4GLH DNA dodecamer containing 5-hydroxymethyl cytosine date
authors Spingler, B., Renciuk, D., Vorlickova, M.
compound source
symmetry
R_factor
R_Free 0.276
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.66
ligand 5HC, K enzyme
Primary referenceCrystal structures of B-DNA dodecamer containing the epigenetic modifications 5-hydroxymethylcytosine or 5-methylcytosine., Renciuk D, Blacque O, Vorlickova M, Spingler B, Nucleic Acids Res. 2013 Aug 20. PMID:23963698
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (26 Kb) [Save to disk]
  • Biological Unit Coordinates (4glh.pdb1.gz) 22 Kb
  • LPC: Ligand-Protein Contacts for 4GLH
  • CSU: Contacts of Structural Units for 4GLH
  • Structure Factors (162 Kb)
  • Retrieve 4GLH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4GLH from S2C, [Save to disk]
  • Re-refined 4glh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4GLH 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 4GLH
  • 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 4GLH, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4glh] [4glh_A] [4glh_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4GLH
  • Community annotation for 4GLH at PDBWiki (http://pdbwiki.org)

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