2R5Z Transcription Dna date Sep 04, 2007
title Structure Of Screxd Complex Bound To A Dna Sequence Derived From The Fkh Gene
authors A.K.Aggarwal, J.M.Passner, R.Jain
compound source
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

Molecule: Dna (5'- D(Dapdcpdtpdcpdtpdapdapdgpdapdtpdtpdapdapdtp Dcpdgpdgpdcpdtpdg)-3');
Chain: C
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'- D(Dtpdcpdapdgpdcpdcpdgpdapdtpdtpdapdapdtpdcp Dtpdtpdapdgpdapdg)-3');
Chain: D
Engineered: Yes

Synthetic: Yes
symmetry Space Group: C 2 2 21
R_factor 0.233 R_Free 0.303
crystal
cell
length a length b length c angle alpha angle beta angle gamma
88.840 92.600 78.840 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] (47 Kb) [Save to disk]
  • Biological Unit Coordinates (2r5z.pdb1.gz) 42 Kb
  • CSU: Contacts of Structural Units for 2R5Z
  • Likely Quarternary Molecular Structure file(s) for 2R5Z
  • Structure Factors (91 Kb)
  • Retrieve 2R5Z in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2R5Z from S2C, [Save to disk]
  • Re-refined 2r5z structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2R5Z 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 2R5Z
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2R5Z, from MSDmotif at EBI
  • Fold representative 2r5z from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2r5z_C] [2r5z_B] [2r5z_D] [2r5z_A] [2r5z]
  • SWISS-PROT database: [P40427] [P09077]
  • Domain organization of [EXD_DROME] [SCR_DROME] by SWISSPFAM
  • Domain found in 2R5Z: [HOX ] by SMART
  • Other resources with information on 2R5Z
  • Community annotation for 2R5Z 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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