5XU8 Hydrolase date Jun 22, 2017
title Crystal Structure Of Human Usp2 In Complex With Ubiquitin An Thioguanine
authors C.Y.Chou, S.J.Chuang
compound source
Molecule: Ubiquitin Carboxyl-Terminal Hydrolase 2
Chain: A
Fragment: Unp Residues 258-605
Synonym: 41 Kda Ubiquitin-Specific Protease,Deubiquitinatin 2,Ubiquitin Thioesterase 2,Ubiquitin-Specific-Processing Pr
Ec: 3.4.19.12
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Usp2, Ubp41
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta (De3)
Expression_system_plasmid: Pet-24d

Molecule: Ubiquitin-40s Ribosomal Protein S27a
Chain: B
Fragment: Unp Residues 1-76
Synonym: Ubiquitin Carboxyl Extension Protein 80

Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
symmetry Space Group: C 1 2 1
R_factor 0.179 R_Free 0.238
crystal
cell
length a length b length c angle alpha angle beta angle gamma
102.953 54.650 72.687 90.00 107.54 90.00
method X-Ray Diffractionresolution 1.81 Å
ligand CL, DX4, NA, ZN enzyme Hydrolase E.C.3.4.19.12 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary reference6-Thioguanine is a noncompetitive and slow binding inhibitor of human deubiquitinating protease USP2., Chuang SJ, Cheng SC, Tang HC, Sun CY, Chou CY, Sci Rep. 2018 Feb 15;8(1):3102. doi: 10.1038/s41598-018-21476-w. PMID:29449607
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk]
  • Biological Unit Coordinates (5xu8.pdb1.gz) 74 Kb
  • LPC: Ligand-Protein Contacts for 5XU8
  • CSU: Contacts of Structural Units for 5XU8
  • Structure Factors (579 Kb)
  • Retrieve 5XU8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5XU8 from S2C, [Save to disk]
  • View 5XU8 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 5XU8
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5xu8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5xu8_A] [5xu8_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5XU8
  • Community annotation for 5XU8 at PDBWiki (http://pdbwiki.org)

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