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structure nameCRYSTAL STRUCTURE OF VDR DNA-BINDING DOMAIN BOUND TO MOUSE OSTEOPONTIN (SPP) RESPONSE ELEMENT
(Vitamin D3 Receptor)
referenceShaffer et al. 'EMBO 21 2242 2002
sourceHomo sapiens
experimentX-ray (resolution=2.70, R-factor=?)
structural superfamilyGlucocorticoid receptor-like DNA-binding domain;
sequence familyZinc finger, C4 type two domains;
multimeric complexes1kb2_AB 1kb4_AB 1kb6_AB 1ynw_AB
redundant complexes1kb4_A 1kb6_A 1ynw_A
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureEKRR

Estimated binding specificities ?

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# IC=3.673 IC/col=0.735 n_of_columns=5 specificity:   
A |   7   0   7   7  73
C |   7   0   7  75   7
G |  73   0   7   7   9
T |   9  96  75   7   7
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: VDR
TGAACTCAAAGGAGGTCAPubMed1kb2_B(4.45e-05), 1kb4_B(4.47e-05)
AGGTCAPubMed1kb2_B(2.62e-03), 1kb6_AB(7.07e-04), 1ynw_AB(2.69e-04), ... (total=5)
GGGTCAGCAAGTTCAPubMed1kb2_B(2.99e-05), 1kb6_AB(9.24e-06), 1ynw_AB(1.82e-04), ... (total=5)

Dendrogram of similar interfaces ?

matrix format
  
  CAECKG--KGRG--RT   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 14:22:11 2026