2OB4 Ligase date Dec 18, 2006
title Human Ubiquitin-Conjugating Enzyme Cdc34
authors D.Neculai, G.V.Avvakumov, S.Xue, J.R.Walker, F.Mackenzie, J.Weige M.Sundstrom, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, F.Sicher Paganon, Structural Genomics Consortium (Sgc)
compound source
Molecule: Ubiquitin-Conjugating Enzyme E2-32 Kda Complement
Chain: A
Fragment: Catalytic Domain: Residues 7-184
Synonym: Ubiquitin-Protein Ligase, Ubiquitin Carrier Protei Cdc34;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cdc34, Ube2r1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28-Lic
symmetry Space Group: I 2 2 2
R_factor 0.223 R_Free 0.284
length a length b length c angle alpha angle beta angle gamma
42.280 66.310 124.610 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
enzyme Ligase E.C. BRENDA
Primary referenceA human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen., Sheng Y, Hong JH, Doherty R, Srikumar T, Shloush J, Avvakumov GV, Walker JR, Xue S, Neculai D, Wan JW, Kim SK, Arrowsmith CH, Raught B, Dhe-Paganon S, Mol Cell Proteomics. 2012 Aug;11(8):329-41. Epub 2012 Apr 10. PMID:22496338
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (32 Kb) [Save to disk]
  • Biological Unit Coordinates (2ob4.pdb1.gz) 28 Kb
  • CSU: Contacts of Structural Units for 2OB4
  • Structure Factors (59 Kb)
  • Retrieve 2OB4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2OB4 from S2C, [Save to disk]
  • Re-refined 2ob4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2OB4 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 2OB4
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2OB4, from MSDmotif at EBI
  • Fold representative 2ob4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ob4_A] [2ob4]
  • SWISS-PROT database: [P49427]
  • Domain organization of [UB2R1_HUMAN] by SWISSPFAM
  • Domain found in 2OB4: [UBCc ] by SMART
  • Other resources with information on 2OB4
  • Community annotation for 2OB4 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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