5gnj_I : 3D-footprint complex

structure name	STRUCTURE OF A TRANSCRIPTION FACTOR AND DNA COMPLEX (Transcription factor MYC2)
reference	Lian et al. 'Cell 19 1334 2017
source	Arabidopsis thaliana
experiment	X-ray (resolution=2.70, R-factor=0.209)
structural superfamily	HLH, helix-loop-helix DNA-binding domain;
sequence family	Helixloophelix DNAbinding domain;
multimeric complexes	5gnj_AB 5gnj_GIN
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 5gnj_I interface=5,9,12,13, eplnHveaErqRReklnqrfyalravvpnvskmdkasllgdaiayinelkskvvkteseklqiknqleevklela
interface signature	HERR

Estimated binding specificities ?

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# IC=4.007 IC/col=0.801 n_of_columns=5

specificity:

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

scan!

Related DNA sequences reported in the literature ?

site	source	matches (E-value)
term: MYC2
CACATG	PubMed	5gnj_I(2.62e-03), 5gnj_AB(1.16e-04), 5gnj_GIN(7.77e-05)
CANNTG	PubMed	5gnj_AB(6.34e-03), 5gnj_GIN(3.42e-03)
ATACGTGT	PubMed	5gnj_I(1.62e-06), 5gnj_AB(1.22e-06), 5gnj_GIN(1.87e-04)
AACGTG	PubMed	5gnj_I(3.55e-04), 5gnj_AB(1.83e-05), 5gnj_GIN(7.27e-06)

Dendrogram of similar interfaces ?

matrix format

  
  HG----ETRCRG   L                    +5gnj_I    
                                    +-1 
  HGNT--ECRCRG   L                +-2 +1nkp_E    
                                  ! ! 
  HGNT--ECRCRG   L        +-------3 +1nkp_A    
                          !       ! 
  HGNTMTEARCRG   L   +----4       +-1nlw_D    
                     !    ! 
  --RG--------   L --5    +---------6od3_F    
                     ! 
  HGNTLGECRCRC   L   +--------------5i50_B

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updated Tue Dec 19 10:26:35 2023