4JIO Bro1 V domain and ubiquitin date 2013-03-06
authors Pashkova, N., Gakhar, L., Piper, R.C.
compound source
symmetry
R_factor
R_Free 0.4211
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.60
ligand MSE enzyme
Gene NCAS
Primary referenceThe yeast alix homolog bro1 functions as a ubiquitin receptor for protein sorting into multivesicular endosomes., Pashkova N, Gakhar L, Winistorfer SC, Sunshine AB, Rich M, Dunham MJ, Yu L, Piper RC, Dev Cell. 2013 Jun 10;25(5):520-33. doi: 10.1016/j.devcel.2013.04.007. Epub 2013 , May 30. PMID:23726974
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (172 Kb) [Save to disk]
  • Biological Unit Coordinates (4jio.pdb1.gz) 70 Kb
  • Biological Unit Coordinates (4jio.pdb2.gz) 72 Kb
  • Biological Unit Coordinates (4jio.pdb3.gz) 18 Kb
  • LPC: Ligand-Protein Contacts for 4JIO
  • CSU: Contacts of Structural Units for 4JIO
  • Structure Factors (231 Kb)
  • Retrieve 4JIO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4JIO from S2C, [Save to disk]
  • Re-refined 4jio structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4JIO 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 4JIO
  • 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 4JIO, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4jio_U] [4jio_B] [4jio_A] [4jio]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4JIO: [UBQ ] by SMART
    • Other resources with information on 4JIO
  • Community annotation for 4JIO at PDBWiki (http://pdbwiki.org)

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