462D Rna date Mar 18, 1999
title Crystal Structure Of The Hiv-1 Genomic Rna Dimerization Init Site
authors E.Ennifar, M.Yusupov, P.Walter, R.Marquet, C.Ehresmann, B.Ehresma P.Dumas
compound source
Molecule: Rna (5'- R(Cpupupgpcpupgpapgpgpupgpcpapcpapcpapgp G) -3');
Chain: A, B
Synonym: Hiv-1(Mal) Genomic Rna Dimerization Initiation Sit
Engineered: Yes
Synthetic: Yes
symmetry Space Group: P 31 2 1
R_factor 0.211 R_Free 0.212
crystal
cell
length a length b length c angle alpha angle beta angle gamma
59.100 59.100 64.000 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
ligand MG enzyme
Primary referenceThe crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges., Ennifar E, Yusupov M, Walter P, Marquet R, Ehresmann B, Ehresmann C, Dumas P, Structure Fold Des 1999 Nov 15;7(11):1439-49. PMID:10574792
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (31 Kb) [Save to disk]
  • Biological Unit Coordinates (462d.pdb1.gz) 26 Kb
  • LPC: Ligand-Protein Contacts for 462D
  • CSU: Contacts of Structural Units for 462D
  • Likely Quarternary Molecular Structure file(s) for 462D
  • Structure Factors (56 Kb)
  • Retrieve 462D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 462D from S2C, [Save to disk]
  • Re-refined 462d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 462D 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 462D
  • 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 462D, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [462d_B] [462d_A] [462d]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 462D
  • Community annotation for 462D 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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