5AF6 Structure of Lys33-linked diUb bound to Trabid NZF1 date
authors Michel, M.A., Elliott, P.R., Swatek, K.N., Simicek, M., Pruneda, J.N., Wagstaff, J.L., Freund, S.M.V., Komander, D.
compound source
symmetry
R_factor
R_Free 0.2216
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.40
ligand ZN enzyme
Primary referenceAssembly and Specific Recognition of K29- and K33-Linked Polyubiquitin., Michel MA, Elliott PR, Swatek KN, Simicek M, Pruneda JN, Wagstaff JL, Freund SM, Komander D, Mol Cell. 2015 Mar 4. pii: S1097-2765(15)00091-X. doi:, 10.1016/j.molcel.2015.01.042. PMID:25752577
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (182 Kb) [Save to disk]
  • Biological Unit Coordinates (5af6.pdb1.gz) 37 Kb
  • Biological Unit Coordinates (5af6.pdb2.gz) 36 Kb
  • Biological Unit Coordinates (5af6.pdb3.gz) 37 Kb
  • Biological Unit Coordinates (5af6.pdb4.gz) 36 Kb
  • Biological Unit Coordinates (5af6.pdb5.gz) 37 Kb
  • LPC: Ligand-Protein Contacts for 5AF6
  • CSU: Contacts of Structural Units for 5AF6
  • Structure Factors (711 Kb)
  • Retrieve 5AF6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5AF6 from S2C, [Save to disk]
  • Re-refined 5af6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5AF6 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 5AF6
  • 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 5AF6, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5af6_A] [5af6_E] [5af6_B] [5af6_D] [5af6_I] [5af6_J] [5af6_G] [5af6_H] [5af6_F] [5af6] [5af6_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5AF6: [UBQ] [ZnF_RBZ ] by SMART
    • Other resources with information on 5AF6
  • Community annotation for 5AF6 at PDBWiki (http://pdbwiki.org)

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