4I1F Ligase date Nov 20, 2012
title Structure Of Parkin-S223p 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
Mutation: 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 0.205 R_Free 0.245
crystal
cell
length a length b length c angle alpha angle beta angle gamma
86.955 133.155 65.385 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.58 Å
ligand BA, 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] (62 Kb) [Save to disk]
  • Biological Unit Coordinates (4i1f.pdb1.gz) 56 Kb
  • LPC: Ligand-Protein Contacts for 4I1F
  • CSU: Contacts of Structural Units for 4I1F
  • Structure Factors (737 Kb)
  • Retrieve 4I1F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4I1F from S2C, [Save to disk]
  • Re-refined 4i1f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4I1F 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 4I1F
  • 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 4I1F, from MSDmotif at EBI
  • Fold representative 4i1f from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4i1f] [4i1f_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4I1F: [IBR ] by SMART
  • Other resources with information on 4I1F
  • Community annotation for 4I1F at PDBWiki (http://pdbwiki.org)

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