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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 |  13   0  54   0   0
C |  16   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
  
  CAECKG--KGRG--   L                          +----1cit_A    
                                +-------------3 
  --EAKG--KTRG--   L            !             !    +4umm_A    
                                !             +----1 
  ----KGVG--RG--   L            !                  +4tnt_B    
                         +------5 
  ----KGVT--RG--   L     !      !                  +5emc_A    
                         !      !  +---------------2 
  --ECKGAGKGRG--   L   +-6      +--4               +1hcq_E    
                       ! !         ! 
  --ECKGAG--KTRG   L   ! !         +---------------4aa6_B    
                     --7 ! 
  ----KGVT--RG--   L   ! +-------------------------2c7a_B    
                       ! 
  --ECKGAG--RG--   L   +--------------------------4ond_A

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updated Mon Jun 29 14:08:53 2026