3K9P Ligase Signaling Protein date Oct 16, 2009
title The Crystal Structure Of E2-25k And Ubiquitin Complex
authors G.B.Kang, S.Ko, S.M.Song, W.Lee, S.H.Eom
compound source
Molecule: Ubiquitin-Conjugating Enzyme E2 K
Chain: A
Synonym: Ubiquitin-Conjugating Enzyme E2-25 Kda, E2(25k), E Ubiquitin-Protein Ligase, Ubiquitin Carrier Protein, Huntin Interacting Protein 2, Hip-2;
Ec: 6.3.2.19
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ube2k, Hip2, Lig
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ubiquitin
Chain: B
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.232 R_Free 0.296
crystal
cell
length a length b length c angle alpha angle beta angle gamma
43.554 50.974 63.906 90.00 102.62 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand
enzyme Ligase E.C.6.3.2.19 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural basis of E2-25K/UBB+1 interaction leading to proteasome inhibition and neurotoxicity., Ko S, Kang GB, Song SM, Lee JG, Shin DY, Yoon J, Sheng Y, Cheong C, Jeon YH, Jung YK, Arrowsmith CH, Avvakumov GV, Dhe-Paganon S, Yoo YJ, Eom SH, Lee W, J Biol Chem. 2010 Sep 8. PMID:20826778
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (47 Kb) [Save to disk]
  • Biological Unit Coordinates (3k9p.pdb1.gz) 43 Kb
  • Biological Unit Coordinates (3k9p.pdb2.gz) 32 Kb
  • Biological Unit Coordinates (3k9p.pdb3.gz) 13 Kb
  • CSU: Contacts of Structural Units for 3K9P
  • Structure Factors (45 Kb)
  • Retrieve 3K9P in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3K9P from S2C, [Save to disk]
  • Re-refined 3k9p structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3K9P 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 3K9P
  • 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 3K9P, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3k9p] [3k9p_B] [3k9p_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3K9P: [UBA] [UBCc] [UBQ ] by SMART
  • Other resources with information on 3K9P
  • Community annotation for 3K9P 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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