2QEK

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.265
R-Value Work: 0.251
R-Value Observed: 0.251

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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

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.

Macromolecule Content

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

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K Query on K Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	C [auth A], D [auth A], F [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.265
R-Value Work: 0.251
R-Value Observed: 0.251
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

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Entry History

Deposition Data

Released Date: 2008-05-06

Deposition Author(s):

Freisz, S.

Ennifar, E.

Dumas, P.

Revision History (Full details and data files)

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

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