7PNL

Complex between monomolecular human telomeric G-quadruplex and a sulfonamide derivative of the natural alkaloid Berberine

• PDB DOI: https://doi.org/10.2210/pdb7PNL/pdb
• NAKB: 7PNL

• Classification: DNA
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2021-09-07 Released: 2022-09-21 
• Deposition Author(s): Bazzicalupi, C., Gratteri, P., Petreni, A., Nocentini, A.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.321 
• R-Value Work: 0.204 
• R-Value Observed: 0.209 

Literature

Complex between monomolecular human telomeric G-quadruplex and a sulfonamide derivative of the natural alkaloid Berberine

Bazzicalupi, C., Gratteri, P., Petreni, A., Nocentini, A., Supuran, C., Randazzo, A.

To be published.

Biological Assembly 1  

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

Macromolecule Content

• Total Structure Weight: 8.64 kDa 
• Atom Count: 598 
• Modelled Residue Count: 23 
• Deposited Residue Count: 23 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
G-guadruplex DNA (23-mer)	A	23	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7VE (Subject of Investigation/LOI)	E [auth A], F [auth A]	4-[[1-[3-[(17-methoxy-5,7-dioxa-13-azoniapentacyclo[11.8.0.0^{2,10}.0^{4,8}.0^{15,20}]henicosa-1(21),2(10),3,8,13,15,17,19-octaen-16-yl)oxy]propyl]triazol-4-yl]methoxy]benzenesulfonamide C31 H30 N5 O7 S ZPZQYKHNQSCVCG-UHFFFAOYSA-N
K	B [auth A], C [auth A], D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.321 
• R-Value Work: 0.204 
• R-Value Observed: 0.209 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.842	α = 90
b = 72.717	β = 90.1
c = 27.028	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-09-21 
Deposition Author(s): Bazzicalupi, C., Gratteri, P., Petreni, A., Nocentini, A.

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Funding Organization	Location	Grant Number
Other government		FFARB2018
Other government		CARLABAZZICALUPIRICATEN2020

Revision History  

• Version 1.0: 2022-09-21
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description