4PQT Insights into the mechanism of deubiquitination by JAMM deubiquitinases from co-crystal structures of enzyme with substrate and product date
authors Shrestha, R.K., Ronau, J.A., Das, C.
compound source
symmetry
R_factor
R_Free 0.2525
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.05
ligand EDO, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceInsights into the Mechanism of Deubiquitination by JAMM Deubiquitinases from Cocrystal Structures of the Enzyme with the Substrate and Product., Shrestha RK, Ronau JA, Davies CW, Guenette RG, Strieter ER, Paul LN, Das C, Biochemistry. 2014 May 20;53(19):3199-217. doi: 10.1021/bi5003162. Epub 2014 May , 9. PMID:24787148
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (48 Kb) [Save to disk]
  • Biological Unit Coordinates (4pqt.pdb1.gz) 31 Kb
  • Biological Unit Coordinates (4pqt.pdb2.gz) 14 Kb
  • Biological Unit Coordinates (4pqt.pdb3.gz) 43 Kb
  • LPC: Ligand-Protein Contacts for 4PQT
  • CSU: Contacts of Structural Units for 4PQT
  • Structure Factors (287 Kb)
  • Retrieve 4PQT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4PQT from S2C, [Save to disk]
  • Re-refined 4pqt structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4PQT 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 4PQT
  • 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
  • 3D motif for 4PQT, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4pqt_A] [4pqt] [4pqt_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4PQT: [JAB_MPN] [UBQ ] by SMART
    • Other resources with information on 4PQT
  • Community annotation for 4PQT at PDBWiki (http://pdbwiki.org)

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