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structure nameCRYSTAL STRUCTURE OF HOXA9 AND PBX1 HOMEODOMAINS BOUND TO DNA
(PRE-B-CELL LEUKEMIA TRANSCRIPTION FACTOR-1)
referenceLaronde-Leblanc et al. 'Genes 17 2060 2003
sourceHOMO SAPIENS
experimentX-ray (resolution=1.90, R-factor=0.233)
structural superfamilyHomeodomain-like;
sequence familyHomeobox domain;
multimeric complexes1b72_AB 1b8i_AB 1puf_AB 2r5y_AB 2r5z_AB 4cyc_AB 4uus_AB 4uus_EF 5zjq_AB 5zjr_AB 5zjs_AB
redundant complexes1lfu_P 5zjr_B 1b72 1b8i 2r5y 2r5z 4cyc 4uus 5zjq 5zjs
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureRNNIR

Estimated binding specificities ?

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# IC=5.354 IC/col=0.892 n_of_columns=6 specificity:   
A |  72   0   0  96  10  69
C |   8   0   0   0   8  11
G |   8   0  96   0  17   8
T |   8  96   0   0  61   8
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: PBX1
ATCAATCAAPubMed1puf_B(1.14e-02), 1puf_AB(1.49e-03)
TGATTGACPubMed1puf_B(7.15e-03), 1puf_AB(7.14e-07)
TGATTGATPubMed1puf_B(7.15e-03), 1puf_AB(3.42e-04)
TTGATPubMed1puf_B(4.18e-04), 1puf_AB(7.82e-03)
TGATTAATPubMed1puf_B(7.15e-03), 1puf_AB(3.42e-04)
TTGATTGATPubMed1puf_B(1.14e-02), 1puf_AB(1.49e-03)
ATCAATCAPubMed1puf_B(7.15e-03), 1puf_AB(3.42e-04)

Dendrogram of similar interfaces ?

matrix format
  
  RCRT------------------NT--NAITRG------------   L                         +----5zjt_B    
                                                        +------------------5 
  --RA------------------ITQTNAMG--------------   L      !                  +----5zjt_E    
                                                        !  
  --RT------------------NT--NAIARG------------   L      !                    +----1b72_B    
                                                        !             +------4 
  ----------------------NCITNA----------RGRG--   L      !             !      +----6fqq_E    
                                                        !          +--7 
  --RT----------------KTIAQCNA----RT----------   L      !          !  !          +1ig7_A    
                                                        !          !  +----------2 
  --RT------------------ITQCNAACRG------------   L      !          !             +6a8r_A    
                                                     +-12        +-8 
  --RT------------------NT--NA--RG------------   L   !  !        ! !            +-1b8i_B    
                                                     !  !        ! !   +--------3 
  --RT------------------IAKGNA----------------   L   !  !        ! !   !        ! +2hdd_A    
                                                     !  !      +-9 +---6        +-1 
  ----------------------IA--NA----------------       !  !      ! !     !          +4qtr_D    
                                                     !  !      ! !     ! 
  --------------YTVC--KGDCKC------------------   L -13  !   +-10 !     +----------2qhb_A    
                                                     !  !   !  ! ! 
  --RA------YA----------IAQCNAYCKG------------   L   !  !   !  ! +----------------5flv_I    
                                                     !  +--11  !  
  ----------------RTQT--ITQANA------VTKT----KT   L   !      !  +-----------------2ld5_A    
                                                     !      !  
  ----NGRGTG--LG--LCRG------------------------       !      +-------------------4e9f_A    
                                                     !  
  --RA----------------KGSAQA------------------   L   +-------------------------6j5b_C

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updated Tue Dec 19 06:02:14 2023