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structure nameHOMEODOMAIN FROM THE DROSOPHILA PAIRED PROTEIN BOUND TO A DNA OLIGONUCLEOTIDE
(PAIRED PROTEIN)
referenceWilson et al. 'Cell(Cambridge,Mass.)' 82 709 1995
sourceDrosophila melanogaster
experimentX-ray (resolution=2.00, R-factor=0.198)
structural superfamilyHomeodomain-like;
sequence familyHomeobox domain;
redundant complexes1pdn_C
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureRRVQN

Estimated binding specificities ?

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# IC=5.300 IC/col=0.757 n_of_columns=7 specificity:   
A |   9   0  96  96   9  24  67
C |   9   0   0   0   9  24   9
G |  67   0   0   0  11  24  11
T |  11  96   0   0  67  24   9
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Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: PAIRED
GTTATPubMed1fjl_B(6.06e-03)
TAATTPubMed1fjl_B(1.01e-03)
TAATGTTATTAPubMed1fjl_B(1.06e-03)

Dendrogram of similar interfaces ?

matrix format
  
  RART----VTKGNA--KA   L         +--------------------2lkx_A    
                                 ! 
  --RT----IAQCNAMG--   L   +-----6               +----1b72_A    
                           !     !        +------4 
  --RC----IAQCNAYC--   L   !     !        !      +----3rkq_B    
                           !     +--------5 
  --RT--QTVAQTNA----   L   !              !       +---8osb_E    
                           !              !       ! 
  --------NCICNARGRG   L --7              +-------3    +4xrm_B    
                           !                      !  +-1 
  --------NCITNARGRG   L   !                      +--2 +6fqq_E    
                           !                         ! 
  ----RT--NT--NAIARG   L   !                         +4cyc_B    
                           ! 
  --------VTCCNAQA--   L   +--------------------------8g87_X

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updated Mon Jun 29 14:12:19 2026