9JA7 | pdb_00009ja7

Crystal structure of theophylline aptamer obtained in the presence of caffeine

• PDB DOI: https://doi.org/10.2210/pdb9JA7/pdb
• NAKB: 9JA7

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


• Deposited: 2024-08-24 Released: 2025-09-03 
• Deposition Author(s): Kondo, J., Ohtani, Y.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 
  0.260 (Depositor), 0.291 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Crystal structure of theophylline aptamer obtained in the presence of caffeine

Kondo, J., Ohtani, Y.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 11.64 kDa 
• Atom Count: 748 
• Modeled Residue Count: 33 
• Deposited Residue Count: 33 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Theophylline aptamer	A	33	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N
K	H [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free:  0.260 (Depositor), 0.291 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.925	α = 90
b = 46.925	β = 90
c = 180.258	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Kondo, J., Ohtani, Y.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP23ama121014

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release