9U3I | pdb_00009u3i

Crystal structure of a phenylalanine-modifi ed thrombin-binding DNA aptamer

• PDB DOI: https://doi.org/10.2210/pdb9U3I/pdb
• NAKB: 9U3I

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


• Deposited: 2025-03-18 Released: 2026-03-25 
• Deposition Author(s): Park, S., Kanazawa, H., Kondo, J.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.205 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a phenylalanine-modifi ed thrombin-binding DNA aptamer

Park, S., Kanazawa, H., Kondo, J.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 4.91 kDa 
• Atom Count: 383 
• Modeled Residue Count: 15 
• Deposited Residue Count: 15 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*G*(FNH)P*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')	A [auth B]	15	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PHE (Subject of Investigation/LOI)	B	PHENYLALANINE C9 H11 N O2 COLNVLDHVKWLRT-QMMMGPOBSA-N
BA	C [auth B]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.205 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.055	α = 90
b = 54.44	β = 90
c = 21.419	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-03-25 
Deposition Author(s): Park, S., Kanazawa, H., Kondo, J.

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

Revision History  

• Version 1.0: 2026-03-25
  Type: Initial release