3O65 Hydrolase Protein Binding date Jul 28, 2010
title Crystal Structure Of A Josephin-Ubiquitin Complex: Evolution Restraints On Ataxin-3 Deubiquitinating Activity
authors S.D.Weeks, K.C.Grasty, L.Hernandez-Cuebas, P.J.Loll
compound source
Molecule: Putative Ataxin-3-Like Protein
Chain: A, C, E, G
Fragment: Josephin Domain
Synonym: Machado-Joseph Disease Protein 1-Like
Ec: 3.1.2.15
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Atx3l, Atxn3l, Mjdl
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pethsul

Molecule: Ubiquitin
Chain: B, D, F, H
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ubb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petxsh
symmetry Space Group: P 3 2 1
R_factor 0.176 R_Free 0.224
crystal
cell
length a length b length c angle alpha angle beta angle gamma
159.150 159.150 146.290 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.70 Å
ligand MSE, NA, NEH enzyme Hydrolase E.C.3.1.2.15 BRENDA
note 3O65 is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A, C, G, E


Primary referenceCrystal Structure of a Josephin-Ubiquitin Complex: EVOLUTIONARY RESTRAINTS ON ATAXIN-3 DEUBIQUITINATING ACTIVITY., Weeks SD, Grasty KC, Hernandez-Cuebas L, Loll PJ, J Biol Chem. 2011 Feb 11;286(6):4555-65. Epub 2010 Nov 30. PMID:21118805
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (374 Kb) [Save to disk]
  • Biological Unit Coordinates (3o65.pdb1.gz) 92 Kb
  • Biological Unit Coordinates (3o65.pdb2.gz) 92 Kb
  • Biological Unit Coordinates (3o65.pdb3.gz) 95 Kb
  • Biological Unit Coordinates (3o65.pdb4.gz) 93 Kb
  • Biological Unit Coordinates (3o65.pdb5.gz) 1076 Kb
  • Biological Unit Coordinates (3o65.pdb6.gz) 272 Kb
  • Biological Unit Coordinates (3o65.pdb7.gz) 766 Kb
  • LPC: Ligand-Protein Contacts for 3O65
  • CSU: Contacts of Structural Units for 3O65
  • Structure Factors (1045 Kb)
  • Retrieve 3O65 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3O65 from S2C, [Save to disk]
  • Re-refined 3o65 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3O65 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 3O65
  • 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 3O65, from MSDmotif at EBI
  • Fold representative 3o65 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3o65_E] [3o65_B] [3o65] [3o65_C] [3o65_F] [3o65_G] [3o65_A] [3o65_H] [3o65_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3O65: [Josephin] [UBQ ] by SMART
  • Other resources with information on 3O65
  • Community annotation for 3O65 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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