3NOB Protein Binding date Jun 25, 2010
title Structure Of K11-Linked Di-Ubiquitin
authors K.C.Dong, M.L.Matsumoto, S.G.Hymowitz
compound source
Molecule: Ubiquitin
Chain: A, B, C, D, E, F, G, H
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Gene: Rps27a, Uba80, Ubcep1, Uba52, Ubb, Ubc
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Vector
Expression_system_plasmid: Pet15b
symmetry Space Group: C 1 2 1
R_factor 0.245 R_Free 0.281
crystal
cell
length a length b length c angle alpha angle beta angle gamma
155.597 56.059 65.772 90.00 95.21 90.00
method X-Ray Diffractionresolution 2.19 Å
ligand SO4 enzyme
Primary referenceK11-Linked Polyubiquitination in Cell Cycle Control Revealed by a K11 Linkage-Specific Antibody., Matsumoto ML, Wickliffe KE, Dong KC, Yu C, Bosanac I, Bustos D, Phu L, Kirkpatrick DS, Hymowitz SG, Rape M, Kelley RF, Dixit VM, Mol Cell. 2010 Jul 21. PMID:20655260
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (104 Kb) [Save to disk]
  • Biological Unit Coordinates (3nob.pdb1.gz) 27 Kb
  • Biological Unit Coordinates (3nob.pdb2.gz) 26 Kb
  • Biological Unit Coordinates (3nob.pdb3.gz) 26 Kb
  • Biological Unit Coordinates (3nob.pdb4.gz) 26 Kb
  • LPC: Ligand-Protein Contacts for 3NOB
  • CSU: Contacts of Structural Units for 3NOB
  • Structure Factors (216 Kb)
  • Retrieve 3NOB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NOB from S2C, [Save to disk]
  • Re-refined 3nob structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3NOB 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 3NOB
  • 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 3NOB, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3nob] [3nob_E] [3nob_B] [3nob_A] [3nob_D] [3nob_C] [3nob_H] [3nob_F] [3nob_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3NOB: [UBQ ] by SMART
    • Other resources with information on 3NOB
  • Community annotation for 3NOB at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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