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legend  pdf

structure nameCRYSTAL STRUCTURE OF THE DNA-BINDING DOMAINS OF YVOA IN COMPLEX WITH PALINDROMIC OPERATOR DNA
(HTH-type transcriptional repressor YvoA)
referenceFillenberg et al. 'Nucleic 43 1283 2015
sourceBacillus subtilis subsp. subtilis str. 168
experimentX-ray (resolution=1.91, R-factor=0.181)
structural superfamily"Winged helix" DNA-binding domain;
sequence familyBacterial regulatory proteins, gntR family;
multimeric complexes4u0y_ABCD
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureRSRMTR

Estimated binding specificities ?

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# IC=5.620 IC/col=0.803 n_of_columns=7 specificity:   
A |   2  59   7  81   0   0  63
C |   1  11  25   0  96  96  11
G |   0   2  42  13   0   0  11
T |  93  24  22   2   0   0  11
scan!

Dendrogram of similar interfaces ?

matrix format
  
  ----------------EGRGSARGMCTTRT------------------   L                                +-------------------4wwc_B    
                                                                                 +----4 
  ----------------ETNTSCRGHC--RT--------QA--------   L                        +--5    +-------------------5d4s_B    
                                                                              !  ! 
  ------------------------------RCYG--KT----------                            !  +------------------------2acj_B    
                                                                              ! 
  ----------------RA--ST--ECTTRAKA------HT--------   L                      +-7          +-----------------7oz3_B    
                                                                            ! ! +--------3 
  ------------------------TTHT--KG------RC--------   L                      ! ! !        +-----------------7b0c_A    
                                                                            ! +-6 
  --------------------------------YGRG------------                          !   !                         +4wcg_A    
                                                                          +-8   !          +--------------1 
  --------------------STRGQTQAST------HG------KT--   L                    ! !   +----------2              +7t8k_B    
                                                                          ! !              ! 
  --------------------TT--PTTCSTNT----------------   L                  +-9 !              +---------------4lln_I    
                                                                        ! ! ! 
  --------------------HT--STATSTRG----------------   L                  ! ! +-----------------------------5lej_A    
                                                                     +-10 ! 
  --------LAHAKARA------------------------------IA                   !  ! +-----------------------------6dta_A    
                                                                  +-11  !  
  ------------------------KGTA--TA--RG------------   L            !  !  +-----------------------------1xsd_A    
                                                               +-12  !  
  --------------------ST--PTTCSTQC--RA------------   L         !  !  +-----------------------------1ddn_B    
                                                            +-13  !  
  IARTQTNA----------------------------------------   L      !  !  +-----------------------------6d5f_d    
                                                         +-14  !  
  ----------------------------------------NG------       !  !  +-----------------------------7k63_U    
                                                       -15  !  
  ----------------------AT----NT------------------   L   !  +-----------------------------7c7l_A    
                                                         !  
  --------------------NTHG--RTYTPT----------RT----   L   +-----------------------------6qil_A    
                                                       

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updated Tue Dec 19 09:29:59 2023