3BZH Ligase date Jan 18, 2008
title Crystal Structure Of Human Ubiquitin-Conjugating Enzyme E2 E
authors J.R.Walker, G.V.Avvakumov, S.Xue, Y.Li, J.Weigelt, C.H.Arrowsmith A.M.Edwards, A.Bochkarev, S.Dhe-Paganon, Structural Genomics C (Sgc)
compound source
Molecule: Ubiquitin-Conjugating Enzyme E2 E1
Chain: A
Synonym: Ubiquitin-Protein Ligase E1, Ubiquitin Carrier Pro Ubch6;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ube2e1, Ubch6
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28-Mhl
symmetry Space Group: P 31 2 1
R_factor 0.205 R_Free 0.226
length a length b length c angle alpha angle beta angle gamma
51.630 51.630 109.437 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.60 Å
ligand GOL 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] (63 Kb) [Save to disk]
  • Biological Unit Coordinates (3bzh.pdb1.gz) 110 Kb
  • LPC: Ligand-Protein Contacts for 3BZH
  • CSU: Contacts of Structural Units for 3BZH
  • Likely Quarternary Molecular Structure file(s) for 3BZH
  • Structure Factors (331 Kb)
  • Retrieve 3BZH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BZH from S2C, [Save to disk]
  • Re-refined 3bzh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BZH 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 3BZH
  • 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 3BZH, from MSDmotif at EBI
  • Fold representative 3bzh from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bzh] [3bzh_A]
  • SWISS-PROT database: [P51965]
  • Domain organization of [UB2E1_HUMAN] by SWISSPFAM
  • Domain found in 3BZH: [UBCc ] by SMART
  • Other resources with information on 3BZH
  • Community annotation for 3BZH 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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