8ZD8 | pdb_00008zd8

NMR structure of the (CGG-dsDNA:ND=) 1:1 complex

• PDB DOI: https://doi.org/10.2210/pdb8ZD8/pdb
• NAKB: 8ZD8

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


• Deposited: 2024-05-01 Released: 2025-04-30 
• Deposition Author(s): Sakurabayashi, S., Furuita, K., Yamada, T., Nomura, M., Nakatani, K., Kojima, C.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED), Japan Science and Technology

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

NMR structure of the (CGG-dsDNA:ND=) 1:1 complex

Sakurabayashi, S., Furuita, K., Yamada, T., Nomura, M., Nakatani, K., Kojima, C.

To be published.

Biological Assembly 1  

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

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 7.19 kDa 
• Atom Count: 481 
• Modeled Residue Count: 22 
• Deposited Residue Count: 22 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*AP*AP*TP*G)-3')	A [auth 1]	11	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*TP*TP*CP*GP*GP*TP*TP*AP*G)-3')	B [auth 2]	11	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L1S (Subject of Investigation/LOI)	C [auth 1]	~{N}-(7-methyl-1,8-naphthyridin-2-yl)-3-[[3-[(7-methyl-1,8-naphthyridin-2-yl)amino]-3-oxidanylidene-propyl]amino]propanamide C24 H25 N7 O2 QZBZQIYEBGGLJT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-30 
Deposition Author(s): Sakurabayashi, S., Furuita, K., Yamada, T., Nomura, M., Nakatani, K., Kojima, C.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP22H05536
Japan Society for the Promotion of Science (JSPS)	Japan	JP23J02416
Japan Agency for Medical Research and Development (AMED)	Japan	JP23ama121001
Japan Science and Technology	Japan	JPMJFS2125
Japan Society for the Promotion of Science (JSPS)	Japan	JP21K06047

Revision History  

• Version 1.0: 2025-04-30
  Type: Initial release