2itl_B : 3D-footprint complex

structure name	THE ORIGIN BINDING DOMAIN OF THE SV40 LARGE T ANTIGEN BOUND TO THE FUNCTIONAL PEN PALINDROME DNA (23 BP) (large T antigen)
reference	Bochkareva et al. 'Embo 25 5961 2006
source	Simian virus 40
experiment	X-ray (resolution=1.65, R-factor=0.204)
structural superfamily	Origin of replication-binding domain, RBD-like;
sequence family	Origin of replication binding protein;
multimeric complexes	2itl_AB 2ntc_AB 4fgn_AB 5d9i_AB
redundant complexes	2nl8_A 2ntc_A 4fgn_A 5d9i_A
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 2itl_B interface=18,19,20,70, pkdfpsellsflshavfSNRtlacfaiyttkekaallykkimekysvtfisrhnsynhnilffltphrhRvsainnyaqklctfsflickgvnkeylmysaltrdpfsvieeslp
interface signature	SNRR

Estimated binding specificities ?

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# IC=5.766 IC/col=0.961 n_of_columns=6

specificity:

A |  54   0  96   0   0  13
C |  16   0   0   0   0  54
G |  13  96   0  96  96  13
T |  13   0   0   0   0  16

scan!

Dendrogram of similar interfaces ?

matrix format

  
  FGSANGRGTC------------RG--------   L                 +-------------------4gdf_A    
                                             +---------1 
  --SANGKGTC------------RG--------   L     +-2         +-------------------3qfq_B    
                                           ! ! 
  --------------RT--RTYT--VTQT----       +-3 +-----------------------------1uut_A    
                                         ! ! 
  ----------KTTGYCNG--RT----------   L --4 +-----------------------------1b3t_A    
                                         ! 
  ----------------------------YCAG       +-----------------------------2bcq_A

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updated Fri Sep 13 16:25:56 2024