5ZJQ Transcription Dna date Mar 22, 2018
title Structure Of Abdbexd Complex Bound To A 'Red14' Dna Sequenc
authors N.Baburajendran, T.Zeiske, 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(Gptpcpaptpapapaptpcpaptpgp
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Drosophila Melanogaster
Organism_taxid: 7227

Molecule: Dna (5'-D(Gpcpaptpgpaptptptpaptpgpap
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Drosophila Melanogaster
Organism_taxid: 7227
symmetry Space Group: C 1 2 1
R_factor 0.223 R_Free 0.252
crystal
cell
length a length b length c angle alpha angle beta angle gamma
77.056 49.440 95.194 90.00 109.33 90.00
method X-Ray Diffractionresolution 2.44 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] (77 Kb) [Save to disk]
  • Biological Unit Coordinates (5zjq.pdb1.gz) 73 Kb
  • CSU: Contacts of Structural Units for 5ZJQ
  • Structure Factors (319 Kb)
  • Retrieve 5ZJQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5ZJQ from S2C, [Save to disk]
  • View 5ZJQ 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 5ZJQ
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5zjq from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5zjq_D] [5zjq_A] [5zjq_B] [5zjq_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5ZJQ
  • Community annotation for 5ZJQ at PDBWiki (http://pdbwiki.org)

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