2Y6E Hydrolase date Jan 20, 2011
title Structure Of The D1d2 Domain Of Usp4, The Conserved Catalyti
authors M.P.A.Luna-Vargas, A.C.Faesen, W.J.Van Dijk, M.Rape, A.Fish, T.K.
compound source
Molecule: Ubiquitin Carboxyl-Terminal Hydrolase 4
Chain: A, B, C, D, E, F
Fragment: Catalytic Domain, Residues 296-490,765-932
Synonym: Ubiquitin-Specific-Processing Protease 4, Deubiqui Enzyme 4, Ubiquitin Thiolesterase 4, Ubiquitous Nuclear Pro Homolog, Usp4;
Ec: 3.1.2.15
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta2(De3) Plyss-T1r
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-Nki-B3clic And Pet46-Eklic
symmetry Space Group: P 21 21 21
R_factor 0.178 R_Free 0.210
crystal
cell
length a length b length c angle alpha angle beta angle gamma
110.500 151.030 178.670 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand CME, SO4, ZN enzyme Hydrolase E.C.3.1.2.15 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceThe DUSP-Ubl domain of USP4 enhances its catalytic efficiency by promoting ubiquitin exchange., Clerici M, Luna-Vargas MP, Faesen AC, Sixma TK, Nat Commun. 2014 Nov 18;5:5399. doi: 10.1038/ncomms6399. PMID:25404403
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (690 Kb) [Save to disk]
  • Biological Unit Coordinates (2y6e.pdb1.gz) 679 Kb
  • LPC: Ligand-Protein Contacts for 2Y6E
  • CSU: Contacts of Structural Units for 2Y6E
  • Structure Factors (1533 Kb)
  • Retrieve 2Y6E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2Y6E from S2C, [Save to disk]
  • Re-refined 2y6e structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2Y6E 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 2Y6E
  • 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 2Y6E, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2y6e_F] [2y6e_A] [2y6e_B] [2y6e_D] [2y6e] [2y6e_C] [2y6e_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 2Y6E
  • Community annotation for 2Y6E 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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