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structure nameANTPHD WITH 15BP DNA DUPLEX R-MONOTHIOATED AT CYTIDINE-8
(Homeotic protein antennapedia)
referenceZandarashvili et al. Chembiochem 17 1636 2016
sourceDrosophila melanogaster
experimentX-ray (resolution=2.09, R-factor=0.219)
structural superfamilyHomeodomain-like;
sequence familyHomeobox domain;
redundant complexes1ahd_P 4xic_D 4xid_D 5jlx_D 9ant_B
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureRRIQN

Estimated binding specificities ?

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# IC=5.379 IC/col=0.896 n_of_columns=6 specificity:   
A |   0  11  96  96   9   9
C |  96   9   0   0   9   9
G |   0   9   0   0   9  69
T |   0  67   0   0  69   9
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: ANTENNAPEDIA
TAATGPubMed5jlw_D(1.20e-07), 4xic_A(3.59e-04), 4xid_D(7.10e-07), ... (total=5)
CCAATPubMed5jlw_D(2.85e-03), 4xic_A(2.64e-03), 4xid_D(6.05e-03), ... (total=5)
TTAATTPubMed5jlw_D(1.12e-03), 4xic_A(1.13e-03), 4xid_D(3.38e-03), ... (total=5)

Dendrogram of similar interfaces ?

matrix format
  
  RT------------------IAQCNAYA--RT   L                                       +1nk2_P    
                                                             +---------------2 
  RT------------------NT--NAITRG--                      +----6               +5zjt_B    
                                                        !    ! 
  RA----------------RCVTCTNAQTRC--   L            +-----8    +----------------1au7_A    
                                                  !     ! 
  RT------------------NT--NAIARG--   L            !     +---------------------1b72_B    
                                                  !  
  RT------------------IAKGNA------   L         +-10           +---------------6m3d_C    
                                               !  !     +-----5 
  ------------------RTVAITNAMCRG--   L         !  !     !     +---------------1yrn_A    
                                               !  !     ! 
  RT------------------VAQTNA------   L         !  !     !                   +-5hod_A    
                                               !  +-----9        +----------3 
  RT------------------ITQCNAACRG--   L         !        !        !          ! +6a8r_A    
                                            +-11        !    +---4          +-1 
  ----RT--------------NCSTNARG----   L      !  !        !    !   !            +1mnm_C    
                                            !  !        +----7   ! 
  ------------------RCVACTNAQA----   L      !  !             !   +------------7xrc_C    
                                         +-12  !             ! 
  --NGRGTGLG----LC----------------       !  !  !             +----------------6vjw_A    
                                         !  !  !  
  RA------------------YAQTNAAARG--   L -13  !  +-----------------------------6wig_A    
                                         !  !  
  --------------------ITKGNARGRA--   L   !  +-----------------------------1zq3_P    
                                         !  
  ----------STRGQTQAST------------   L   +-----------------------------7t8k_B    
                                       

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updated Tue Dec 19 10:48:02 2023