2R5Y Transcription Dna date Sep 04, 2007
title Structure Of Screxd Complex Bound To A Consensus Hox-Exd Si
authors A.K.Aggarwal, J.M.Passner, R.Jain
compound source
Molecule: Dna (5'- D(Dapdcpdtpdcpdtpdapdtpdgpdapdtpdtpdtpdapdtp Pdcpdtpdg)-3');
Chain: C
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'- D(Dtpdcpdapdgpdcpdcpdcpdapdtpdapdapdapdtpdcp Pdgpdapdg)-3');
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Homeotic Protein Sex Combs Reduced
Chain: A
Fragment: Homeobox Dna-Binding Domain
Engineered: Yes

Organism_scientific: Drosophila Melanogaster
Organism_common: Fruit Fly
Organism_taxid: 7227
Gene: Scr
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-3a

Molecule: Homeobox Protein Extradenticle
Chain: B
Fragment: Homeobox Tale-Type Dna-Binding Domain
Synonym: Dpbx
Engineered: Yes

Organism_scientific: Drosophila Melanogaster
Organism_common: Fruit Fly
Organism_taxid: 7227
Gene: Exd
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-3a
symmetry Space Group: P 43 21 2
R_factor 0.255 R_Free 0.299
crystal
cell
length a length b length c angle alpha angle beta angle gamma
65.310 65.310 200.300 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceFunctional specificity of a Hox protein mediated by the recognition of minor groove structure., Joshi R, Passner JM, Rohs R, Jain R, Sosinsky A, Crickmore MA, Jacob V, Aggarwal AK, Honig B, Mann RS, Cell. 2007 Nov 2;131(3):530-43. PMID:17981120
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (46 Kb) [Save to disk]
  • Biological Unit Coordinates (2r5y.pdb1.gz) 41 Kb
  • CSU: Contacts of Structural Units for 2R5Y
  • Likely Quarternary Molecular Structure file(s) for 2R5Y
  • Structure Factors (110 Kb)
  • Retrieve 2R5Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2R5Y from S2C, [Save to disk]
  • Re-refined 2r5y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2R5Y 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 2R5Y
  • 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
  • 3D motif for 2R5Y, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2r5y_D] [2r5y] [2r5y_C] [2r5y_B] [2r5y_A]
  • SWISS-PROT database: [P40427] [P09077]
  • Domain organization of [EXD_DROME] [SCR_DROME] by SWISSPFAM
  • Domain found in 2R5Y: [HOX ] by SMART
  • Other resources with information on 2R5Y
  • Community annotation for 2R5Y at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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