2XSD Transcription Dna date Sep 28, 2010
title Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain Bound To 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
Synthetic: Yes

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

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, Oc
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 0.1940 R_Free 0.2317
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

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] (70 Kb) [Save to disk]
  • Biological Unit Coordinates (2xsd.pdb1.gz) 64 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
  • 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 2XSD, from MSDmotif at EBI
  • Fold representative 2xsd from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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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