4BM9 Ligase date May 07, 2013
title Structure Of The Autoinhibited Parkin Catalytic Domain
authors T.Wauer, D.Komander
compound source
Molecule: E3 Ubiquitin-Protein Ligase Parkin
Chain: A
Fragment: Upd And Rbr Domain, Residues 137-465
Synonym: Parkinson Juvenile Disease Protein 2, Parkinson Di Protein 2, Parkin;
Ec: 6.3.2.-
Engineered: Yes
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_variant: Rosetta2
symmetry Space Group: H 3 2
R_factor 0.1903 R_Free 0.2178
length a length b length c angle alpha angle beta angle gamma
168.420 168.420 97.181 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.25 Å
ligand GOL, SO4, ZN enzyme Ligase E.C.6.3.2 BRENDA

Primary referenceStructure of the human Parkin ligase domain in an autoinhibited state., Wauer T, Komander D, EMBO J. 2013 May 31. doi: 10.1038/emboj.2013.125. PMID:23727886
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (106 Kb) [Save to disk]
  • Biological Unit Coordinates (4bm9.pdb1.gz) 588 Kb
  • LPC: Ligand-Protein Contacts for 4BM9
  • CSU: Contacts of Structural Units for 4BM9
  • Structure Factors (1032 Kb)
  • Retrieve 4BM9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4BM9 from S2C, [Save to disk]
  • Re-refined 4bm9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4BM9 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 4BM9
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4BM9, from MSDmotif at EBI
  • Fold representative 4bm9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4bm9_A] [4bm9]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4BM9: [IBR ] by SMART
  • Other resources with information on 4BM9
  • Community annotation for 4BM9 at PDBWiki (http://pdbwiki.org)

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