5LRV Hydrolase date Aug 22, 2016
title Structure Of Cezanneotud7b Otu Domain Bound To Lys11-Linked Diubiquitin
authors T.E.T.Mevissen, Y.Kulathu, M.P.C.Mulder, P.P.Geurink, S.L.Maslen M.Gersch, P.R.Elliott, J.E.Burke, B.D.M.Van Tol, M.Akutsu, F.El M.Kawasaki, S.M.V.Freund, H.Ovaa, D.Komander
compound source
Molecule: Otu Domain-Containing Protein 7b
Chain: A
Synonym: Cellular Zinc Finger Anti-Nf-Kappa-B Protein,Zinc Domain-Containing Protein 1,Zinc Finger Protein Cezanne;
Ec: 3.4.19.12
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Otud7b, Za20d1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Polyubiquitin-B
Chain: B
Engineered: Yes
Mutation: Yes
Other_details: Lys11 Was Replaced With A Diaminobutyric Aci Residue;
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Polyubiquitin-B
Chain: C
Engineered: Yes
Mutation: Yes
Other_details: Gly76 Was Replaced With A Ligation Handle Fo Diubiquitin Probe Generation
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 21 21 21
R_factor 0.207 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
92.030 56.520 91.750 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand ABU, DAB, GOL, PO4 enzyme Hydrolase E.C.3.4.19.12 BRENDA
Primary referenceMolecular basis of Lys11-polyubiquitin specificity in the deubiquitinase Cezanne., Mevissen TE, Kulathu Y, Mulder MP, Geurink PP, Maslen SL, Gersch M, Elliott PR, Burke JE, van Tol BD, Akutsu M, El Oualid F, Kawasaki M, Freund SM, Ovaa H, Komander D, Nature. 2016 Oct 12;538(7625):402-405. doi: 10.1038/nature19836. PMID:27732584
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (142 Kb) [Save to disk]
  • Biological Unit Coordinates (5lrv.pdb1.gz) 136 Kb
  • LPC: Ligand-Protein Contacts for 5LRV
  • CSU: Contacts of Structural Units for 5LRV
  • Structure Factors (713 Kb)
  • Retrieve 5LRV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5LRV from S2C, [Save to disk]
  • Re-refined 5lrv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5LRV 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 5LRV
  • 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: [5lrv] [5lrv_B] [5lrv_C] [5lrv_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5LRV: [UBQ ] by SMART
    • Other resources with information on 5LRV
  • Community annotation for 5LRV at PDBWiki (http://pdbwiki.org)

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