interface graph thumbnail
legend  pdf

structure nameMOUSE GABP ALPHA/BETA DOMAIN BOUND TO DNA
(PROTEIN GA BINDING PROTEIN ALPHA)
referenceBatchelor et al. Science 279 1037 1998
sourceMUS MUSCULUS
experimentX-ray (resolution=2.15, R-factor=?)
structural superfamily"Winged helix" DNA-binding domain;
sequence familyEtsdomain;
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureKRARY

Estimated binding specificities ?

contactlogo
# IC=5.582 IC/col=0.930 n_of_columns=6 specificity:   
A |  12   0   0  84  96  12
C |  60   0   0  12   0  12
G |  12  96  96   0   0  60
T |  12   0   0   0   0  12
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: GABP
CCGGAAGTPubMed1awc_A(6.34e-03)
CAGGAAGTPubMed1awc_A(6.34e-03)
CGGAAPubMed1awc_A(3.54e-04)
ACTTCCGPubMed1awc_A(3.37e-03)
CCGGAAPubMed1awc_A(1.12e-03)
CGGAAAPubMed1awc_A(1.12e-03)
CACTTCCGPubMed1awc_A(6.34e-03)
GGAAGPubMed1awc_A(3.54e-04)
GAGGAAPubMed1awc_A(1.12e-03)

Dendrogram of similar interfaces ?

matrix format
  
  ------KT--RGAT--RGYT------------   L                                               +--1awc_A    
                                                                          +----------5 
  ------KT--RG----RGYA------------   L                                    !          ! +4l18_B    
                                                                          !          +-4 
  ------KT--RG----RGYA------------   L                             +------7            +3wts_C    
                                                                   !      ! 
  ----DCKT--RG----RGYA------------   L                             !      !            +1dux_F    
                                                                 +-9      +------------3 
  ----ECKT--RGAT--RGNT------------   L                           ! !                   +1pue_E    
                                                              +-10 ! 
  ----DCKT--RGST--RGYA------------   L                        !  ! +--------------------4bnc_A    
                                                           +-11  !  
  ----DCKT--RGAT--RCYA------------   L                     !  !  +----------------------5e8i_D    
                                                           !  !  
  ----DCKT--RG----RGYA----KA------   L                     !  +-----------------------5jvt_A    
                                                           !  
  ------KT--RGSA--RGQA----------RA   L                     !                          +1yo5_C    
                                                        +-13                +---------1 
  ------KT--RGAT--RGYA------------   L                  !  !      +---------6         +4iri_A    
                                                        !  !      !         ! 
  ----------NT--RGCT--NGST--------   L                  !  !  +---8         +---------1if1_B    
                                                        !  !  !   ! 
  ------KT--RG----RAYA------------   L               +-14  +-12   +-------------------6vge_A    
                                                     !  !     !  
  ------STVT------RGQTNT--MT------   L               !  !     !                       +5d5v_B    
                                                     !  !     +-----------------------2 
  ------ST--------RTQT----KG------                +-15  !                             +5d5w_B    
                                                  !  !  !  
  KTHG----------------------------                !  !  +--------------------------5hdn_C    
                                               +-16  !  
  ----EAKT--RGAT--RGYA----------RT   L         !  !  +--------------------------3jtg_A    
                                            +-17  !  
  ----ECKT--RGAT--RGHT----------RA   L      !  !  +---------------------------4mhg_A    
                                         +-18  !  
  --------------------------YGKC--   L   !  !  +---------------------------6lui_A    
                                       -19  !  
  ----DCKT--RG----RGYA------------   L   !  +----------------------------3zp5_A    
                                         !  
  ----EC----RG----RGYC------------   L   +----------------------------2stw_A    
                                       

home
updated Fri Sep 13 15:25:21 2024