4GY5 Crystal structure of the tandem tudor domain and plant homeodomain of UHRF1 with Histone H3K9me3 date 2012-09-05
authors Cheng, J., Yang, Y., Fang, J., Xiao, J., Zhu, T., Chen, F., Wang, P., Xu, Y.
compound source
symmetry
R_factor
R_Free 0.2876
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.96
ligand M3L, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, E


Primary referenceStructural insight into coordinated recognition of trimethylated histone H3 lysine 9 (H3K9me3) by the plant homeodomain (PHD) and tandem tudor domain (TTD) of UHRF1 (ubiquitin-like, containing PHD and RING finger domains, 1) protein., Cheng J, Yang Y, Fang J, Xiao J, Zhu T, Chen F, Wang P, Li Z, Yang H, Xu Y, J Biol Chem. 2013 Jan 11;288(2):1329-39. doi: 10.1074/jbc.M112.415398. Epub 2012 , Nov 16. PMID:23161542
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (133 Kb) [Save to disk]
  • Biological Unit Coordinates (4gy5.pdb1.gz) 39 Kb
  • Biological Unit Coordinates (4gy5.pdb2.gz) 38 Kb
  • Biological Unit Coordinates (4gy5.pdb3.gz) 28 Kb
  • Biological Unit Coordinates (4gy5.pdb4.gz) 27 Kb
  • LPC: Ligand-Protein Contacts for 4GY5
  • CSU: Contacts of Structural Units for 4GY5
  • Structure Factors (373 Kb)
  • Retrieve 4GY5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4GY5 from S2C, [Save to disk]
  • Re-refined 4gy5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4GY5 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 4GY5
  • 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 4GY5, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4gy5_F] [4gy5_D] [4gy5] [4gy5_C] [4gy5_B] [4gy5_A] [4gy5_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4GY5: [PHD] [RING ] by SMART
    • Other resources with information on 4GY5
  • Community annotation for 4GY5 at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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