3NX5 Dna date Jul 13, 2010
title The Crystal Structure Of Sanguinarine Bound To Dna D(Cgtacg)
authors M.Ferraroni, C.Bazzicalupi, P.Gratteri, A.R.Bilia
compound source
Molecule: 5'-D(Cpgptpapcpg)-3'
Chain: A, B, C, D
Engineered: Yes
 Synthetic: Yes
Other_details: Synthetic Dna
symmetry Space Group: P 32 2 1
R_factor 0.252 R_Free 0.283
crystal
cell
length a length b length c angle alpha angle beta angle gamma
29.992 29.992 119.069 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.31 Å
ligand CA, SAU enzyme
Primary referenceX-Ray diffraction analyses of the natural isoquinoline alkaloids Berberine and Sanguinarine complexed with double helix DNA d(CGTACG)., Ferraroni M, Bazzicalupi C, Bilia AR, Gratteri P, Chem Commun (Camb). 2011 May 7;47(17):4917-9. Epub 2011 Mar 22. PMID:21431128
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (14 Kb) [Save to disk]
  • Biological Unit Coordinates (3nx5.pdb1.gz) 5 Kb
  • Biological Unit Coordinates (3nx5.pdb2.gz) 6 Kb
  • LPC: Ligand-Protein Contacts for 3NX5
  • CSU: Contacts of Structural Units for 3NX5
  • Structure Factors (152 Kb)
  • Retrieve 3NX5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NX5 from S2C, [Save to disk]
  • Re-refined 3nx5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3NX5 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 3NX5
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3NX5, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3nx5_A] [3nx5_D] [3nx5_B] [3nx5_C] [3nx5]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3NX5
  • Community annotation for 3NX5 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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