2QEK | pdb_00002qek

HIV-1 subtype F DIS RNA extended duplex form

• PDB DOI: https://doi.org/10.2210/pdb2QEK/pdb
• NAKB: 2QEK

• Classification: RNA
• Mutation(s): No 


• Deposited: 2007-06-26 Released: 2008-05-06 
• Deposition Author(s): Freisz, S., Ennifar, E., Dumas, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.265 (Depositor) 
• R-Value Work: 
  0.251 (Depositor), 0.261 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

Starting Model: experimental

Literature

Binding of aminoglycoside antibiotics to the duplex form of the HIV-1 genomic RNA dimerization initiation site.

Freisz, S., Lang, K., Micura, R., Dumas, P., Ennifar, E.

(2008) Angew Chem Int Ed Engl 47: 4110-4113

• PubMed: 18435520 
• DOI: https://doi.org/10.1002/anie.200800726
• Primary Citation Related Structures: 
  2QEK, 3C3Z, 3C44, 3C5D, 3C7R

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Organizational Affiliation: 
• Architecture et Réactivité de l'ARN, Université Louis Pasteur/CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg, France.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 14.91 kDa 
• Atom Count: 1,055 
• Modeled Residue Count: 46 
• Deposited Residue Count: 46 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
HIV-1 subtype F DIS genomic RNA	A, B	23	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	C [auth A], D [auth A], F [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.265 (Depositor) 
• R-Value Work:  0.251 (Depositor), 0.261 (DCC) 
• R-Value Observed: 0.251 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.773	α = 90
b = 37.355	β = 111.24
c = 44.965	γ = 90

Software Package:

Software Name	Purpose
MX	data collection
CNS	refinement
DENZO	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-06 
Deposition Author(s): Freisz, S., Ennifar, E., Dumas, P.

Revision History  

• Version 1.0: 2008-05-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description