2GJD Ligase date Mar 30, 2006
title Distinct Functional Domains Of Ubc9 Dictate Cell Survival An Resistance To Genotoxic Stress
authors R.C.Van Waardenburg, D.M.Duda, C.S.Lancaster, B.A.Schulman, M.A.
compound source
Molecule: Ubiquitin-Conjugating Enzyme E2-18 Kda
Chain: A, B, C, D
Synonym: Ubiquitin- Protein Ligase, Ubiquitin Carrier Prote
Ec: 6.3.2.19
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Ubc9
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Gold
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex
symmetry Space Group: P 1 21 1
R_factor 0.210 R_Free 0.230
crystal
cell
length a length b length c angle alpha angle beta angle gamma
59.304 60.141 95.287 90.00 105.01 90.00
method X-Ray Diffractionresolution 1.75 Å
ligand
enzyme Ligase E.C.6.3.2.19 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceDistinct functional domains of Ubc9 dictate cell survival and resistance to genotoxic stress., van Waardenburg RC, Duda DM, Lancaster CS, Schulman BA, Bjornsti MA, Mol Cell Biol. 2006 Jul;26(13):4958-69. PMID:16782883
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (112 Kb) [Save to disk]
  • Biological Unit Coordinates (2gjd.pdb1.gz) 107 Kb
  • CSU: Contacts of Structural Units for 2GJD
  • Likely Quarternary Molecular Structure file(s) for 2GJD
  • Structure Factors (925 Kb)
  • Retrieve 2GJD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2GJD from S2C, [Save to disk]
  • Re-refined 2gjd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2GJD 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 2GJD
  • 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 2GJD, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2gjd] [2gjd_C] [2gjd_A] [2gjd_D] [2gjd_B]
  • SWISS-PROT database: [P50623]
  • Domain organization of [UBC9_YEAST] by SWISSPFAM
  • Domain found in 2GJD: [UBCc ] by SMART
  • Other resources with information on 2GJD
  • Community annotation for 2GJD 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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