419D Dna-Rna Hybrid date Aug 12, 1998
title Octamer 5'-R(Gpupapupapcpa)-D(Pc)-3' With Six Watson Base-Pairs And Two 3' Overhang Residues
authors S.M.Mitra, K.Shi, R.Biswas, M.Sundaralingam
compound source
Molecule: Dnarna (5'-R(Gpupapupapcpa)-D(Pc)-3')
Chain: A, B, C, D
Engineered: Yes
 Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.186 R_Free 0.278
crystal
cell
length a length b length c angle alpha angle beta angle gamma
24.190 45.530 74.200 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
Primary referenceThe crystal structure of the octamer [r(guauaca)dC]2 with six Watson-Crick base-pairs and two 3' overhang residues., Shi K, Biswas R, Mitra SN, Sundaralingam M, J Mol Biol 2000 May 26;299(1):113-22. PMID:10860726
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (17 Kb) [Save to disk]
  • Biological Unit Coordinates (419d.pdb1.gz) 7 Kb
  • Biological Unit Coordinates (419d.pdb2.gz) 8 Kb
  • CSU: Contacts of Structural Units for 419D
  • Likely Quarternary Molecular Structure file(s) for 419D
  • Structure Factors (25 Kb)
  • Retrieve 419D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 419D from S2C, [Save to disk]
  • Re-refined 419d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 419D 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 419D
  • 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 419D, 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: [419d_B] [419d] [419d_D] [419d_A] [419d_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 419D
  • Community annotation for 419D at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science