9CKA | pdb_00009cka

[7F1F-AgP63-inter] Tensegrity triangle with 2-thiothymidine in the junction and Ag+ intercalating between base pair stacks with P63 symmetry

• PDB DOI: https://doi.org/10.2210/pdb9CKA/pdb
• NAKB: 9CKA

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


• Deposited: 2024-07-08 Released: 2026-03-18 
• Deposition Author(s): Vecchioni, S., Lu, B., Sha, R., Ohayon, Y.P.
• Funding Organization(s): National Science Foundation (NSF, United States), Department of Energy (DOE, United States), Office of Naval Research (ONR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 6.63 Å
• R-Value Free: 
  0.222 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Thiopyrimidine metal base pairs

Vecchioni, S., Sha, R., Lu, B., Ohayon, Y.P.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 12.92 kDa 
• Atom Count: 856 
• 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(*AP*GP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')	A	21	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-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*(2PS))-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 D]	SILVER ION Ag FOIXSVOLVBLSDH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 6.63 Å
• R-Value Free:  0.222 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.476	α = 90
b = 127.476	β = 90
c = 52.673	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: 2026-03-18 
Deposition Author(s): Vecchioni, S., Lu, B., Sha, R., Ohayon, Y.P.

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

Revision History  

• Version 1.0: 2026-03-18
  Type: Initial release