5C1Z Ligase date Jun 15, 2015
title Parkin (Ublr0rbr)
authors A.Kumar, J.D.Aguirre, T.E.C.Condos, R.J.Martinez-Torres, V.K.Cha R.Toth, R.Sundaramoorthy, P.Mercier, A.Knebel, D.E.Spratt, K.R.B G.S.Shaw, H.Walden
compound source
Molecule: E3 Ubiquitin-Protein Ligase Parkin
Chain: A, B
Synonym: Parkin,Parkinson Juvenile Disease Protein 2,Parkin Disease 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 Bl21(De3)
Expression_system_taxid: 469008
symmetry Space Group: P 21 21 21
R_factor 0.192 R_Free 0.212
crystal
cell
length a length b length c angle alpha angle beta angle gamma
67.310 67.320 206.230 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.79 Å
ligand CL, GOL, SO4, ZN enzyme Ligase E.C.6.3.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceDisruption of the autoinhibited state primes the E3 ligase parkin for activation and catalysis., Kumar A, Aguirre JD, Condos TE, Martinez-Torres RJ, Chaugule VK, Toth R, Sundaramoorthy R, Mercier P, Knebel A, Spratt DE, Barber KR, Shaw GS, Walden H, EMBO J. 2015 Aug 7. pii: e201592337. PMID:26254304
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (283 Kb) [Save to disk]
  • Biological Unit Coordinates (5c1z.pdb1.gz) 139 Kb
  • Biological Unit Coordinates (5c1z.pdb2.gz) 140 Kb
  • LPC: Ligand-Protein Contacts for 5C1Z
  • CSU: Contacts of Structural Units for 5C1Z
  • Structure Factors (4505 Kb)
  • Retrieve 5C1Z in mmCIF format [Save to disk]
  • Re-refined 5c1z structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5C1Z 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 5C1Z
  • 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
  • Fold representative 5c1z from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5c1z_A] [5c1z] [5c1z_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5C1Z: [IBR] [UBQ ] by SMART
  • Other resources with information on 5C1Z
  • Community annotation for 5C1Z at PDBWiki (http://pdbwiki.org)

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