interface graph thumbnail
legend  pdf

structure nameCRYSTAL STRUCTURE OF FULL-LENGTH CBNR COMPLEXED WITH THE TARGET DNA COMPLEX
(LysR-type regulatory protein)
referenceGiannopoulou et al. 'Febs 288 4560 2021
sourceCupriavidus necator
experimentX-ray (resolution=3.60, R-factor=0.237)
structural superfamilyPeriplasmic binding protein-like II;"Winged helix" DNA-binding domain;
sequence familyLysR substrate binding domain; Bacterial regulatory helixturnhelix;
multimeric complexes7d98_BPQ
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureSPPTH

Estimated binding specificities ?

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# IC=3.863 IC/col=0.552 n_of_columns=7 specificity:   
A |   0   8  96  16  24  24   8
C |   0  72   0   8  24  24  72
G |  88   8   0   8  24  24   8
T |   8   8   0  64  24  24   8
scan!

Dendrogram of similar interfaces ?

matrix format
  
  ----SG--PTPG--TT--------------HG--   L                   +--------------------7d98_Q    
                                                         +-4 
  ----ATQAPTPG----RGQG------------RT   L                 ! !         +----------4iht_D    
                                                      +--6 +---------2 
  ------------------------YGRG------                  !  !           +----------4wcg_A    
                                                    +-7  ! 
  ----TC--KTTC--KGTCHT--ST----------   L            ! !  +---------------------7ve5_B    
                                                    ! ! 
  ----STPTATAT--TTKG----------------   L            ! +------------------------5yi2_J    
                                                +---8 
  ----ST--PTTC----QG--------RG------   L        !   !   +--------------------1f5t_A    
                                                !   !   ! 
  ------------------RC----YG--KT----            !   +---5                    +2acj_B    
                                              +-9       !     +--------------1 
  ----------TTHT----KG--------------   L      ! !       +-----3              +7b0c_A    
                                              ! !             ! 
  ------------------RG----YG--------       +-10 !             +--------------1qbj_C    
                                           !  ! ! 
  FGNATTQGKGIG--VT------------------   L   !  ! +----------------------------7bzg_B    
                                         -11  !  
  --------RGTCTA----RGNT------------   L   !  +----------------------------4fx4_B    
                                           !  
  ------------------------YG--------       +----------------------------3eyi_B    
                                         

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updated Sat Sep 14 02:15:36 2024