6YOV OCT4-SOX2-bound nucleosome - SHL+6 date
authors Michael, A.K., Kempf, G., Cavadini, S., Bunker, R.D., Thoma, N.H.
compound source
symmetry
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.42
ligand PTD enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


K
  • DNA binding


  • Primary referenceMechanisms of OCT4-SOX2 motif readout on nucleosomes., Michael AK, Grand RS, Isbel L, Cavadini S, Kozicka Z, Kempf G, Bunker RD, Schenk AD, Graff-Meyer A, Pathare GR, Weiss J, Matsumoto S, Burger L, Schubeler D, Thoma NH, Science. 2020 Apr 23. pii: science.abb0074. doi: 10.1126/science.abb0074. PMID:32327602
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (258 Kb) [Save to disk]
  • Biological Unit Coordinates (6yov.pdb1.gz) 246 Kb
  • LPC: Ligand-Protein Contacts for 6YOV
  • CSU: Contacts of Structural Units for 6YOV
  • Retrieve 6YOV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6YOV from S2C, [Save to disk]
  • View 6YOV 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 6YOV
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6yov from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6yov_I] [6yov_L] [6yov_G] [6yov_E] [6yov_C] [6yov_H] [6yov_D] [6yov_F] [6yov_J] [6yov_B] [6yov_A] [6yov_K]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6YOV
  • Community annotation for 6YOV at PDBWiki (http://pdbwiki.org)

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