2A4D Ligase date Jun 28, 2005
title Structure Of The Human Ubiquitin-Conjugating Enzyme E2 Varia 1)
authors J.R.Walker, G.V.Avvakumov, S.Xue, E.M.Newman, F.Mackenzie, J.Weig M.Sundstrom, C.Arrowsmith, A.Edwards, A.Bochkarev, S.Dhe-Pagano Structural Genomics Consortium (Sgc)
compound source
Molecule: Ubiquitin-Conjugating Enzyme E2 Variant 1
Chain: A
Fragment: Catalytic Domain, Residues 82-220
Synonym: Uev-1, Croc-1, Ubiquitin-Conjugating Enzyme Varian Traf6-Regulated Ikk Activator 1 Beta Uev1a, Pokcl.19;
Ec: 6.3.2.19
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ube2v1, Croc1, Ube2v, Uev1
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: C 2 2 21
R_factor 0.183 R_Free 0.240
crystal
cell
length a length b length c angle alpha angle beta angle gamma
43.058 53.910 108.034 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.69 Å
ligand
enzyme Ligase E.C.6.3.2.19 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


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] (52 Kb) [Save to disk]
  • Biological Unit Coordinates (2a4d.pdb1.gz) 47 Kb
  • CSU: Contacts of Structural Units for 2A4D
  • Likely Quarternary Molecular Structure file(s) for 2A4D
  • Structure Factors (97 Kb)
  • Retrieve 2A4D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2A4D from S2C, [Save to disk]
  • Re-refined 2a4d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2A4D 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 2A4D
  • 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 2A4D, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2a4d_A] [2a4d]
  • SWISS-PROT database: [Q13404]
  • Domain organization of [UB2V1_HUMAN] by SWISSPFAM
  • Domain found in 2A4D: [UBCc ] by SMART
  • Other resources with information on 2A4D
  • Community annotation for 2A4D 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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