interface graph thumbnail
legend  pdf

structure nameSTRUCTURE OF SOX17 BOUND TO DNA
(Transcription factor SOX-17)
referencePalasingam et al. J.Mol.Biol. 388 619 2009
sourceMus musculus
experimentX-ray (resolution=2.75, R-factor=0.243)
structural superfamilyHMG-box;
sequence familyHMG high mobility group box;
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureRNFMRHNSY

Estimated binding specificities ?

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# IC=6.241 IC/col=1.040 n_of_columns=6 specificity:   
A |  96   0  96  96   0  39
C |   0  96   0   0  19  19
G |   0   0   0   0   0  19
T |   0   0   0   0  77  19
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: SOX17
CACAATGPubMed3f27_D(7.85e-06)
CCAATPubMed3f27_D(4.30e-04)

Dendrogram of similar interfaces ?

matrix format
  
  RCNGFTMARTHTNG--ST--YA--   L     +-----------------------------6t90_L    
                                 +-4 
  RTNGFTIARA--NASGST--YAPG   L   ! +-----------------------------1j46_A    
                                 ! 
  RTNTFTMARA--NGACST--YA--   L --5                             +4s2q_D    
                                 !                    +--------1 
  RCNAFTIARG--NC--SALTYAKT   L   !         +----------2        +2gzk_A    
                                 !         !          ! 
  RGNTFTMART--NGRTSA--WANT   L   +---------3          +--------7m5w_A    
                                           ! 
  RCNTFTMARAHGNAACST------   L             +-------------------4euw_A

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updated Fri Sep 13 16:59:56 2024