6ycq_A : 3D-footprint complex

structure name	CRYSTAL STRUCTURE OF THE DNA BINDING DOMAIN OF ARABIDOPSIS THALIANA AUXIN RESPONSE FACTOR 1 (ATARF1) IN COMPLEX WITH HIGH AFFINITY DNA (Auxin response factor 1)
reference	Weijers et al. Proc.Natl.Acad.Sci.USA 117 24557 2020
source	Arabidopsis thaliana
experiment	X-ray (resolution=1.65, R-factor=0.173)
structural superfamily	DNA-binding pseudobarrel domain;
sequence family	Auxin response factor; B3 DNA binding domain;
multimeric complexes	4ldx_AB 6ycq_AB
redundant complexes	4ldx_A
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 6ycq_A interface=123,128,173,176,178, gkpggvlsdalcrelwhacagplvtlpregervyyfpeghmeqleasmhqgleqqmpsfnlpskilckviniqrraepetdevyaqitllpeldqseptspdapvqepekctvhsfcktltaSdtstHggfsvlrrhaddclppldmsqqppwqelvatdlhnsewhfrhifRgqPrRhllttgwsvfvsskklvagdafiflrgeneelrvgvrrhmrqqtnipssvisshsmhigvlataahaittgtifsvfykprtsrsefivsvnryleaktqklsvgmrfkmrfegeeapekrfsgtivgvqenkssvwhdsewrslkvqwdepssvfrpervspwelepl
interface signature	SHRPR

Estimated binding specificities ?

readout + contact

# IC=8.004 IC/col=1.001 n_of_columns=8

specificity:

A |   0   0   0   9   0   0   9  11
C |   0   0   0   9  96   0   9  67
G |   0   0  96   9   0  96  67   9
T |  96  96   0  69   0   0  11   9

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Related DNA sequences reported in the literature ?

site	source	matches (E-value)
term: ARF1
TGTCTC	PubMed	6ycq_A(6.36e-03), 4ldx_AB(8.04e-04), 4ldx_A(3.92e-05)

Dendrogram of similar interfaces ?

matrix format

  
  --STHG------RG----PTRG--   L                  +---6ycq_A    
                                 +--------------2 
  --STHG--ST--RC----PTRG--   L   !              +---6sdg_B    
                               --3 
  --STITRGVTWC--NCNG----MA   L   !                +-5yzz_C    
                                 +----------------1 
  KASTLTRGIT--WC--NTNT--MA   L                    +-6j9b_A

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updated Sat Sep 14 00:52:35 2024