2EKE Ligase Protein Binding date Mar 23, 2007
title Structure Of A Sumo-Binding-Motif Mimic Bound To Smt3p-Ubc9p Conservation Of A Noncovalent Ubiquitin-Like Protein-E2 Com Platform For Selective Interactions Within A Sumo Pathway
authors D.M.Duda, B.A.Schulman
compound source
Molecule: Sumo-Conjugating Enzyme Ubc9
Chain: A, B
Synonym: Ubiquitin-Conjugating Enzyme E2-18 Kda, Ubiquitin- Ligase, Ubiquitin Carrier Protein 9;
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: Prsf-Duet

Molecule: Ubiquitin-Like Protein Smt3
Chain: C, D
Engineered: Yes
Mutation: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Smt3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Gold
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prsf-Duet
symmetry Space Group: C 1 2 1
R_factor 0.225 R_Free 0.250
crystal
cell
length a length b length c angle alpha angle beta angle gamma
120.891 84.578 80.141 90.00 124.31 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand
enzyme Ligase E.C.6.3.2.19 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructure of a SUMO-binding-motif Mimic Bound to Smt3p-Ubc9p: Conservation of a Non-covalent Ubiquitin-like Protein-E2 Complex as a Platform for Selective Interactions within a SUMO Pathway., Duda DM, van Waardenburg RC, Borg LA, McGarity S, Nourse A, Waddell MB, Bjornsti MA, Schulman BA, J Mol Biol. 2007 Jun 8;369(3):619-30. Epub 2007 Apr 10. PMID:17475278
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (90 Kb) [Save to disk]
  • Biological Unit Coordinates (2eke.pdb1.gz) 44 Kb
  • Biological Unit Coordinates (2eke.pdb2.gz) 43 Kb
  • CSU: Contacts of Structural Units for 2EKE
  • Likely Quarternary Molecular Structure file(s) for 2EKE
  • Structure Factors (804 Kb)
  • Retrieve 2EKE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2EKE from S2C, [Save to disk]
  • Re-refined 2eke structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2EKE 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 2EKE
  • 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 2EKE, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2eke_A] [2eke_B] [2eke_C] [2eke] [2eke_D]
  • SWISS-PROT database: [Q12306] [P50623]
  • Domain organization of [SMT3_YEAST] [UBC9_YEAST] by SWISSPFAM
  • Domains found in 2EKE: [UBCc] [UBQ ] by SMART
  • Other resources with information on 2EKE
  • Community annotation for 2EKE 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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