9FT8 | pdb_00009ft8

Crystal structure of d(CGTGAATTCACG) with HT1

• PDB DOI: https://doi.org/10.2210/pdb9FT8/pdb
• NAKB: 9FT8

• Classification: DNA
• Organism(s): DNA molecule
• Mutation(s): No 


• Deposited: 2024-06-24 Released: 2025-01-22 
• Deposition Author(s): Sbirkova-Dimitrova, H.I., Shivachev, B.L.
• Funding Organization(s): Bulgarian National Science Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.246 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.227 (DCC) 

Starting Model: experimental

Literature

Structural Characterization of B-DNA d(CGTGAATTCACG)2 in Complex with the Specific Minor Groove Binding Fluorescent Marker Hoechst 33342

Sbirkova-Dimitrova, H., Rusew, R., Gerginov, H., Heroux, A., Shivachev, B.L.

(2025) Crystals (Basel) 15

• DOI: https://doi.org/10.3390/cryst15010020

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.9 kDa 
• Atom Count: 542 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*TP*GP*AP*AP*TP*TP*CP*AP*CP*G)-3')	A [auth AAA], B [auth BBB]	12	DNA molecule

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HT1 (Subject of Investigation/LOI)	G [auth BBB]	2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE C27 H28 N6 O PRDFBSVERLRRMY-UHFFFAOYSA-N
CL	E [auth AAA], F [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth AAA], D [auth AAA]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.246 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.227 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.593	α = 90
b = 40.406	β = 90
c = 65.033	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Sbirkova-Dimitrova, H.I., Shivachev, B.L.

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Funding Organization	Location	Grant Number
Bulgarian National Science Fund	Bulgaria	KP-06-KOCT/5

Revision History  

• Version 1.0: 2025-01-22
  Type: Initial release