3DD9 Ribosome Inhibitor date Jun 05, 2008
title Structure Of Doch66y Dimer
authors A.Garcia-Pino, R.Loris
compound source
Molecule: Death On Curing Protein
Chain: A, B, C, D, E, F, G, H
Engineered: Yes
Mutation: Yes
 Organism_scientific: Enterobacteria Phage P1
Organism_taxid: 10678
Gene: Doc
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21b
symmetry Space Group: P 1 21 1
R_factor 0.211 R_Free 0.245
crystal
cell
length a length b length c angle alpha angle beta angle gamma
53.084 197.988 54.109 90.00 93.04 90.00
method X-Ray Diffractionresolution 2.45 Å
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B, H, C, D, G
  • protein serine/threonine kin...


    • Primary referenceThe intrinsically disordered domain of the antitoxin Phd chaperones the toxin Doc against irreversible inactivation and misfolding., De Gieter S, Konijnenberg A, Talavera A, Butterer A, Haesaerts S, De Greve H, Sobott F, Loris R, Garcia-Pino A, J Biol Chem. 2014 Dec 5;289(49):34013-23. doi: 10.1074/jbc.M114.572396. Epub 2014, Oct 16. PMID:25326388
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (142 Kb) [Save to disk]
  • Biological Unit Coordinates (3dd9.pdb1.gz) 36 Kb
  • Biological Unit Coordinates (3dd9.pdb2.gz) 36 Kb
  • Biological Unit Coordinates (3dd9.pdb3.gz) 34 Kb
  • Biological Unit Coordinates (3dd9.pdb4.gz) 36 Kb
  • CSU: Contacts of Structural Units for 3DD9
  • Likely Quarternary Molecular Structure file(s) for 3DD9
  • Structure Factors (631 Kb)
  • Retrieve 3DD9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DD9 from S2C, [Save to disk]
  • Re-refined 3dd9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3DD9 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 3DD9
  • 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
  • 3D motif for 3DD9, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dd9_E] [3dd9_B] [3dd9_G] [3dd9_H] [3dd9_C] [3dd9_F] [3dd9_D] [3dd9] [3dd9_A]
  • SWISS-PROT database: [Q06259]
  • Domain organization of [DOC_BPP1] by SWISSPFAM
    • Other resources with information on 3DD9
  • Community annotation for 3DD9 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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