4DDG Crystal structure of human OTUB1/UbcH5b~Ub/Ub date
authors Juang, Y.C., Sanches, M., Sicheri, F.
compound source
symmetry
R_factor
R_Free 0.2802
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.30
Gene
Ontology
ChainFunctionProcessComponent
A, J, C, K, L, B


Primary referenceOTUB1 Co-opts Lys48-Linked Ubiquitin Recognition to Suppress E2 Enzyme Function., Juang YC, Landry MC, Sanches M, Vittal V, Leung CC, Ceccarelli DF, Mateo AR, Pruneda JN, Mao DY, Szilard RK, Orlicky S, Munro M, Brzovic PS, Klevit RE, Sicheri F, Durocher D, Mol Cell. 2012 Feb 10;45(3):384-97. PMID:22325355
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1141 Kb) [Save to disk]
  • Biological Unit Coordinates (4ddg.pdb1.gz) 569 Kb
  • Biological Unit Coordinates (4ddg.pdb2.gz) 569 Kb
  • CSU: Contacts of Structural Units for 4DDG
  • Structure Factors (1012 Kb)
  • Retrieve 4DDG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DDG from S2C, [Save to disk]
  • Re-refined 4ddg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4DDG 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 4DDG
  • 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 4DDG, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ddg_F] [4ddg_G] [4ddg_J] [4ddg_W] [4ddg_D] [4ddg_E] [4ddg_A] [4ddg] [4ddg_T] [4ddg_L] [4ddg_X] [4ddg_N] [4ddg_P] [4ddg_R] [4ddg_K] [4ddg_M] [4ddg_S] [4ddg_V] [4ddg_U] [4ddg_Q] [4ddg_O] [4ddg_I] [4ddg_C] [4ddg_B] [4ddg_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4DDG: [UBCc] [UBQ ] by SMART
    • Other resources with information on 4DDG
  • Community annotation for 4DDG at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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