8T4N | pdb_00008t4n

DB1976 Bound to the DNA Sequence 5'-CGCGAATTCGCG-3

• PDB DOI: https://doi.org/10.2210/pdb8T4N/pdb
• NAKB: 8T4N

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


• Deposited: 2023-06-09 Released: 2024-06-12 
• Deposition Author(s): Terrell, J.R., Poon, G.M.K., Wilson, W.D.
• Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.247 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Structural studies on the PU.1 inhibitory mechanism by diamidine minor groove binders

Terrell, J.R., Paul, A., Ogbonna, E.N., Farahat, A.A., Poon, G.M.K., Wilson, W.D.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.77 kDa 
• Atom Count: 547 
• 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*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')	A, B	12	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y5U (Subject of Investigation/LOI)	C [auth A]	(2M,2'M)-2,2'-(selenophene-2,5-diyl)di(1H-benzimidazole-6-carboximidamide) C20 H16 N8 Se NXECULIQZLOKFU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.247 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.442	α = 90
b = 41.286	β = 90
c = 65.719	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-06-12 
Deposition Author(s): Terrell, J.R., Poon, G.M.K., Wilson, W.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL155178
National Science Foundation (NSF, United States)	United States	MCB2028902
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM137160
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM111749

Revision History  

• Version 1.0: 2024-06-12
  Type: Initial release