4x9j_A : 3D-footprint complex

structure name	EGR-1 WITH DOUBLY METHYLATED DNA (Early growth response protein 1)
reference	Zandarashvili et al.
source	Homo sapiens
experiment	X-ray (resolution=1.41, R-factor=0.174)
structural superfamily	beta-beta-alpha zinc fingers;
sequence family	Zinc finger, C2H2 type;
multimeric complexes	1p47_AB
redundant complexes	1a1f_A 1a1g_A 1a1h_A 1a1i_A 1a1j_A 1a1k_A 1a1l_A 1aay_A 1jk1_A 1jk2_A 1p47_A 1zaa_C 4r2a_A 4r2c_A 4r2d_A
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 4x9j_A interface=17,19,23,45,47,48,73,75,79, erpyacpvescdrrfsRsDeltRhirihtgqkpfqcricmrnfsRsDHltthirthtgekpfacdicgrkfaRsDerkRhtkihlr
interface signature	RDRRDHRDR

Estimated binding specificities ?

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# IC=9.424 IC/col=0.942 n_of_columns=10

specificity:

A |   0  24   0  10   0   0   0  10   0  10
C |   0  24   0   1   0   0   0  53   0  23
G |  96  24  96   0  96  96  96  12  96  10
T |   0  24   0  85   0   0   0  21   0  53

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Related DNA sequences reported in the literature ?

site	source	matches (E-value)
term: ZIF268
GCGTGGGCG	PubMed	4x9j_A(3.18e-11), 1p47_AB(2.76e-12), 4r2a_A(2.53e-10), ... (total=17)
GCGTGGGGCG	PubMed	4x9j_A(2.13e-04), 1p47_AB(1.52e-05), 4r2a_A(5.33e-07), ... (total=17)
AGCGTGGGCGT	PubMed	4x9j_A(1.92e-09), 1p47_AB(1.92e-12), 4r2a_A(1.15e-08), ... (total=17)

Dendrogram of similar interfaces ?

matrix format

  
  RGDC--SCHG----DC--SANA----WCSCVG--RG--   L           +-------------------5v3g_A    
                                                       ! 
  ------SA--MT--VT----NARG----ETTG------             +-5                +--6e94_A    
                                                     ! !   +------------2 
  --EC--SGKGRG--DG--YCKGRG--QA--TC------   L         ! +---4            +--5k5h_A    
                                                   +-6     ! 
  --------------QA----TCRG--RGYCRT------   L       ! !     +---------------7txc_E    
                                                 +-7 ! 
  --CT--STQTLTITST--STHTRG--RG--EA--RA--   L     ! ! +---------------------5v3j_F    
                                               +-8 ! 
  --NT--STNAVT--QTSTSGKGRG--------------   L   ! ! +-----------------------6u9q_A    
                                               ! ! 
  QT--AG--KGRG--RG--DCKG----------------   L   ! +------------------------7n5w_A    
                                             --9 
  --KG--WTKA--------HCHGRG--TAACNA--KGRG   L   !                          +1tf6_A    
                                               !              +-----------1 
  NGKT--WTKG--------HTHGRGTGTTACNA--KGRG   L   +--------------3           +1tf3_A    
                                                              ! 
  ------------RGST--YGYC----QCTGSTRGYT--                      +-----------4is1_C

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updated Tue Dec 19 09:41:54 2023