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legend  pdf

structure nameNFKB P50 HOMODIMER BOUND TO DNA
(PROTEIN NUCLEAR FACTOR KAPPA-B NF-KB)
referenceHarrison et al. Nature 373 311 1995
sourceHomo sapiens
experimentX-ray (resolution=2.60, R-factor=0.225)
structural superfamilyp53-like transcription factors;E set domains;
sequence familyRel homology domain RHD; IPT/TIG domain;
multimeric complexes1le5_AB 1le5_EF 1le9_AB 1le9_EF 1lei_AB 1nfk_AB 1vkx_AB 2i9t_AB 2o61_AB 3gut_ABD 3gut_CF 3gut_EGH 8tkl_AB 8tkm_AB
reference complex1nfk_A
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureRRYEHKR

Estimated binding specificities ?

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# IC=4.434 IC/col=0.633 n_of_columns=7 specificity:   
A |  16  24  24   0   0   0  13
C |  13  24  24   0  96  96  54
G |  54  24  24   0   0   0  13
T |  13  24  24  96   0   0  16
scan!

Dendrogram of similar interfaces ?

matrix format
  
  RCRCYC--EC------HC--KT----RG   L                        +1svc_P    
                                                        +-1 
  RGRGYTCCEC------HTKTKTPTKTRG   L                      ! +1nfk_A    
                                                     +--6 
  RGRGYACCEC----SAHG--KG------   L                   !  !   +7cli_B    
                                                     !  ! +-3 
  RGRGYA--EC------HG--KG------   L                   !  +-5 +7w7l_B    
                                               +-----7    ! 
  RGRGYTCCEC------HG--KG------   L             !     !    +1a3q_A    
                                               !     ! 
  RGRG----EC----------RGPTKT--   L             !     !    +2ram_A    
                                     +---------8     +----2 
  RGRGYTCTEC----------RT------   L   !         !          +1gji_A    
                                     !         ! 
  RGRGYTCCEC----------KT------   L   !         !          +2v2t_A    
                                   -10         +----------4 
  RGRGYTCTEC--RT------RT--KA--   L   !                    +2o61_A    
                                     !  
  RGRG----EG--RG--------------   L   !      +-------------1bvo_A    
                                     +------9 
  RG--YT--TTEC----RG----------   L          +-------------1imh_C    
                                   

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updated Thu Sep 12 15:32:09 2024