3C5D | pdb_00003c5d

Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to lividomycin

• PDB DOI: https://doi.org/10.2210/pdb3C5D/pdb
• NAKB: 3C5D

• Classification: RNA
• Mutation(s): No 


• Deposited: 2008-01-31 Released: 2008-05-06 
• Deposition Author(s): Freisz, S., Lang, K., Micura, R., Dumas, P., Ennifar, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.245 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.246 (DCC) 
• R-Value Observed: 
  0.232 (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: 16.53 kDa 
• Atom Count: 1,226 
• Modeled Residue Count: 46 
• Deposited Residue Count: 46 
• Unique hybrid chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LIV	D [auth B], E [auth B]	(2R,3S,4S,5S,6R)-2-((2S,3S,4R,5R,6R)-5-AMINO-2-(AMINOMETHYL)-6-((2R,3S,4R,5S)-5-((1R,2R,3S,5R,6S)-3,5-DIAMINO-2-((2S,3R ,5S,6R)-3-AMINO-5-HYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-6-HYDROXYCYCLOHEXYLOXY)-4-HYDROXY-2-(HYDROXYMET HYL)-TETRAHYDROFURAN-3-YLOXY)-4-HYDROXY-TETRAHYDRO-2H-PYRAN-3-YLOXY)-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-3,4,5-TRIOL C29 H55 N5 O18 DBLVDAUGBTYDFR-SWMBIRFSSA-N
K	C [auth A], F [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.245 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.246 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.086	α = 90
b = 29.294	β = 120.84
c = 59.607	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DNA	data collection
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2008-05-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary