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
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
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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