5J7D De Novo Protein date Apr 06, 2016
title Computationally Designed Thioredoxin Df106
authors S.Horowitz, N.Johansen, J.G.Olsen, J.R.Winther
compound source
Molecule: Designed Thioredoxin Df106
Chain: A, B, C, D, E, F, G, H
Engineered: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.201 R_Free 0.273
crystal
cell
length a length b length c angle alpha angle beta angle gamma
58.070 67.950 229.451 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand CU enzyme
Primary referenceComputational redesign of thioredoxin is hypersensitive towards minor conformational changes in the backbone template., Johansson KE, Johansen NT, Christensen S, Horowitz S, Bardwell JC, Olsen JG, Willemoes M, Lindorff-Larsen K, Ferkinghoff-Borg J, Hamelryck T, Winther JR, J Mol Biol. 2016 Sep 19. pii: S0022-2836(16)30378-3. doi:, 10.1016/j.jmb.2016.09.013. PMID:27659562
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (289 Kb) [Save to disk]
  • Biological Unit Coordinates (5j7d.pdb1.gz) 38 Kb
  • Biological Unit Coordinates (5j7d.pdb2.gz) 38 Kb
  • Biological Unit Coordinates (5j7d.pdb3.gz) 38 Kb
  • Biological Unit Coordinates (5j7d.pdb4.gz) 38 Kb
  • Biological Unit Coordinates (5j7d.pdb5.gz) 38 Kb
  • Biological Unit Coordinates (5j7d.pdb6.gz) 38 Kb
  • Biological Unit Coordinates (5j7d.pdb7.gz) 27 Kb
  • Biological Unit Coordinates (5j7d.pdb8.gz) 38 Kb
  • LPC: Ligand-Protein Contacts for 5J7D
  • CSU: Contacts of Structural Units for 5J7D
  • Structure Factors (758 Kb)
  • Retrieve 5J7D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5J7D from S2C, [Save to disk]
  • Re-refined 5j7d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5J7D 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 5J7D
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5j7d_F] [5j7d_C] [5j7d_D] [5j7d_G] [5j7d_A] [5j7d_H] [5j7d_B] [5j7d_E] [5j7d]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5J7D
  • Community annotation for 5J7D 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