2Z5D Ligase date Jul 06, 2007
title Human Ubiquitin-Conjugating Enzyme E2 H
authors A.Bochkarev, H.Cui, J.R.Walker, E.M.Newman, F.Mackenzie, K.P.Batt M.Sundstrom, C.Arrowsmith, A.Edwards, S.Dhe-Paganon, Structural Consortium (Sgc)
compound source
Molecule: Ubiquitin-Conjugating Enzyme E2 H
Chain: A, B
Fragment: Residues 1-179
Synonym: Ubiquitin-Protein Ligase H, Ubiquitin Carrier Prot Ubch2, E2-20k;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ube2h
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a-Lic
symmetry Space Group: P 21 21 21
R_factor 0.181 R_Free 0.223
length a length b length c angle alpha angle beta angle gamma
42.959 85.861 102.558 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand NA enzyme Ligase E.C. BRENDA
note 2Z5D supersedes 1YH6
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] (59 Kb) [Save to disk]
  • Biological Unit Coordinates (2z5d.pdb1.gz) 54 Kb
  • LPC: Ligand-Protein Contacts for 2Z5D
  • CSU: Contacts of Structural Units for 2Z5D
  • Likely Quarternary Molecular Structure file(s) for 2Z5D
  • Structure Factors (447 Kb)
  • Retrieve 2Z5D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2Z5D from S2C, [Save to disk]
  • Re-refined 2z5d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2Z5D 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 2Z5D
  • 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 2Z5D, from MSDmotif at EBI
  • Fold representative 2z5d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2z5d] [2z5d_B] [2z5d_A]
  • SWISS-PROT database: [P62256]
  • Domain organization of [UBE2H_HUMAN] by SWISSPFAM
  • Domain found in 2Z5D: [UBCc ] by SMART
  • Other resources with information on 2Z5D
  • Community annotation for 2Z5D 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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