4I1H Ligase date Nov 20, 2012
title Structure Of Parkin E3 Ligase
authors J.C.Lougheed, E.Brecht, N.H.Yao
compound source
Molecule: E3 Ubiquitin-Protein Ligase Parkin
Chain: A
Fragment: R0rbr (Unp Residues 141-465)
Synonym: Parkinson Juvenile Disease Protein 2, Parkinson Di Protein 2;
Ec: 6.3.2.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Park2, Prkn
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 2 2 21
R_factor 0.181 R_Free 0.215
crystal
cell
length a length b length c angle alpha angle beta angle gamma
87.110 133.930 66.210 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand ZN enzyme Ligase E.C.6.3.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructure and function of Parkin E3 ubiquitin ligase reveals aspects of RING and HECT ligases., Riley BE, Lougheed JC, Callaway K, Velasquez M, Brecht E, Nguyen L, Shaler T, Walker D, Yang Y, Regnstrom K, Diep L, Zhang Z, Chiou S, Bova M, Artis DR, Yao N, Baker J, Yednock T, Johnston JA, Nat Commun. 2013 Jun 17;4:1982. doi: 10.1038/ncomms2982. PMID:23770887
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (60 Kb) [Save to disk]
  • Biological Unit Coordinates (4i1h.pdb1.gz) 55 Kb
  • LPC: Ligand-Protein Contacts for 4I1H
  • CSU: Contacts of Structural Units for 4I1H
  • Structure Factors (370 Kb)
  • Retrieve 4I1H in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4I1H from S2C, [Save to disk]
  • Re-refined 4i1h structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4I1H 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 4I1H
  • 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 4I1H, from MSDmotif at EBI
  • Fold representative 4i1h from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4i1h] [4i1h_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4I1H: [IBR ] by SMART
  • Other resources with information on 4I1H
  • Community annotation for 4I1H at PDBWiki (http://pdbwiki.org)

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