1Z3D Ligase date Mar 11, 2005
title Protein Crystal Growth Improvement Leading To The 2.5a Crystallographic Structure Of Ubiquitin-Conjugating Enzyme From Caenorhabditis Elegans
authors J.A.Gavira, E.Digiammarino, W.Tempel, D.Toh, Z.J.Liu, B.C.Wang, E. J.D.Ng, Southeast Collaboratory For Structural Genomics (Sec
compound source
Molecule: Ubiquitin-Conjugating Enzyme E2 1
Chain: A
Synonym: Ubiquitin-Protein Ligase 1, Ubiquitin Carrier Prot
Ec: 6.3.2.19
Engineered: Yes
 Organism_scientific: Caenorhabditis Elegans
Organism_taxid: 6239
Gene: Ubc-1
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet26
symmetry Space Group: P 65
R_factor 0.242 R_Free 0.273
crystal
cell
length a length b length c angle alpha angle beta angle gamma
100.550 100.550 35.840 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.50 Å
ligand
enzyme Ligase E.C.6.3.2.19 BRENDA
related structures by homologous chain: 1AYZ, 2AAK
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (29 Kb) [Save to disk]
  • Biological Unit Coordinates (1z3d.pdb1.gz) 25 Kb
  • CSU: Contacts of Structural Units for 1Z3D
  • Likely Quarternary Molecular Structure file(s) for 1Z3D
  • Structure Factors (53 Kb)
  • Retrieve 1Z3D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Z3D from S2C, [Save to disk]
  • Re-refined 1z3d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1Z3D 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 1Z3D
  • 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 1Z3D, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1z3d_A] [1z3d]
  • SWISS-PROT database: [P52478]
  • Domain organization of [UBC1_CAEEL] by SWISSPFAM
  • Domain found in 1Z3D: [UBCc ] by SMART
    • Other resources with information on 1Z3D
  • Community annotation for 1Z3D at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science