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structure nameCRYSTAL STRUCTURE OF HOXA9 AND PBX1 HOMEODOMAINS BOUND TO DNA
(HOMEOBOX PROTEIN HOX-A9)
referenceLaronde-Leblanc et al. 'Genes 17 2060 2003
sourceMUS MUSCULUS
experimentX-ray (resolution=1.90, R-factor=0.233)
structural superfamilyHomeodomain-like;
sequence familyHomeobox domain;
multimeric complexes1puf_AB
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureRRIQNM

Estimated binding specificities ?

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# IC=5.339 IC/col=0.763 n_of_columns=7 specificity:   
A |   9   9  24   0   0  96  67
C |   9  11  24   0   0   0   9
G |  69   9  24  96   0   0  11
T |   9  67  24   0  96   0   9
scan!

Dendrogram of similar interfaces ?

matrix format
  
  RA----RA----------------IAQTNAMC----   L                            +----1puf_A    
                                                                +----10  
  RG----------------------ITKGNARGRA--   L                      !     !  +-1zq3_P    
                                                                !     +--8 
  ----YARA----------------IAQTNA------   L                   +-13        +-6es3_K    
                                                             !  !  
  ------RT----------RT----IAQCNA------   L                   !  !          +5jlw_D    
                                                             !  +----------4 
  ------RT----------------NT--NA------   L                   !             +1b72_B    
                                                             !  
  --KG--RT----------------IAQCNAYA--RT   L                +-14             +1nk2_P    
                                                          !  !           +-1 
  ------RT----------RTQT--ITQANAVTKTKT   L                !  !           ! +2ld5_A    
                                                          !  !     +-----7 
  RT----RT--------------KTIAQCNA----RT   L                !  !     !     ! +1ig7_A    
                                                          !  !     !     +-5 
  RC----RT----------------ITQCNAACRG--   L                !  +----12       +6a8r_A    
                                                    +----16        !  
  ------RA----------------ITQTNAMG----   L          !     !        !       +5zjt_E    
                                                    !     !        +-------3 
  --RC--RT----------------NT--NAIT----   L          !     !                +5zjt_B    
                                                    !     !  
  ------RT----------------IAKGNA------   L          !     !                 +2hdd_A    
                                                    !     !  +--------------2 
  ------------------------IA--NA------          +--17     !  !              +4qtr_D    
                                                !   !     +-15  
  ------RT----------------NT--NA--RG--   L      !   !        !              +1b8i_B    
                                                !   !        +--------------6 
  ------------------------NCITNARGRG--   L      !   !                       +6fqq_E    
                                             +-18   !  
  ------RA--------------KGSAQA--------   L   !  !   !                 +--6j5b_C    
                                             !  !   +-----------------9 
  ------RT--------STVC--KGDCRG--------   L   !  !                     +--1w0t_A    
                                           -19  !  
  ------RA----------------IAQCNAMC----   L   !  +------------------------4cyc_A    
                                             !  
  RA----RA----------------IAQTNA------   L   !                   +------5ego_B    
                                             +------------------11  
  ------YTRTTGRGSTATEA--ST------------   L                       +------6xg8_A    
                                           

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updated Tue Dec 19 06:02:05 2023