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legend  pdf

structure nameSTRUCTURE OF SCR/EXD COMPLEX BOUND TO A CONSENSUS HOX-EXD SITE
(HOMEOTIC PROTEIN SEX COMBS REDUCED)
referenceAggarwal et al. 'Cell(Cambridge,Mass.)' 131 530 2007
sourceDROSOPHILA MELANOGASTER
experimentX-ray (resolution=2.60, R-factor=0.255)
structural superfamilyHomeodomain-like;
sequence familyHomeobox domain;
multimeric complexes2r5y_AB 2r5z_AB
redundant complexes2r5z_A
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureRIQNM

Estimated binding specificities ?

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# IC=6.472 IC/col=0.925 n_of_columns=7 specificity:   
A |   0  17  45   0  96  96  80
C |  96  54  17   0   0   0   8
G |   0  17  17   0   0   0   8
T |   0   8  17  96   0   0   0
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: EXD
ATCAATCAAPubMed2r5y_A(5.29e-03), 2r5y_AB(1.57e-06), 2r5z_AB(7.85e-04)
TGATNNATPubMed2r5y_AB(1.78e-05), 2r5z_AB(4.39e-03)
TGATTAATPubMed2r5y_AB(1.75e-07), 2r5z_AB(2.04e-08)
TGATTNATGGPubMed2r5y_A(1.52e-06), 2r5y_AB(5.83e-14), 2r5z_AB(1.90e-05)
TTGATTGATPubMed2r5y_A(5.29e-03), 2r5y_AB(1.57e-06), 2r5z_AB(7.85e-04)

Dendrogram of similar interfaces ?

matrix format
  
  --RT------------IAKGNA----   L         +-----------------------------2hdd_A    
                                       +-1 
  --RA------------NAMANARARG   L     +-2 +-----------------------------2d5v_B    
                                     ! ! 
  --RA----------KGSAQA------   L   +-3 +-----------------------------6j5b_C    
                                   ! ! 
  --RG------------VA--NAQA--   L --4 +-----------------------------3l1p_A    
                                   ! 
  SA--RGSGVTSCSGNTRTRT------   L   +-----------------------------6pax_A

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updated Fri Sep 13 16:40:55 2024