, X., Luo, Y., Ren, Y., Huang, L.

To be published.

Macromolecule Content

Total Structure Weight: 48.78 kDa
Atom Count: 3,368
Modeled Residue Count: 152
Deposited Residue Count: 152
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
DNA (38-MER)	A, B, C, D	38	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP (Subject of Investigation/LOI) Query on AMP Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain J [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth D] MOL2 format, chain J [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth D] mmCIF format, chain J [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], J [auth C], N [auth D]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain J [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain J [auth C] Focus chain N [auth D]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain G [auth B] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B]	G [auth B] H [auth B] K [auth C] L [auth C] M [auth C] G [auth B], H [auth B], K [auth C], L [auth C], M [auth C], O [auth D], P [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D]
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain I [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain I [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain I [auth B]	I [auth B], Q [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain Q [auth D] Interactions & Density Focus chain I [auth B] Focus chain Q [auth D]