1r71_B : 3D-footprint complex

structure name	CRYSTAL STRUCTURE OF THE DNA BINDING DOMAIN OF KORB IN COMPLEX WITH THE OPERATOR DNA (Transcriptional repressor protein korB)
reference	Heinemann et al. Nat.Struct.Mol.Biol. 11 656 2004
source	Escherichia coli
experiment	X-ray (resolution=2.20, R-factor=0.198)
structural superfamily	KorB DNA-binding domain-like;
sequence family	KorB domain;
multimeric complexes	1r71_AB 1r71_CD
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 1r71_B interface=45,46,47,48,50,51,73,75,79,104, yneadqvienlqrneltpreiadfigrelakgkkkgdiakeigkSPAFiTQhvtlldlpekiadafntgrvrDvTvvnElvtafkkrpeeveawldddtqeitRgtvkllreflde
interface signature	SPAFTQDTER

Estimated binding specificities ?

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# IC=6.271 IC/col=0.697 n_of_columns=9

specificity:

A |   0  16  72   0   0   0  24  24  16
C |   0   8   8   0  96  96  24  24  16
G |   0  16   8  96   0   0  24  24  16
T |  96  56   8   0   0   0  24  24  48

scan!

Related DNA sequences reported in the literature ?

site	source	matches (E-value)
term: KORB
TTTAGC	PubMed	1r71_B(4.61e-05), 1r71_AB(8.94e-08), 1r71_CD(1.20e-07)
GCTAAA	PubMed	1r71_B(4.61e-05), 1r71_AB(8.94e-08), 1r71_CD(1.20e-07)

Dendrogram of similar interfaces ?

matrix format

  
  --STPTATFTTTQT--DGTC------RG----   L                +-1r71_B    
                                                  +---1 
  ----QASATAATNTRT----RG--RG------   L   +--------2   +-6y93_B    
                                         !        ! 
  STSTRGKGIG--RG----RG------------   L --3        +-----3mkw_B    
                                         ! 
  ETSGRGAT--ATNTRT------KC--VTRTEC   L   +--------------4umk_D

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updated Sat Jan 10 04:54:45 2026