Macromolecule Content

Total Structure Weight: 16.23 kDa
Atom Count: 1207
Modelled Residue Count: 46
Deposited Residue Count: 46
Unique nucleic acid chains: 1

3C44

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

PDB DOI: 10.2210/pdb3C44/pdb
NDB: DR0042

Classification: RNA
Mutation(s): No

Deposited: 2008-01-29 Released: 2008-05-06
Deposition Author(s): Freisz, S., Ennifar, E., Dumas, P.

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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: 10.1002/anie.200800726
Primary Citation of Related Structures:
2QEK, 3C3Z, 3C44, 3C5D, 3C7R

Macromolecules

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PAR Query on PAR Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B]	C [auth A], F [auth B]	PAROMOMYCIN C₂₃ H₄₅ N₅ O₁₄ UOZODPSAJZTQNH-LSWIJEOBSA-N		Ligand Interaction
K Query on K Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth B]	D [auth A], G [auth B], H [auth B], J [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B]	E [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction

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 = 30.818	α = 90
b = 95.703	β = 90
c = 47.856	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Deposited Date: 2008-01-29
Released Date: 2008-05-06

Deposition Author(s):

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

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.