4KSK Gumby/Fam105B in complex with ubiquitin date 2013-05-17
authors Ceccarelli, D.F., Juang, Y.C., Sicheri, F.
compound source
symmetry
R_factor
R_Free 0.26764
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.40
ligand SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceThe linear ubiquitin-specific deubiquitinase gumby regulates angiogenesis., Rivkin E, Almeida SM, Ceccarelli DF, Juang YC, MacLean TA, Srikumar T, Huang H, Dunham WH, Fukumura R, Xie G, Gondo Y, Raught B, Gingras AC, Sicheri F, Cordes SP, Nature. 2013 Jun 20;498(7454):318-24. doi: 10.1038/nature12296. Epub 2013 May 24. PMID:23708998
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (230 Kb) [Save to disk]
  • Biological Unit Coordinates (4ksk.pdb1.gz) 113 Kb
  • Biological Unit Coordinates (4ksk.pdb2.gz) 113 Kb
  • LPC: Ligand-Protein Contacts for 4KSK
  • CSU: Contacts of Structural Units for 4KSK
  • Structure Factors (427 Kb)
  • Retrieve 4KSK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4KSK from S2C, [Save to disk]
  • Re-refined 4ksk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4KSK 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 4KSK
  • 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 4KSK, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ksk_C] [4ksk_A] [4ksk] [4ksk_D] [4ksk_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4KSK: [UBQ ] by SMART
    • Other resources with information on 4KSK
  • Community annotation for 4KSK at PDBWiki (http://pdbwiki.org)

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