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
  • Alignments of the sequence of 4BM9 with the sequences similar proteins can be viewed for 4BM9's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 4BM9
  • Community annotation for 4BM9 at PDBWiki (http://pdbwiki.org)

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