4O5Y O6-carboxymethylguanine in DNA forms a sequence context dependent wobble base pair structure with thymine date
authors Zhang, F., Tsunoda, M., Suzuki, K., Kikuchi, Y., Wilkinson, O., Millington, C.L., Margison, G.P., Williams, D.M., Takenaka, A.
compound source
symmetry
R_factor
R_Free 0.26859
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.75
ligand BA, C6G, K enzyme
Primary referenceO(6)-Carboxymethylguanine in DNA forms a sequence context-dependent wobble base-pair structure with thymine., Zhang F, Tsunoda M, Kikuchi Y, Wilkinson O, Millington CL, Margison GP, Williams DM, Takenaka A, Acta Crystallogr D Biol Crystallogr. 2014 Jun;70(Pt 6):1669-79. doi:, 10.1107/S1399004714006178. Epub 2014 May 30. PMID:24914978
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (18 Kb) [Save to disk]
  • Biological Unit Coordinates (4o5y.pdb1.gz) 13 Kb
  • LPC: Ligand-Protein Contacts for 4O5Y
  • CSU: Contacts of Structural Units for 4O5Y
  • Structure Factors (137 Kb)
  • Retrieve 4O5Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4O5Y from S2C, [Save to disk]
  • Re-refined 4o5y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4O5Y 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 4O5Y
  • 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 4O5Y, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4o5y] [4o5y_B] [4o5y_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4O5Y
  • Community annotation for 4O5Y at PDBWiki (http://pdbwiki.org)

    • 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