5M93 Signaling Protein date Oct 31, 2016
title Crystal Structure Of Sdea-Modified Ubiquitin.
authors S.Kalayil, S.Bhogaraju, I.Dikic
compound source
Molecule: Polyubiquitin-B
Chain: A, B, C
Engineered: Yes
Mutation: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ubb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Pgex-6p1
symmetry Space Group: P 1 21 1
R_factor 0.189 R_Free 0.231
crystal
cell
length a length b length c angle alpha angle beta angle gamma
31.596 81.073 51.287 90.00 105.72 90.00
method X-Ray Diffractionresolution 1.79 Å
ligand RIB, SO4 enzyme
Primary referencePhosphoribosylation of Ubiquitin Promotes Serine Ubiquitination and Impairs Conventional Ubiquitination., Bhogaraju S, Kalayil S, Liu Y, Bonn F, Colby T, Matic I, Dikic I, Cell. 2016 Dec 1;167(6):1636-1649.e13. doi: 10.1016/j.cell.2016.11.019. PMID:27912065
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (44 Kb) [Save to disk]
  • Biological Unit Coordinates (5m93.pdb1.gz) 13 Kb
  • Biological Unit Coordinates (5m93.pdb2.gz) 14 Kb
  • Biological Unit Coordinates (5m93.pdb3.gz) 14 Kb
  • LPC: Ligand-Protein Contacts for 5M93
  • CSU: Contacts of Structural Units for 5M93
  • Structure Factors (364 Kb)
  • Retrieve 5M93 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5M93 from S2C, [Save to disk]
  • Re-refined 5m93 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5M93 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 5M93
  • 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: [5m93] [5m93_A] [5m93_C] [5m93_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5M93
  • Community annotation for 5M93 at PDBWiki (http://pdbwiki.org)

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