5XIS Transferase Ribosomal Protein date Apr 27, 2017
title Crystal Structure Of Rnf168 Udm1 In Complex With Lys63-Linke Diubiquitin, Form I
authors T.S.Takahashi, Y.Sato, S.Fukai
compound source
Molecule: E3 Ubiquitin-Protein Ligase Rnf168
Chain: A, D
Fragment: Unp Residues 110-188
Synonym: Hrnf168,Ring Finger Protein 168,Ring-Type E3 Ubiqu Transferase Rnf168;
Ec: 2.3.2.27
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rnf168
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcold-Gst

Molecule: Ubiquitin-40s Ribosomal Protein S27a
Chain: B, E
Synonym: Ubiquitin Carboxyl Extension Protein 80
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Rps27a, Uba80, Ubcep1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet26b

Molecule: Ubiquitin-40s Ribosomal Protein S27a
Chain: C, F
Synonym: Ubiquitin Carboxyl Extension Protein 80
Engineered: Yes
Mutation: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Rps27a, Uba80, Ubcep1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet26b
symmetry Space Group: P 1
R_factor 0.219 R_Free 0.245
crystal
cell
length a length b length c angle alpha angle beta angle gamma
35.273 66.291 74.173 76.47 79.29 80.49
method X-Ray Diffractionresolution 1.78 Å
ligand MG, XYZ enzyme Transferase E.C.2.3.2.27 BRENDA
Primary referenceStructural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168., Takahashi TS, Hirade Y, Toma A, Sato Y, Yamagata A, Goto-Ito S, Tomita A, Nakada S, Fukai S, Nat Commun. 2018 Jan 12;9(1):170. doi: 10.1038/s41467-017-02345-y. PMID:29330428
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (87 Kb) [Save to disk]
  • Biological Unit Coordinates (5xis.pdb1.gz) 41 Kb
  • Biological Unit Coordinates (5xis.pdb2.gz) 42 Kb
  • LPC: Ligand-Protein Contacts for 5XIS
  • CSU: Contacts of Structural Units for 5XIS
  • Structure Factors (1432 Kb)
  • Retrieve 5XIS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5XIS from S2C, [Save to disk]
  • View 5XIS 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 5XIS
  • 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: [5xis_A] [5xis_F] [5xis_E] [5xis_B] [5xis_C] [5xis_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5XIS
  • Community annotation for 5XIS at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science