1kb2_B : 3D-footprint complex

structure name	CRYSTAL STRUCTURE OF VDR DNA-BINDING DOMAIN BOUND TO MOUSE OSTEOPONTIN (SPP) RESPONSE ELEMENT (Vitamin D3 Receptor)
reference	Shaffer et al. 'EMBO 21 2242 2002
source	Homo sapiens
experiment	X-ray (resolution=2.70, R-factor=?)
structural superfamily	Glucocorticoid receptor-like DNA-binding domain;
sequence family	Zinc finger, C4 type two domains;
multimeric complexes	1kb2_AB 1kb4_AB 1kb6_AB 1ynw_AB
redundant complexes	1kb4_A 1kb6_A 1ynw_A
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 1kb2_B interface=21,24,28,29, ricgvcgdratgfhfnamtcEgcKgffRRsmkrkalftcpfngdcritkdnrrhcqacrlkrcvdigmmkefiltdeevqrkrem
interface signature	EKRR

Estimated binding specificities ?

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# IC=3.627 IC/col=0.725 n_of_columns=5

specificity:

A |   7   0   7   7  73
C |   9   0   9  75   7
G |  73   0   7   7   9
T |   7  96  73   7   7

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Related DNA sequences reported in the literature ?

site	source	matches (E-value)
term: VDR
TGAACTCAAAGGAGGTCA	PubMed	1kb2_B(4.45e-05), 1kb4_B(4.47e-05)
AGGTCA	PubMed	1kb2_B(2.62e-03), 1kb6_AB(7.07e-04), 1ynw_AB(2.69e-04), ... (total=5)
GGGTCAGCAAGTTCA	PubMed	1kb2_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    
                                  +-------------2 
  --EAKG--KTRG----   L        +---3             +---4umm_A    
                              !   ! 
  ----KGVT--RG----   L   +----4   +-----------------2c7a_B    
                         !    ! 
  --ECKGAG--RG----   L --5    +---------------------4ond_A    
                         ! 
  --ECKGAGKGRG----   L   !                         +1hcq_E    
                         +-------------------------1 
  --ECKGAG--KTRG--   L                             +4aa6_B

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updated Sat Jan 10 04:44:47 2026