4UP0 Ternary crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and a H3K4me2 peptide date
authors Miller, T.C.R., Fiedler, M., Rutherford, T.J., Birchall, K., Chugh, J., Bienz, M.
compound source
symmetry
R_factor
R_Free 0.16611
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.28
ligand MLY, ZN enzyme
Primary referenceCompetitive Binding of a Benzimidazole to the Histone-Binding Pocket of the Pygo PHD Finger., Miller TC, Rutherford TJ, Birchall K, Chugh J, Fiedler M, Bienz M, ACS Chem Biol. 2014 Oct 24. PMID:25323450
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (38 Kb) [Save to disk]
  • Biological Unit Coordinates (4up0.pdb1.gz) 32 Kb
  • LPC: Ligand-Protein Contacts for 4UP0
  • CSU: Contacts of Structural Units for 4UP0
  • Structure Factors (407 Kb)
  • Retrieve 4UP0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4UP0 from S2C, [Save to disk]
  • Re-refined 4up0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4UP0 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 4UP0
  • 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 4UP0, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4up0_F] [4up0] [4up0_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4UP0: [PHD ] by SMART
    • Other resources with information on 4UP0
  • Community annotation for 4UP0 at PDBWiki (http://pdbwiki.org)

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