2BF8 Ligase date Dec 06, 2004
title Crystal Structure Of Sumo Modified Ubiquitin Conjugating Enz 25k
authors A.Pichler, P.Knipscheer, E.Oberhofer, W.J.Van Dijk, R.Korner, J.V Olsen, S.Jentsch, F.Melchior, T.K.Sixma
compound source
Molecule: Ubiquitin-Conjugating Enzyme E2-25 Kda
Chain: A
Fragment: Conserved Core Domain, Residues 1-154
Synonym: E2-25k, Ubiquitin-Protein Ligase, Ubiquitin Carrie E2(25k), Huntingtin Interacting Protein 2, Hip-2;
Ec: 6.3.2.19
Engineered: Yes
Other_details: Covalent Isopeptide Link Between E2-25k Lysi Sumo C-Terminus;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector: Petm30

Molecule: Ubiquitin-Like Protein Smt3c
Chain: B
Fragment: Residues 21-97
Synonym: Sumo, Ubiquitin-Homology Domain Protein Pic1, Ubiq Protein Ubl1, Ubiquitin-Related Protein Sumo-1, Gap Modifyi 1, Gmp1, Sentrin;
Engineered: Yes
Other_details: Covalent Isopeptide Link Between E2-25k Lysi Sumo C-Terminus

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector: Pet11a
symmetry Space Group: P 43 21 2
R_factor 0.210 R_Free 0.279
crystal
cell
length a length b length c angle alpha angle beta angle gamma
58.391 58.391 162.842 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand
enzyme Ligase E.C.6.3.2.19 BRENDA
related structures by homologous chain: 1WYW, 1Y8R, 1YLA, 2BEP
Primary referenceSUMO modification of the ubiquitin-conjugating enzyme E2-25K., Pichler A, Knipscheer P, Oberhofer E, van Dijk WJ, Korner R, Olsen JV, Jentsch S, Melchior F, Sixma TK, Nat Struct Mol Biol. 2005 Mar;12(3):264-9. Epub 2005 Feb 20. PMID:15723079
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (45 Kb) [Save to disk]
  • Biological Unit Coordinates (2bf8.pdb1.gz) 39 Kb
  • CSU: Contacts of Structural Units for 2BF8
  • Likely Quarternary Molecular Structure file(s) for 2BF8
  • Structure Factors (90 Kb)
  • Retrieve 2BF8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2BF8 from S2C, [Save to disk]
  • Re-refined 2bf8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2BF8 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 2BF8
  • 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 2BF8, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2bf8] [2bf8_A] [2bf8_B]
  • SWISS-PROT database: [P63165] [P61085]
  • Domain organization of [SUMO1_HUMAN] [UBE2K_BOVIN] by SWISSPFAM
  • Domains found in 2BF8: [UBCc] [UBQ ] by SMART
  • Other resources with information on 2BF8
  • Community annotation for 2BF8 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