5YWR Signaling Protein date Nov 30, 2017
title Crystal Structure Of Ring E3 Ligase Znrf1 In Complex With Ub (Ubc13)
authors A.P.Behera, P.Naskar, A.B.Datta
compound source
Molecule: Ubiquitin-Conjugating Enzyme E2 N
Chain: A
Synonym: Bendless-Like Ubiquitin-Conjugating Enzyme,E2 Ubiq Conjugating Enzyme N,Ubc13,Ubch13,Ubiquitin Carrier Protein Ubiquitin-Protein Ligase N;
Ec: 2.3.2.23
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ube2n, Blu
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta2(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petsumo2

Molecule: E3 Ubiquitin-Protein Ligase Znrf1
Chain: B
Synonym: Nerve Injury-Induced Gene 283 Protein,Ring-Type E3 Transferase Znrf1,Zincring Finger Protein 1;
Ec: 2.3.2.27
Engineered: Yes
Other_details: First 137 Amino Acids Deleted From The Prote

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Znrf1, Nin283
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta2(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petsumo2
symmetry Space Group: P 21 21 21
R_factor 0.165 R_Free 0.184
crystal
cell
length a length b length c angle alpha angle beta angle gamma
47.430 59.548 94.792 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.47 Å
ligand
enzyme Transferase E.C.2.3.2.23 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural insights into the nanomolar affinity of RING E3 ligase ZNRF1 for Ube2N and its functional implications., Behera AP, Naskar P, Agarwal S, Banka PA, Poddar A, Datta AB, Biochem J. 2018 May 9;475(9):1569-1582. doi: 10.1042/BCJ20170909. PMID:29626159
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (97 Kb) [Save to disk]
  • Biological Unit Coordinates (5ywr.pdb1.gz) 90 Kb
  • CSU: Contacts of Structural Units for 5YWR
  • Structure Factors (1947 Kb)
  • Retrieve 5YWR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YWR from S2C, [Save to disk]
  • View 5YWR 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 5YWR
  • 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 5ywr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ywr_B] [5ywr_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5YWR
  • Community annotation for 5YWR 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
    Bioinformatics Unit
    Weizmann Institute of Science