2XSD Transcription Dna date Sep 28, 2010
title Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain B Palindromic More Dna
authors R.Jauch, S.H.Choo, C.K.L.Ng, P.R.Kolatkar
compound source
Molecule: 5'-D(Aptpgpcpaptpgpapgpgpap)-3'
Chain: A
Engineered: Yes
 Synthetic: Yes

Molecule: 5'-D(Cpcptpcpaptpgpcpaptpap)-3'
Chain: B
Engineered: Yes
Synthetic: Yes

Molecule: Pou Domain, Class 3, Transcription Factor 1
Chain: C
Fragment: Residues 240-402
Synonym: Octamer-Binding Transcription Factor 6, Octamer-Bi Protein 6, Pou Domain Transcription Factor Scip, Otf-6, Oct
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_plasmid: Pdest-Hismbp
symmetry Space Group: C 1 2 1
R_factor 0.194 R_Free 0.232
crystal
cell
length a length b length c angle alpha angle beta angle gamma
93.497 52.009 69.013 90.00 129.03 90.00
method X-Ray Diffractionresolution 2.05 Å
ligand EDO enzyme
Gene
Ontology
ChainFunctionProcessComponent
C


Primary referenceCrystal structure of the dimeric Oct6 (POU3f1) POU domain bound to palindromic MORE DNA., Jauch R, Choo SH, Ng CK, Kolatkar PR, Proteins. 2010 Oct 19. PMID:21117060
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (69 Kb) [Save to disk]
  • Biological Unit Coordinates (2xsd.pdb1.gz) 62 Kb
  • LPC: Ligand-Protein Contacts for 2XSD
  • CSU: Contacts of Structural Units for 2XSD
  • Structure Factors (109 Kb)
  • Retrieve 2XSD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2XSD from S2C, [Save to disk]
  • Re-refined 2xsd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2XSD 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 2XSD
  • 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 2XSD, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2xsd] [2xsd_A] [2xsd_B] [2xsd_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 2XSD: [HOX] [POU ] by SMART
    • Other resources with information on 2XSD
  • Community annotation for 2XSD 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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