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=3.968 IC/col=0.794 n_of_columns=5

specificity:

A |   0  11  67  96   9
C |   0   9   9   0  67
G |   0  67   9   0  11
T |  96   9  11   0   9

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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

  
  ----ECKG--RGRG------KA   L                                   +2nll_B    
                                                 +-------------5 
  ----EAKG--RTRTRT------                         !             +4umm_E    
                                                 !  
  ----EAKG--KTRG--------   L                     !               +2han_A    
                                                 !             +-2 
  ----ECKG--KGRG--RC----   L                     !         +---7 +2ff0_A    
                                                 !         !   ! 
  ------KGVT--RG--------   L                  +-12         !   +5cbz_E    
                                              !  !   +-----9 
  ----DGKG--RTRG--------   L                  !  !   !     !     +3cbb_A    
                                              !  !   !     !   +-4 
  ----ECKG--KGRG--------                      !  !   !     +---6 +3dzy_A    
                                              !  !   !         ! 
  ----ETKGAT--RG--------   L                  !  !   !         +1lat_A    
                                              !  +--11  
  HA--ECKG--RGRG--------   L                  !      !           +1a6y_A    
                                        +----13      !         +-3 
  ----ECKG--RGRG----FT--   L            !     !      !    +----8 +3dzy_D    
                                        !     !      !    !    ! 
  ------KGVT--RG--------                !     !      +---10    +1r4i_A    
                                        !     !           !  
  ----ECKG--KGRG--------   L         +-14     !           !     +1ynw_B    
                                     !  !     !           +-----1 
  ----ECKG--RGRG--------   L         !  !     !                 +5uan_B    
                                     !  !     !  
  ----ECKG--KTRG--------   L      +-15  !     +-----------------2nll_A    
                                  !  !  !  
  ------KGVG--RG--------   L      !  !  +-----------------------4tnt_B    
                               +-16  !  
  ----ECKG--KGRA--RT----   L   !  !  +--------------------------5l0m_A    
                             -17  !  
  ----ECKA--RGRG--------   L   !  +-----------------------------4nqa_I    
                               !  
  --YGECKGAGKGRG--------   L   +-----------------------------4oln_B

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updated Fri Sep 13 15:44:37 2024