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structure nameSTRUCTURE OF THE RXR/RAR DNA-BINDING DOMAIN HETERODIMER IN COMPLEX WITH THE RETINOIC ACID RESPONSE ELEMENT DR1
(RETINOIC ACID RECEPTOR ALPHA)
referenceKhorasanizadeh et al. 'EMBO 19 1045 2000
sourceHOMO SAPIENS
experimentX-ray (resolution=1.70, R-factor=0.201)
structural superfamilyGlucocorticoid receptor-like DNA-binding domain;
sequence familyZinc finger, C4 type two domains;
multimeric complexes1dsz_AB 6xwg_CD
redundant complexes6xwg
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureEKRR

Estimated binding specificities ?

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# IC=4.434 IC/col=0.887 n_of_columns=5 specificity:   
A |  16   0  54   0   0
C |  13   0  13  96  96
G |  13  96  13   0   0
T |  54   0  16   0   0
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: RAR
TGACCPubMed1dsz_A(2.59e-08), 1dsz_AB(1.44e-05), 6xwg_D(1.20e-03)
TGATGTCAPubMed1dsz_A(1.79e-03)
AGGTCAPubMed1dsz_A(1.21e-07), 1dsz_AB(1.67e-04), 6xwg_CD(2.53e-03), ... (total=4)

Dendrogram of similar interfaces ?

matrix format
  
  EAKG--RTRTRT                               +---4umm_E    
                                 +-----------7 
  ECKG--KGRG--   L               !           +---2ff0_A    
                          +------9 
  DGKG--RTRG--   L        !      !               +3cbb_A    
                          !      +---------------1 
  ECKG--KGRG--            !                      +3dzy_A    
                          !  
  ECKG--RGRG--   L        !                  +---2nll_B    
                     +---12            +-----6 
  --KGVT--RG--   L   !    !            !     +---5cbz_E    
                     !    !    +-------8 
  ECKG--KGRG--   L   !    !    !       !         +1ynw_B    
                     !    !    !       +---------3 
  ECKG--RGRG--   L   !    !    !                 +3dzy_D    
                     !    +---11  
  EAKG--KTRG--   L   !         !                  +2han_A    
                   -13         !  +---------------2 
  ECKA--RGRG--   L   !         !  !               +4nqa_I    
                     !         +-10  
  --KGVT--RG--       !            !               +1r4i_A    
                     !            !             +-4 
  ETKGAT--RG--   L   !            +-------------5 +1lat_A    
                     !                          ! 
  ECKG--KTRG--   L   !                          +-2nll_A    
                     !  
  ECKG--RGRG--   L   +---------------------------5uan_B    
                   

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updated Tue Dec 19 05:32:42 2023