5L8H Hydrolase date Jun 07, 2016
title Structure Of Usp46-Ubvme
authors M.Clerici, T.Sixma, S.Dharadhar
compound source
Molecule: Ubiquitin Carboxyl-Terminal Hydrolase 46
Chain: A
Synonym: Deubiquitinating Enzyme 46,Ubiquitin Thioesterase Ubiquitin-Specific-Processing Protease 46;
Ec: 3.4.19.12
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Usp46
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Polyubiquitin-B
Chain: B
Engineered: Yes
Other_details: Recombinant Expression Followed By Chemical
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ubb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 2 2 21
R_factor 0.166 R_Free 0.194
crystal
cell
length a length b length c angle alpha angle beta angle gamma
91.950 104.660 135.310 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.85 Å
ligand GVE, ZN enzyme Hydrolase E.C.3.4.19.12 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceA conserved two-step binding for the UAF1 regulator to the USP12 deubiquitinating enzyme., Dharadhar S, Clerici M, van Dijk WJ, Fish A, Sixma TK, J Struct Biol. 2016 Sep 17. pii: S1047-8477(16)30200-3. doi:, 10.1016/j.jsb.2016.09.011. PMID:27650958
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (139 Kb) [Save to disk]
  • Biological Unit Coordinates (5l8h.pdb1.gz) 133 Kb
  • LPC: Ligand-Protein Contacts for 5L8H
  • CSU: Contacts of Structural Units for 5L8H
  • Structure Factors (660 Kb)
  • Retrieve 5L8H in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5L8H from S2C, [Save to disk]
  • Re-refined 5l8h structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5L8H 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 5L8H
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5l8h] [5l8h_B] [5l8h_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5L8H: [UBQ ] by SMART
    • Other resources with information on 5L8H
  • Community annotation for 5L8H at PDBWiki (http://pdbwiki.org)

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