4YM6 Crystal structure of the human nucleosome containing 6-4PP (outside) date
authors Osakabe, A., Tachiwana, H., Kagawa, W., Horikoshi, N., Matsumoto, S., Hasegawa, M., Matsumoto, N., Toga, T., Yamamoto, J., Hanaoka, F., Thoma, N.H., Sugasawa, K., Iwai, S., Kurumizaka, H.
compound source
symmetry
R_factor
R_Free 0.2868
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.51
ligand T64 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceStructural basis of pyrimidine-pyrimidone (6-4) photoproduct recognition by UV-DDB in the nucleosome., Osakabe A, Tachiwana H, Kagawa W, Horikoshi N, Matsumoto S, Hasegawa M, Matsumoto N, Toga T, Yamamoto J, Hanaoka F, Thoma NH, Sugasawa K, Iwai S, Kurumizaka H, Sci Rep. 2015 Nov 17;5:16330. doi: 10.1038/srep16330. PMID:26573481
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (246 Kb) [Save to disk]
  • Biological Unit Coordinates (4ym6.pdb1.gz) 239 Kb
  • LPC: Ligand-Protein Contacts for 4YM6
  • CSU: Contacts of Structural Units for 4YM6
  • Structure Factors (820 Kb)
  • Retrieve 4YM6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4YM6 from S2C, [Save to disk]
  • Re-refined 4ym6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4YM6 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 4YM6
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ym6_G] [4ym6_J] [4ym6_E] [4ym6_F] [4ym6] [4ym6_I] [4ym6_D] [4ym6_A] [4ym6_B] [4ym6_C] [4ym6_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4YM6: [H2A] [H2B] [H3] [H4 ] by SMART
    • Other resources with information on 4YM6
  • Community annotation for 4YM6 at PDBWiki (http://pdbwiki.org)

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