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structure nameNKX2.5 HOMEODOMAIN DIMER BOUND TO ANF-242 DNA
(Homeobox protein Nkx-2.5)
referenceKasahara et al. Biochemistry 51 6312 2012
sourceHomo sapiens
experimentX-ray (resolution=1.70, R-factor=?)
structural superfamilyHomeodomain-like;
sequence familyHomeobox domain;
multimeric complexes3rkq_AB 4s0h_AB 4s0h_EF
redundant complexes4s0h_B
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureRIQNY

Estimated binding specificities ?

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# IC=6.313 IC/col=0.902 n_of_columns=7 specificity:   
A |   0   0   0   0  22  22  84
C |  91   0  90   0  16   5   0
G |   0   0   0   0  13  56  12
T |   5  96   6  96  45  13   0
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: NKX2.5
CAAGTGPubMed3rkq_B(7.04e-05), 3rkq_AB(5.82e-04), 4s0h_EF(2.07e-04), ... (total=5)
TNNAGTGPubMed3rkq_AB(6.04e-03), 4s0h_B(1.14e-02)

Dendrogram of similar interfaces ?

matrix format
  
  --KG--RT------------------IAQCNAYA--   L                                         +1nk2_P    
                                                                    +--------------3 
  RC----RT------------------ITQCNAACRG   L                          !              ! +6a8r_A    
                                                                    !              +-1 
  --RC--RT------------------NT--NAITRG                         +----9                +5zjt_B    
                                                               !    ! 
  ----RC----RT--------------NCSTNARG--   L                     !    !              +1mnm_C    
                                                               !    +--------------4 
  ------RT------------------NT--NAIARG   L                     !                   +1b72_B    
                                                            +-10  
  ------RT------------------VAQTNA----   L                  !  !                   +5hod_A    
                                                            !  !         +---------2 
  --RT--RT------------------IAKGNA----   L                  !  !     +---7         +6m3d_C    
                                                            !  !     !   ! 
  ------------------------RTVAITNAMCRG   L                  !  +-----8   +----------1yrn_A    
                                                         +-11        ! 
  ------RT----------------FTYAQTNAATRG   L               !  !        !         +----6ryd_F    
                                                         !  !        +---------6 
  ------------------------RCVACTNAQA--   L               !  !                  +----7xrc_C    
                                                      +-12  !  
  ------RA----------------RCVTCTNAQTRC   L            !  !  !                    +--1au7_A    
                                                      !  !  +--------------------5 
  ------RT----------STVC--KGDCRG------   L         +-13  !                       +--1w0t_A    
                                                   !  !  !  
  ------RA------------------YAQTNAAARG   L         !  !  +------------------------6wig_A    
                                                +-14  !  
  --------NGRGTGLG----LC--------------          !  !  +-------------------------6vjw_A    
                                             +-15  !  
  --------NGRGTGLG----LCRG------------       !  !  +--------------------------7kz0_A    
                                           -16  !  
  RT----RT------------------VAQTNA----   L   !  +-----------------------------1fjl_B    
                                             !  
  ----------------STRGQTQAST----------   L   +-----------------------------7t8k_B    
                                           

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updated Fri Sep 13 17:38:55 2024