6Y5N Ligase date Feb 25, 2020
title Ring-Dtc Domain Of Deltex1
authors M.Gabrielsen, L.Buetow, D.T.Huang
compound source
Molecule: E3 Ubiquitin-Protein Ligase Dtx1
Chain: A, B
Synonym: Protein Deltex-1,Hdtx1,Ring-Type E3 Ubiquitin Tran Dtx1;
Ec: 2.3.2.27
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dtx1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.187 R_Free 0.211
crystal
cell
length a length b length c angle alpha angle beta angle gamma
67.490 86.550 129.830 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.88 Å
ligand CL, EDO, ZN enzyme Transferase E.C.2.3.2.27 BRENDA
Primary referenceStructural insights into ADP-ribosylation of ubiquitin by Deltex family E3 ubiquitin ligases., Chatrin C, Gabrielsen M, Buetow L, Nakasone MA, Ahmed SF, Sumpton D, Sibbet GJ, Smith BO, Huang DT, Sci Adv. 2020 Sep 18;6(38). pii: 6/38/eabc0418. doi: 10.1126/sciadv.abc0418., Print 2020 Sep. PMID:32948590
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (237 Kb) [Save to disk]
  • Biological Unit Coordinates (6y5n.pdb1.gz) 114 Kb
  • Biological Unit Coordinates (6y5n.pdb2.gz) 112 Kb
  • LPC: Ligand-Protein Contacts for 6Y5N
  • CSU: Contacts of Structural Units for 6Y5N
  • Structure Factors (2437 Kb)
  • Retrieve 6Y5N in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6Y5N from S2C, [Save to disk]
    • View 6Y5N 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 6Y5N
  • 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: [6y5n_A] [6y5n_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6Y5N
  • Community annotation for 6Y5N 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