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structure nameHOMEOBOX TRANSCRIPTION FACTOR CDX2 BOUND TO METHYLATED DNA
(Homeobox protein CDX-2)
referenceMorgunova et al. Science 356 ? 2017
sourceHomo sapiens
experimentX-ray (resolution=2.66, R-factor=0.204)
structural superfamilyHomeodomain-like;
sequence familyHomeobox domain;
reference complex6es3_K
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  13
G |  16   0   0   0  24  24  13
T |  54  96  96   0  24  24  16
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: CDX2
TATAAAAPubMed5lty_K(1.05e-02)
TTTTAGGPubMed5lty_K(1.05e-02)
GTTTAGAPubMed5lty_K(1.05e-02)
GTTTATGPubMed5lty_K(1.05e-02)

Dendrogram of similar interfaces ?

matrix format
  
  ----YARA----------IAQTNA--------   L                                   +5lux_L    
                                                                     +--12  
  RA----RA----------IAQTNAMC------   L                               !   +1puf_A    
                                                                     !  
  RA----RT----------IAQTNA------KT   L                               !          +4rdu_A    
                                                                     !        +-1 
  --KG--RC----------IAQCNAYA------   L                               !     +-10 +1nk3_P    
                                                                     !     !  !  
  ------RT----------NT--NAIARG----   L                            +-17     !  +1puf_B    
                                                                  !  !     !  
  ------RT----------VAQTNA--------   L                            !  !  +-15    +5hod_A    
                                                                  !  !  !  !  +-8 
  RA----RT----------VA--NAQT------   L                            !  !  !  !  ! +3d1n_M    
                                                                  !  !  !  +-14  
  RT----RT----------VAQTNA--------   L                            !  !  !     !   +1fjl_B    
                                                                  !  !  !     ! +-2 
  RA----RT----------VASGNA--------   L                            !  +-16     +-3 +3cmy_A    
                                                                  !     !       ! 
  ------RT----------IAQCNAMG------   L                            !     !       +1b72_A    
                                                               +-18     !  
  ------RT------------KGNA--------   L                         !  !     !    +2hos_A    
                                                               !  !     !  +-5 
  ------RA--------RCVTCTNAQTRC----   L                         !  !     !  ! +1au7_A    
                                                               !  !     +-11  
  ------RT----------IAKGNA--------   L                         !  !        !   +2hdd_A    
                                                               !  !        ! +-4 
  --------HTRT------NCSTNARG------   L                      +-19  !        +-9 +1k61_B    
                                                            !  !  !          ! 
  --------RT--------NT--NAIARG----   L                      !  !  !          +4cyc_B    
                                                            !  !  !  
  ----------------RTVAIANAMCRG----   L                      !  !  !     +1le8_A    
                                                            !  !  +-----6 
  ------RT----------VASCNAQA------   L             +-------20  !        +1gt0_C    
                                                   !        !  !  
  RT--RT--------VTKTIAQTNA--------   L             !        !  +-------2me6_A    
                                                   !        !  
  ------RA----RCET--SAQAKG--------   L             !        !       +-5lxu_A    
                                         +--------21        +------13  
  ------RT----STVCKGDCRG----------   L   !         !                ! +1w0t_A    
                                         !         !                +-7 
  ------------YTVCKGDCKC----------   L -22         !                  +2qhb_A    
                                         !         !  
  --------------------KG--NA--EC--   L   !         +------------------1xpx_A    
                                         !  
  ------------RGKGSGSAQAVCRT------   L   +----------------------------5gzb_A    
                                       

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updated Mon Dec 18 13:16:21 2023