5KWD De Novo Protein date Jul 17, 2016
title Computationally Designed Symmetric Homotetramer
authors J.A.Fallas, B.Sankaran, P.Zwart, D.Baker
compound source
Molecule: Ankyrin Repeat-Containing Protein
Chain: A, B, C, D
Engineered: Yes
 Organism_scientific: Metallosphaera Yellowstonensis Mk1
Organism_taxid: 671065
Gene: Metmk1draft_00016260
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
symmetry Space Group: P 21 21 21
R_factor 0.229 R_Free 0.281
crystal
cell
length a length b length c angle alpha angle beta angle gamma
77.770 89.470 99.080 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.75 Å
Gene METMK1DRAFT
Primary referenceComputational design of self-assembling cyclic protein homo-oligomers., Fallas JA, Ueda G, Sheffler W, Nguyen V, McNamara DE, Sankaran B, Pereira JH, Parmeggiani F, Brunette TJ, Cascio D, Yeates TR, Zwart P, Baker D, Nat Chem. 2017 Apr;9(4):353-360. doi: 10.1038/nchem.2673. Epub 2016 Dec 5. PMID:28338692
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (283 Kb) [Save to disk]
  • Biological Unit Coordinates (5kwd.pdb1.gz) 275 Kb
  • CSU: Contacts of Structural Units for 5KWD
  • Structure Factors (364 Kb)
  • Retrieve 5KWD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5KWD from S2C, [Save to disk]
  • Re-refined 5kwd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5KWD 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 5KWD
  • 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: [5kwd_B] [5kwd_C] [5kwd_D] [5kwd] [5kwd_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5KWD
  • Community annotation for 5KWD at PDBWiki (http://pdbwiki.org)

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