1O4X TERNARY COMPLEX OF THE DNA BINDING DOMAINS OF THE OCT1 AND SOX2 TRANSCRIPTION FACTORS WITH A 19MER OLIGONUCLEOTIDE FROM THE HOXB1 REGULATORY ELEMENT date
authors Clore, G.M., Williams, D.C.
compound source
symmetry
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution
note 1O4X (Molecule of the Month:pdb112)
related structures by homologous chain: 1HRZ, 1J46, 1POG
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceMolecular basis for synergistic transcriptional activation by Oct1 and Sox2 revealed from the solution structure of the 42-kDa Oct1.Sox2.Hoxb1-DNA ternary transcription factor complex., Williams DC Jr, Cai M, Clore GM, J Biol Chem 2004 Jan 9;279(2):1449-57. Epub 2003 Oct 14. PMID:14559893
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (91 Kb) [Save to disk]
  • Biological Unit Coordinates (1o4x.pdb1.gz) 84 Kb
  • CSU: Contacts of Structural Units for 1O4X
  • Original NMR restraints for 1O4X from PDB
  • Retrieve 1O4X in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1O4X from S2C, [Save to disk]
    • View 1O4X 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 1O4X
  • 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
  • 3D motif for 1O4X, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1o4xa1, region A:110-163 [Jmol] [rasmolscript] [script source]
        - Domain d1o4xa2, region A:5-79 [Jmol] [rasmolscript] [script source]
        - Domain d1o4xb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1o4x from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1o4x_D] [1o4x_B] [1o4x] [1o4x_A] [1o4x_C]
  • SWISS-PROT database: [P14859] [P48431]
  • Domain organization of [PO2F1_HUMAN] [SOX2_HUMAN] by SWISSPFAM
  • Domains found in 1O4X: [HMG] [HOX] [POU ] by SMART
    • Other resources with information on 1O4X
  • Community annotation for 1O4X 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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