421D Dna-Rna Hybrid date Aug 14, 1998
title 5'-D(Tptpcptptp(Bro)Cptptpc)-3', 5'- R(Gpapapgpapapgpapa)-3'
authors Y.Xiong, M.Sundaralingam
compound source
Molecule: Dna (5'-D(Tptpcptptp(Cbr)Ptptpc)-3')
Chain: A
Engineered: Yes
 Synthetic: Yes

Molecule: Rna (5'-R(Gpapapgpapapgpapa)-3')
Chain: B
Engineered: Yes
Synthetic: Yes
symmetry Space Group: P 61
R_factor 0.201 R_Free 0.237
crystal
cell
length a length b length c angle alpha angle beta angle gamma
48.080 48.080 42.880 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.80 Å
ligand CBR enzyme
Primary referenceCrystal structure and conformation of a DNA-RNA hybrid duplex with a polypurine RNA strand: d(TTCTTBr5CTTC)-r(GAAGAAGAA)., Xiong Y, Sundaralingam M, Structure 1998 Dec 15;6(12):1493-501. PMID:9862803
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (15 Kb) [Save to disk]
  • Biological Unit Coordinates (421d.pdb1.gz) 11 Kb
  • LPC: Ligand-Protein Contacts for 421D
  • CSU: Contacts of Structural Units for 421D
  • Likely Quarternary Molecular Structure file(s) for 421D
  • Structure Factors (31 Kb)
  • Retrieve 421D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 421D from S2C, [Save to disk]
  • Re-refined 421d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 421D 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 421D
  • 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 421D, 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: [421d] [421d_A] [421d_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 421D
  • Community annotation for 421D 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