2nra_C : 3D-footprint complex

structure name	CRYSTAL STRUCTURE OF PI INITIATOR PROTEIN IN COMPLEX WITH ITERON DNA (PI protein)
reference	Swan et al. Proc.Natl.Acad.Sci.Usa 103 18481 2006
source	Escherichia coli
experiment	X-ray (resolution=3.10, R-factor=0.227)
structural superfamily	"Winged helix" DNA-binding domain;
sequence family	Initiator Replication protein;
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 2nra_C interface=61,63,64,66,67,201,205,206,209,210,214, vnkktkirhrnelnhtlaqlplpakrvmymalalidskeplergrvfkiraedlaalakiTpSLaYRqlkeggkllgaskislrgddiialakelnseeldlniiewiayspdegylslkftrtiepyissligkknkfttqlltaslrlssqyssslyqlirkhysnfkkknyfiisvdelkeeliaytfdkdgnieykYpdfPIfkRDvlnKaiaeikkkteisfvgftvhekegrkisklkfefvvded
interface signature	TSLYRYPIRDK

Estimated binding specificities ?

readout + contact

# IC=9.191 IC/col=0.613 n_of_columns=15

specificity:

A |  92  12   8   8  96  76  24  24  24  24  24   0   0   0   0
C |   0  64   8  12   0  16  24  24  24  24  24   0  24   0  96
G |   4   8  72  24   0   4  24  24  24  24  24   0   0   0   0
T |   0  12   8  52   0   0  24  24  24  24  24  96  72  96   0

scan!

Dendrogram of similar interfaces ?

matrix format

  
  ----TT--SGLTYART------YT--PCITRGDCKT--   L                          +-----2nra_C    
                                                 +--------------------1 
  ------SGAAECSAKGRGRGSTYGRTPGDCRGRG--RC   L   +-2                    +-----7rva_C    
                                               ! ! 
  QA------------------------------------     --3 +--------------------------7k63_U    
                                               ! 
  --RC----------------------------------       +---------------------------6l9z_S

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updated Sat Jan 10 05:26:20 2026