4UF6 Hydrolase date Dec 23, 2014
title Uch-L5 In Complex With Ubiquitin-Propargyl Bound To An Activ Fragment Of Ino80g
authors D.D.Sahtoe, W.J.Van Dijk, F.El Oualid, R.Ekkebus, H.Ovaa, T.K.Six
compound source
Molecule: Ubiquitin Carboxyl-Terminal Hydrolase Isozyme L5
Chain: A, D, G, J
Synonym: Uch-L5, Ubiquitin C-Terminal Hydrolase Uch37, Ubiq Thioesterase L5, Uch-L5;
Ec: 3.4.19.12
Engineered: Yes
Other_details: Active Site Cys88 Covalently Linked To Ubiqu Propargyl;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Rosetta 2
Expression_system_vector: Pgex Vector
Expression_system_plasmid: Pgex-Nki-3c-Lic

Molecule: Polyubiquitin-B
Chain: B, E, H, K
Synonym: Ubiquitin
Engineered: Yes
Other_details: Gly76 Of Ubiquitin Is Replaced By Gly-Aye Th Covalently Linked To The Active Site Cys88 Of Uch- L5;

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Nuclear Factor Related To Kappa-B-Binding Protein
Chain: C, F, I, L
Fragment: Activating Fragment Of Ino80g Deubad Domain, Resi 101;
Synonym: Dna-Binding Protein R Kappa-B, Ino80 Complex Subun Ino80g;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Rosetta 2
Expression_system_vector: Pet Vector
Expression_system_plasmid: Pet-Nki-His-3c-Lic
symmetry Space Group: C 1 2 1
R_factor 0.238 R_Free 0.269
crystal
cell
length a length b length c angle alpha angle beta angle gamma
152.084 137.788 98.916 90.00 102.54 90.00
method X-Ray Diffractionresolution 3.69 Å
ligand AYE enzyme Hydrolase E.C.3.4.19.12 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, J, D, G
  • endopeptidase inhibitor acti...


  • F, C, I, L


    Primary referenceMechanism of UCH-L5 Activation and Inhibition by DEUBAD Domains in RPN13 and INO80G., Sahtoe DD, van Dijk WJ, El Oualid F, Ekkebus R, Ovaa H, Sixma TK, Mol Cell. 2015 Feb 17. pii: S1097-2765(14)01017-X. doi:, 10.1016/j.molcel.2014.12.039. PMID:25702870
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (586 Kb) [Save to disk]
  • Biological Unit Coordinates (4uf6.pdb1.gz) 148 Kb
  • Biological Unit Coordinates (4uf6.pdb2.gz) 148 Kb
  • Biological Unit Coordinates (4uf6.pdb3.gz) 145 Kb
  • Biological Unit Coordinates (4uf6.pdb4.gz) 148 Kb
  • LPC: Ligand-Protein Contacts for 4UF6
  • CSU: Contacts of Structural Units for 4UF6
  • Structure Factors (1148 Kb)
  • Retrieve 4UF6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4UF6 from S2C, [Save to disk]
  • Re-refined 4uf6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4UF6 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 4UF6
  • 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 4UF6, from MSDmotif at EBI
  • Fold representative 4uf6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4uf6] [4uf6_J] [4uf6_B] [4uf6_D] [4uf6_I] [4uf6_A] [4uf6_F] [4uf6_E] [4uf6_H] [4uf6_K] [4uf6_L] [4uf6_C] [4uf6_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4UF6: [UBQ ] by SMART
  • Other resources with information on 4UF6
  • Community annotation for 4UF6 at PDBWiki (http://pdbwiki.org)

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