5GG4 Hydrolase Ligase date Jun 15, 2016
title Crystal Structure Of Usp7 With Rnf169 Peptide
authors Y.Jiang, Q.Gong
compound source
Molecule: Ubiquitin Carboxyl-Terminal Hydrolase 7
Chain: A, B, C, D
Fragment: Unp Residues 560-890
Synonym: Deubiquitinating Enzyme 7,Herpesvirus-Associated U Specific Protease,Ubiquitin Thioesterase 7,Ubiquitin-Specif Processing Protease 7;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Usp7, Hausp
Expression_system: Escherichia Coli 'Bl21-Gold(De3)Plyss Ag
Expression_system_taxid: 866768
Expression_system_strain: Bl21-Gold(De3)Plyss Ag
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28asumo

Molecule: Peptide From E3 Ubiquitin-Protein Ligase Rnf169
Chain: E, F, G, H
Synonym: Ring Finger Protein 169
Ec: 6.3.2.-
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: C 1 2 1
R_factor 0.226 R_Free 0.268
length a length b length c angle alpha angle beta angle gamma
162.195 99.965 124.299 90.00 95.54 90.00
method X-Ray Diffractionresolution 3.11 Å
enzyme Hydrolase E.C. BRENDA
Primary referenceDual-utility NLS drives RNF169-dependent DNA damage responses., An L, Jiang Y, Ng HH, Man EP, Chen J, Khoo US, Gong Q, Huen MS, Proc Natl Acad Sci U S A. 2017 Apr 4;114(14):E2872-E2881. doi:, 10.1073/pnas.1616602114. Epub 2017 Mar 21. PMID:28325877
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (184 Kb) [Save to disk]
  • Biological Unit Coordinates (5gg4.pdb1.gz) 103 Kb
  • Biological Unit Coordinates (5gg4.pdb2.gz) 77 Kb
  • CSU: Contacts of Structural Units for 5GG4
  • Structure Factors (737 Kb)
  • Retrieve 5GG4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5GG4 from S2C, [Save to disk]
  • Re-refined 5gg4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5GG4 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 5GG4
  • 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
  • Fold representative 5gg4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5gg4] [5gg4_D] [5gg4_F] [5gg4_A] [5gg4_H] [5gg4_B] [5gg4_C] [5gg4_G] [5gg4_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5GG4
  • Community annotation for 5GG4 at PDBWiki (http://pdbwiki.org)

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