2ypf_A : 3D-footprint complex

structure name	STRUCTURE OF THE AVRBS3-DNA COMPLEX PROVIDES NEW INSIGHTS INTO THE INITIAL THYMINE-RECOGNITION MECHANISM (AVRBS3)
reference	Yefimenko et al. 'Acta 69 1707 2013
source	XANTHOMONAS CAMPESTRIS
experiment	X-ray (resolution=2.55, R-factor=0.239)
structural superfamily	Thiolase-like;
sequence family	Xanthomonas avirulence protein, Avr/PthA;
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 2ypf_A interface=80,115,183,251,285,319,353,387,455,489,523,557,591,659, afthahivalsqhpaalatvavkyqdmiaalpeatheaivavakqwsgaralealltvagelrgpplqldtgqllkiakRggvtaveavhawrnaltgaplnltpeqvvaiashDggkqaletvqrllpvlcqahgltpqqvvaiasngggkqaletvqrllpvlcqahgltpeqvvaiasnIggkqaletvqallpvlcqahgltpqqvvaiasngggkqaletvqrllpvlcqahgltpeqvvaiasnIggkqaletvqallpvlcqahgltpeqvvaiasnIggkqaletvqallpvlcqahgltpeqvvaiasnIggkqaletvqallpvlcqahgltpeqvvaiashDggkqaletvqrllpvlcqahgltpeqvvaiashDggkqaletvqrllpvlcqahgltpqqvvaiasngggkqaletvqrllpvlcqahgltpeqvvaiasnIggkqaletvqallpvlcqahgltpeqvvaiasnIggkqaletvqallpvlcqahgltpeqvvaiashDggkqaletvqrllpvlcqahgltpeqvvaiashDggkqaletvqrllpvlcqahgltpeqvvaiashDggkqaletvqrllpvlcqahgltpqqvvaiasngggkqaletvqrllpvlcqaagltpeqvvaiashDggkqaletvqrllpvl
interface signature	RDIIIIDDIIDDDD

Estimated binding specificities ?

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# IC=21.436 IC/col=1.128 n_of_columns=19

specificity:

A |   0   0  88   2  88   2  88  96  90   0   2   2  96  88   0   0   2   2   5
C |   0   0   2   2   2   2   2   0   2  96  90   4   0   4  96  96  90   2  85
G |   0   0   2   4   2   2   4   0   2   0   2   2   0   2   0   0   2   2   2
T |  96  96   4  88   4  90   2   0   2   0   2  88   0   2   0   0   2  90   4

scan!

Dendrogram of similar interfaces ?

matrix format

  
  RT--RTDA----IA--ITIAIADCDC--ITIADCDCDC--DC   L                +--2ypf_A    
                                                            +---1 
  --IAIANGTG--NGIAIANGDCIAIATARGSADCNG----SA   L   +--------2   +--4cja_A    
                                                   !        ! 
  ----RADCIA----DC----DCDCIC----IADC----IAIC   L --3        +------3ugm_A    
                                                   ! 
  ----RADCDCHTDC------IA--DC--DC------------   L   +---------------4osh_B

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updated Sun Aug 3 06:40:52 2025