1Y3S Rna date Nov 26, 2004
title Hiv-1 Dis Rna Subtype F- Mpd Form
authors E.Ennifar, P.Dumas
compound source
Molecule: 5'-R(Cpup(5bu) Pgpcpupgpapapgpupgpcpapcpapcpapgpcpapap
Chain: A, B
Synonym: Hiv-1 Genomic Rna Dis
Engineered: Yes
 Synthetic: Yes
symmetry Space Group: C 2 2 21
R_factor 0.243 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
27.243 117.794 94.587 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.25 Å
ligand 5BU, K, MG enzyme
Primary referencePolymorphism of Bulged-out Residues in HIV-1 RNA DIS Kissing Complex and Structure Comparison with Solution Studies., Ennifar E, Dumas P, J Mol Biol. 2006 Feb 24;356(3):771-82. Epub 2005 Dec 21. PMID:16403527
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (27 Kb) [Save to disk]
  • Biological Unit Coordinates (1y3s.pdb1.gz) 22 Kb
  • LPC: Ligand-Protein Contacts for 1Y3S
  • CSU: Contacts of Structural Units for 1Y3S
  • Likely Quarternary Molecular Structure file(s) for 1Y3S
  • Structure Factors (96 Kb)
  • Retrieve 1Y3S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Y3S from S2C, [Save to disk]
  • Re-refined 1y3s structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1Y3S in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 1Y3S
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1Y3S, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1y3s_A] [1y3s_B] [1y3s]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 1Y3S
  • Community annotation for 1Y3S at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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