3C44

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
HIV-1 subtype F genomic RNA
A, B
23N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
K
Query on K

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
H [auth B],
J [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.818α = 90
b = 95.703β = 90
c = 47.856γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DNAdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary