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structure nameHOMEOBOX TRANSCRIPTION FACTOR CDX1 BOUND TO METHYLATED DNA
(Homeobox protein CDX-1)
referenceMorgunova et al. Science 356 ? 2017
sourceHomo sapiens
experimentX-ray (resolution=3.23, R-factor=0.247)
structural superfamilyHomeodomain-like;
sequence familyHomeobox domain;
reference complex7q3o_C
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureYRIQN

Estimated binding specificities ?

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# IC=4.434 IC/col=0.633 n_of_columns=7 specificity:   
A |  13   0   0  96  24  24  54
C |  13   0   0   0  24  24  16
G |  16   0   0   0  24  24  13
T |  54  96  96   0  24  24  13
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: CDX1
GTTTAGAPubMed5lux_K(1.05e-02)
TATAAAAPubMed5lux_K(1.05e-02)

Dendrogram of similar interfaces ?

matrix format
  
  --RART--------------VTKGNA--KA--   L                                     +2lkx_A    
                                                                         +-1 
  --KGRT--------------IAQCNAYA--RT   L                      +------------3 +1nk2_P    
                                                            !            ! 
  --RCRT--------------NT--NAITRG--   L                 +----7            +5zjt_B    
                                                       !    ! 
  ------------------RCVACTNAQA----   L                 !    +-------------7xrc_C    
                                                       ! 
  --RTRT--------------VAQTNA------   L            +----8                  +3lnq_A    
                                                  !    !                +-2 
  --RTRT--------------IAKGNA------   L            !    !         +------4 +6m3d_C    
                                                  !    !         !      ! 
  RC--RT--------------ITQCNAACRG--   L         +-10    +---------6      +-6a8r_A    
                                               !  !              ! 
  ------------------RTVAITNAMCRG--   L         !  !              +--------1yrn_A    
                                               !  !  
  ----RA--------------YAQTNAAARG--   L      +-12  +-----------------------6wig_A    
                                            !  !  
  --------------YTVCKGDCKC--------   L      !  !       +--------------------2qhb_A    
                                            !  !  +----9 
  RT--RT--------------VAQTNA------   L      !  !  !    !                 +--1fjl_B    
                                         +-13  +-11    +-----------------5 
  ----RT--------STVCKGDCRG--------   L   !  !     !                      +--1w0t_A    
                                         !  !     !  
  RA--RT--------------VA--NAQT----   L -14  !     +-------------------------3d1n_M    
                                         !  !  
  ----YTRTTGRGSTATEAST------------   L   !  +---------------------------6xg8_A    
                                         !  
  ----------------------KC--YCFAKC       +----------------------------6p5a_B    
                                       

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updated Thu Sep 12 21:46:00 2024