5ZJR Transcription Dna date Mar 22, 2018
title Structure Of Abdbexd Complex Bound To A 'Magenta14' Dna Seq
authors T.Zeiske, N.Baburajendran, A.Kaczynska, R.Mann, B.Honig, L.Shapir A.G.Palmer
compound source
Molecule: Homeobox Protein Abdominal-B
Chain: A
Synonym: Infraabdominal 7,Iab-7,P3,Ph189
Engineered: Yes
 Organism_scientific: Drosophila Melanogaster
Organism_common: Fruit Fly
Organism_taxid: 7227
Gene: Abd-B, Cg10291
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Homeobox Protein Extradenticle
Chain: B
Synonym: Dpbx
Engineered: Yes
Organism_scientific: Drosophila Melanogaster
Organism_common: Fruit Fly
Organism_taxid: 7227
Gene: Exd, Cg8933
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Gptpcpgptpapapaptpcpaptpgp
Chain: C
Engineered: Yes
Synthetic: Yes
Organism_scientific: Drosophila Melanogaster
Organism_taxid: 7227

Molecule: Dna (5'-D(Pgpcpaptpgpaptptptpapcpgpa
Chain: D
Engineered: Yes
Synthetic: Yes
Organism_scientific: Drosophila Melanogaster
Organism_taxid: 7227
symmetry Space Group: C 1 2 1
R_factor 0.269 R_Free 0.288
crystal
cell
length a length b length c angle alpha angle beta angle gamma
77.330 49.445 95.092 90.00 109.18 90.00
method X-Ray Diffractionresolution 3.03 Å
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceIntrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites., Zeiske T, Baburajendran N, Kaczynska A, Brasch J, Palmer AG 3rd, Shapiro L, Honig B, Mann RS, Cell Rep. 2018 Aug 28;24(9):2221-2230. doi: 10.1016/j.celrep.2018.07.100. PMID:30157419
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (73 Kb) [Save to disk]
  • Biological Unit Coordinates (5zjr.pdb1.gz) 68 Kb
  • CSU: Contacts of Structural Units for 5ZJR
  • Structure Factors (71 Kb)
  • Retrieve 5ZJR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5ZJR from S2C, [Save to disk]
    • View 5ZJR 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 5ZJR
  • 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: [5zjr_B] [5zjr_C] [5zjr_D] [5zjr_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5ZJR
  • Community annotation for 5ZJR at PDBWiki (http://pdbwiki.org)

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