4FJV Hydrolase date Jun 12, 2012
title Crystal Structure Of Human Otubain2 And Ubiquitin Complex
authors M.Altun, T.S.Walter, H.B.Kramer, A.Iphofer, Y.David, A.Komsany, N. B.Nicholson, A.Navon, D.I.Stuart, J.Ren, B.M.Kessler
compound source
Molecule: Ubiquitin Thioesterase Otub2
Chain: A, C
Synonym: Deubiquitinating Enzyme Otub2, Otu Domain-Containi Ubiquitin Aldehyde-Binding Protein 2, Otubain-2, Ubiquitin- Processing Protease Otub2;
Ec: 3.4.19.12
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Otub2, C14orf137, Otb2, Otu2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a-Lic

Molecule: Polyubiquitin-C
Chain: B, D
Synonym: Ubiquitin
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ubc
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.206 R_Free 0.267
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.063 76.825 198.847 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.05 Å
ligand GOL, NEH enzyme Hydrolase E.C.3.4.19.12 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


Primary referenceThe human otubain2-ubiquitin structure provides insights into the cleavage specificity of poly-ubiquitin-linkages., Altun M, Walter TS, Kramer HB, Herr P, Iphofer A, Bostrom J, David Y, Komsany A, Ternette N, Navon A, Stuart DI, Ren J, Kessler BM, PLoS One. 2015 Jan 15;10(1):e0115344. doi: 10.1371/journal.pone.0115344., eCollection 2015. PMID:25590432
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (233 Kb) [Save to disk]
  • Biological Unit Coordinates (4fjv.pdb1.gz) 112 Kb
  • Biological Unit Coordinates (4fjv.pdb2.gz) 113 Kb
  • Biological Unit Coordinates (4fjv.pdb3.gz) 223 Kb
  • LPC: Ligand-Protein Contacts for 4FJV
  • CSU: Contacts of Structural Units for 4FJV
  • Structure Factors (407 Kb)
  • Retrieve 4FJV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4FJV from S2C, [Save to disk]
  • Re-refined 4fjv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4FJV 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 4FJV
  • 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 4FJV, from MSDmotif at EBI
  • Fold representative 4fjv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4fjv_D] [4fjv] [4fjv_A] [4fjv_C] [4fjv_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4FJV: [UBQ ] by SMART
  • Other resources with information on 4FJV
  • Community annotation for 4FJV at PDBWiki (http://pdbwiki.org)

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