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legend  pdf

structure nameHUMAN NF-KAPPA-B P52 BOUND TO DNA
(PROTEIN NUCLEAR FACTOR KAPPA-B P52)
referenceVerdine et al.
sourceHomo sapiens
experimentX-ray (resolution=2.10, R-factor=?)
structural superfamilyp53-like transcription factors;E set domains;
sequence familyRel homology domain RHD; IPT/TIG domain;
multimeric complexes1a3q_AB
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureRRYCEHK

Estimated binding specificities ?

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# IC=5.766 IC/col=0.961 n_of_columns=6 specificity:   
A |   0   0   0   0  54  54
C |   0   0   0   0  13  13
G |  96  96  96  96  16  13
T |   0   0   0   0  13  16
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: NF-KAPPA-B P52
GGGACTTTCCPubMed1a3q_AB(5.26e-04)
GGGGATTCCCCPubMed1a3q_A(1.10e-04)
GGGGGCTTTCCCPubMed1a3q_AB(4.53e-09)
TGCCCPubMed1a3q_A(2.64e-03)
GGGGTCTCCCPubMed1a3q_AB(1.93e-07)
GGAAAPubMed1a3q_AB(5.60e-03)
GGGTCTCCCCPubMed1a3q_A(6.84e-05), 1a3q_AB(1.93e-07)
GGGATTTCACPubMed1a3q_AB(2.14e-07)
CAACGGCAGGGGAATCTCCCTCTCCTTPubMed1a3q_A(1.14e-03), 1a3q_AB(3.28e-11)
AGTTGGGATTTCCCAACCPubMed1a3q_AB(2.02e-08)
GGGAAATTCCPubMed1a3q_AB(2.14e-07)
GGGGCTGTCCCPubMed1a3q_AB(7.29e-06)
TGGAGCTTCCPubMed1a3q_AB(1.01e-04)
GGGGACTTTCCGPubMed1a3q_A(1.63e-04), 1a3q_AB(2.41e-05)
GGGGAGTCCCCPubMed1a3q_A(1.10e-04), 1a3q_AB(5.11e-15)
GGGAACTACCPubMed1a3q_AB(5.26e-04)
GGGGAATCTCCCPubMed1a3q_A(1.63e-04), 1a3q_AB(4.74e-14)
TATTCPubMed1a3q_AB(5.61e-03)
sitesourcematches (E-value)

Dendrogram of similar interfaces ?

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

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updated Fri Sep 13 15:22:17 2024