5KEK Dna date Jun 09, 2016
title Structure Determination Of A Self-Assembling Dna Crystal
authors C.R.Simmons, J.J.Birktoft, N.C.Seeman, H.Yan
compound source
Molecule: Dna (5'- D(Gpapgpcpapgpapcpcptpgpapcpgpapcpapcptp 3');
Chain: A
Engineered: Yes
 Synthetic: Yes
Organism_scientific: Endothia Gyrosa
Organism_taxid: 40263

Molecule: Dna (5'-D(Pcpgptpcpa)-3')
Chain: B
Engineered: Yes
Synthetic: Yes
Organism_scientific: Endothia Gyrosa
Organism_taxid: 40263

Molecule: Dna (5'-D(Tpcptpgpapgptpgpt)-3')
Chain: C
Engineered: Yes
Synthetic: Yes
Organism_scientific: Endothia Gyrosa
Organism_taxid: 40263

Molecule: Dna (5'-D(Pgpgptpcptpgpc)-3')
Chain: D
Engineered: Yes
Synthetic: Yes
Organism_scientific: Endothia Gyrosa
Organism_taxid: 40263
symmetry Space Group: P 32 2 1
R_factor 0.205 R_Free 0.260
crystal
cell
length a length b length c angle alpha angle beta angle gamma
67.926 67.926 59.262 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.10 Å
ligand CAC enzyme
Primary referenceConstruction and Structure Determination of a Three-Dimensional DNA Crystal., Simmons CR, Zhang F, Birktoft JJ, Qi X, Han D, Liu Y, Sha R, Abdallah HO, Hernandez C, Ohayon YP, Seeman NC, Yan H, J Am Chem Soc. 2016 Aug 2. PMID:27447429
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (21 Kb) [Save to disk]
  • Biological Unit Coordinates (5kek.pdb1.gz) 17 Kb
  • LPC: Ligand-Protein Contacts for 5KEK
  • CSU: Contacts of Structural Units for 5KEK
  • Structure Factors (46 Kb)
  • Retrieve 5KEK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5KEK from S2C, [Save to disk]
  • Re-refined 5kek structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5KEK 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 5KEK
  • 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: [5kek] [5kek_A] [5kek_C] [5kek_D] [5kek_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5KEK
  • Community annotation for 5KEK at PDBWiki (http://pdbwiki.org)

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