interface graph thumbnail
legend  pdf

3D-footprint cannot reliably estimate the specificity of histones, as they display few contacts over long stretches of DNA.


Related DNA sequences reported in the literature ?


structure nameCCAAT-BINDING COMPLEX FROM ASPERGILLUS NIDULANS WITH DNA
(HAPE)
referenceHortschansky et al. Structure 20 1757 2012
sourceASPERGILLUS NIDULANS
experimentX-ray (resolution=1.80, R-factor=0.158)
structural superfamilyHistone-fold;
sequence familyHistonelike transcription factor CBF/; Core histone H2A/H2B/H3/H4;
multimeric complexes4g92_ABC 6y35_ABC 6y36_ABC 6y37_ABC 6y39_BCEFHI 7aw7_ABCDE 7aw9_ABCDE
redundant complexes6y39_C 6y35 6y36 6y37 7aw7 7aw9
links to other resourcesNAKB PDBSum PDIdb DNAproDB
sitesourcematches (E-value)
term: CCAAT
CCAATPubMed4g92_ABC(1.40e-05), 6y35_ABC(3.75e-04), 6y36_ABC(1.26e-07), ... (total=4)
ATTGGPubMed4g92_ABC(1.40e-05), 6y35_ABC(3.75e-04), 6y36_ABC(1.26e-07), ... (total=4)
CCAACPubMed4g92_ABC(7.23e-03), 6y36_ABC(3.65e-04), 6y37_ABC(7.13e-03)
CTGATTGGCPubMed4g92_ABC(7.98e-07), 6y35_ABC(1.10e-04), 6y36_ABC(1.25e-08), ... (total=4)
GCCAAPubMed4g92_ABC(7.23e-03), 6y36_ABC(3.65e-04), 6y37_ABC(7.13e-03)
TGCCAATCAPubMed4g92_ABC(7.98e-07), 6y35_ABC(1.10e-04), 6y36_ABC(1.25e-08), ... (total=4)
CCAATCGCATPubMed4g92_ABC(9.64e-04), 6y35_ABC(1.84e-04), 6y36_ABC(2.66e-08), ... (total=4)
CAATTPubMed4g92_ABC(7.13e-03), 6y35_ABC(1.40e-04), 6y36_ABC(3.68e-04), ... (total=4)
GCCAATPubMed4g92_ABC(1.63e-04), 6y35_ABC(1.18e-03), 6y36_ABC(9.19e-07), ... (total=4)
GCAATGAPubMed4g92_ABC(9.50e-03), 6y35_ABC(3.53e-03), 6y36_ABC(3.47e-03), ... (total=4)

Dendrogram of similar interfaces ?

matrix format
  
  RG----                 +-----------------------------3x1t_H    
                         ! 
  ----RT                 !                           +---1u35_G    
                         !              +------------2 
  --LTRC                 !            +-5            +---3kwq_E    
                       +-8            ! ! 
  --LC--               ! !    +-------6 +----------------8bvw_e    
                       ! !    !       ! 
  ----RT               ! !    !       !           +----7lyb_G    
                       ! !    !       +-----------3 
  ----RT               ! +----7                   +----8cww_A    
                     +-9      ! 
  --LTRC             ! !      !         +--------------6jm9_A    
                     ! !      +---------4 
  ----RG             ! !                !              +7uv9_E    
                  +-10 !                +--------------1 
  ----RT          !  ! !                               +8g57_E    
                  !  ! ! 
  ----RA       +-11  ! +-----------------------------1kx5_G    
               !  !  !  
  ----RG       !  !  +-----------------------------7yqk_E    
             -12  !  
  --LCRT       !  +-----------------------------8byq_e    
               !  
  ----RT       +-----------------------------7zs9_e    
             

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updated Fri Sep 13 18:15:50 2024