9CKH | pdb_00009ckh

[d2d3-2Ag] Tensegrity triangle with deazapurines on the helical and center strands with two deazaA:Ag+:T base pairs

• PDB DOI: https://doi.org/10.2210/pdb9CKH/pdb
• NAKB: 9CKH

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


• Deposited: 2024-07-08 Released: 2025-07-30 
• Deposition Author(s): Vecchioni, S., Jong, M.A., Woloszyn, K., Sha, R., Ohayon, Y.P., Gallindo, M.A., Lopez Chamorro, C.
• Funding Organization(s): Office of Naval Research (ONR), National Science Foundation (NSF, United States), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 5.92 Å
• R-Value Free: 
  0.179 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Literature

Deazapurine metal-mediated nanostructures

Lopez Chamorro, C., Jong, M.A.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 13 kDa 
• Atom Count: 857 
• Modeled Residue Count: 42 
• Deposited Residue Count: 42 
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')	A	21	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')	B	7	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')	C	6	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')	D	8	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AG (Subject of Investigation/LOI)	E [auth A], F [auth D]	SILVER ION Ag FOIXSVOLVBLSDH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 5.92 Å
• R-Value Free:  0.179 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.277	α = 90
b = 123.277	β = 90
c = 62.265	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
STARANISO	data scaling
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Vecchioni, S., Jong, M.A., Woloszyn, K., Sha, R., Ohayon, Y.P., Gallindo, M.A., Lopez Chamorro, C.

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Funding Organization	Location	Grant Number
Office of Naval Research (ONR)	United States	N000141912596
National Science Foundation (NSF, United States)	United States	CCF-2106790
National Science Foundation (NSF, United States)	United States	GCR-2317843
Department of Energy (DOE, United States)	United States	DE-SC0007991

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release