1nkp_A : 3D-footprint complex

structure name	CRYSTAL STRUCTURE OF MYC-MAX RECOGNIZING DNA (MYC PROTO-ONCOGENE PROTEIN)
reference	Burley et al. 'Cell(Cambridge,Mass.)' 112 193 2003
source	HOMO SAPIENS
experiment	X-ray (resolution=1.80, R-factor=0.219)
structural superfamily	HLH, helix-loop-helix DNA-binding domain;
sequence family	Helixloophelix DNAbinding domain; Myc leucine zipper domain;
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 1nkp_A interface=6,10,11,14,17,18, ghmnvKrrtHNvlErqRRnelkrsffalrdqipelennekapkvvilkkatayilsvqaeeqkliseedllrkrreqlkhkleqlggc
interface signature	KHNERR

Estimated binding specificities ?

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# IC=4.434 IC/col=0.887 n_of_columns=5

specificity:

A |  13   0  96   0  16
C |  16  96   0  96  13
G |  54   0   0   0  54
T |  13   0   0   0  13

scan!

Related DNA sequences reported in the literature ?

site	source	matches (E-value)
term: MYC
CACGTG	PubMed	1nkp_A(4.51e-04), 1nkp_AB(8.79e-10), 1nkp_DE(1.19e-09)
CATGTG	PubMed	1nkp_AB(3.45e-05), 1nkp_DE(8.58e-05)
CACGTGT	PubMed	1nkp_A(1.25e-03), 1nkp_AB(2.57e-08), 1nkp_DE(3.33e-08)
CACCACGTGGTG	PubMed	1nkp_A(8.54e-03), 1nkp_AB(4.28e-06), 1nkp_DE(5.25e-06)
AACGTT	PubMed	1nkp_AB(3.47e-03), 1nkp_DE(4.01e-03)
AACGTG	PubMed	1nkp_A(4.51e-04), 1nkp_AB(6.52e-06), 1nkp_DE(8.14e-06)
CANNTG	PubMed	1nkp_AB(3.37e-03), 1nkp_DE(4.01e-03)
GGCCACGTG	PubMed	1nkp_A(3.55e-03), 1nkp_AB(5.43e-07), 1nkp_DE(6.80e-07)
CAACGTG	PubMed	1nkp_A(1.25e-03), 1nkp_AB(5.35e-05), 1nkp_DE(6.46e-05)

Dendrogram of similar interfaces ?

matrix format

  
  KT----HGNT----ECRCRG   L                               +1nkp_A    
                                                       +-1 
  ------HGNT--LGECRCRC   L                        +----3 +5i50_B    
                                                  !    ! 
  ------HGNT--MTEARCRG   L              +---------5    +-1nlw_D    
                                        !         ! 
  ------HGNT----ECRCRG   L            +-6         +------7d8t_A    
                                      ! ! 
  ------HGNT----ECRCRG   L            ! !              +-1nkp_E    
                               +------8 +--------------4 
  ------HG------ETRCRG   L     !      !                +-5gnj_I    
                             +-9      ! 
  --NTRGEC----RC------       ! !      +-----------------2ql2_A    
                             ! ! 
  ----------NG--SCHTRC     -10 +------------------------5nj8_C    
                             !  
  ------HGNT--ITECYCRC   L   !       +-----------------7f2f_B    
                             +-------7 
  ------HGST--ITETRCRG   L           !                +4h10_A    
                                     +----------------2 
  ------HG------ETRTRG   L                            +5v0l_A

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updated Mon Dec 18 05:31:19 2023