6AQR Hydrolase date Aug 21, 2017
title Saga Dub Module Ubp8(C146a)Sgf11sus1sgf73 Bound To Monoub
authors M.E.Morrow, M.T.Morgan, C.Wolberger
compound source
Molecule: Ubiquitin Carboxyl-Terminal Hydrolase 8
Chain: A
Synonym: Deubiquitinating Enzyme 8,Ubiquitin Thioesterase 8 Ubiquitin-Specific-Processing Protease 8;
Ec: 3.4.19.12
Engineered: Yes
Mutation: Yes
 Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Ubp8, Ymr223w, Ym9959.05
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Transcription And Mrna Export Factor Sus1
Chain: B
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Sus1, Ybr111w-A
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Saga-Associated Factor 11
Chain: C
Synonym: 11 Kda Saga-Associated Factor
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Sgf11, Ypl047w
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Polyubiquitin-C
Chain: D
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ubc
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Saga-Associated Factor 73
Chain: E
Synonym: 73 Kda Saga-Associated Factor,Saga Histone Acetylt Complex 73 Kda Subunit;
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Sgf73, Ygl066w
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.201 R_Free 0.249
crystal
cell
length a length b length c angle alpha angle beta angle gamma
78.755 103.177 112.846 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand ZN enzyme Hydrolase E.C.3.4.19.12 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B
  • enzyme activator activity


    • C
  • enzyme activator activity


    • E


    Primary referenceActive site alanine mutations convert deubiquitinases into high-affinity ubiquitin-binding proteins., Morrow ME, Morgan MT, Clerici M, Growkova K, Yan M, Komander D, Sixma TK, Simicek M, Wolberger C, EMBO Rep. 2018 Aug 27. pii: embr.201745680. doi: 10.15252/embr.201745680. PMID:30150323
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (140 Kb) [Save to disk]
  • Biological Unit Coordinates (6aqr.pdb1.gz) 134 Kb
  • LPC: Ligand-Protein Contacts for 6AQR
  • CSU: Contacts of Structural Units for 6AQR
  • Structure Factors (2225 Kb)
  • Retrieve 6AQR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6AQR from S2C, [Save to disk]
    • View 6AQR 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 6AQR
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6aqr_C] [6aqr_E] [6aqr_D] [6aqr_B] [6aqr_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6AQR
  • Community annotation for 6AQR at PDBWiki (http://pdbwiki.org)

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