6dfb_A : 3D-footprint complex

structure name	KAISO (ZBTB33) K539A ZINC FINGER DNA BINDING DOMAIN IN COMPLEX WITH THE SPECIFIC KAISO BINDING SEQUENCE (KBS) (Transcriptional regulator Kaiso)
reference	Stanfield et al. Biochemistry ? ? 2020
source	Homo sapiens
experiment	X-ray (resolution=1.66, R-factor=0.181)
structural superfamily	beta-beta-alpha zinc fingers;
sequence family	Zinc finger, C2H2 type;
redundant complexes	6v8u 5vmu 5vmv 5vmw 5vmx 5vmy 5vmz 6df5 6df8 6df9 6dfa 6dfc 2lt7 4f6m 4f6n
reference complex	2lt7_A
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 6dfb_A interface=27,28,31,53,55,56,81,82,83,115,117, ddhyelivdgrvyyicivckrsyvclTSlrRhfnihswekkypcrycekvfpLaEYrtaheihhtgerryqclacgksfiNYQfmsshiksvhsqdpsgdsklyrlhpcrslqiRqY
interface signature	TSRLEYNYQRY

Estimated binding specificities ?

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# IC=8.472 IC/col=1.059 n_of_columns=8

specificity:

A |  13   0   0   0  96   0   0  57
C |  16   0   0  96   0   0   0  13
G |  13  96  96   0   0  96  96  13
T |  54   0   0   0   0   0   0  13

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Related DNA sequences reported in the literature ?

site	source	matches (E-value)
term: KAISO
CTGCNA	PubMed	6dfb_A(1.88e-05), 6v8u_A(6.52e-03), 4f6m_A(2.01e-05), ... (total=9)
TCCTGCNA	PubMed	6dfb_A(2.83e-10), 5vmw_A(1.20e-05), 5vmx_A(9.93e-06), ... (total=12)
TNGCAGGA	PubMed	6dfb_A(2.83e-10), 5vmw_A(1.20e-05), 5vmx_A(9.93e-06), ... (total=12)
TCTCGCGAGA	PubMed	5vmw_A(1.18e-07), 5vmx_A(1.14e-07), 5vmy_A(1.14e-07)
NCTGCCA	PubMed	6dfb_A(1.57e-07), 6v8u_A(1.73e-04), 4f6m_A(1.93e-07), ... (total=9)

Dendrogram of similar interfaces ?

matrix format

  
  ECSCKGRG--DCTCYCKGRG--QA--TC----   L          +----------5und_A    
                                         +------2 
  DCYCKGRG--QA----TC----RCSCDC--VT   L   !      ! +--------5k5i_A    
                                       --3      +-1 
  ----------DC--SCQGKTTTATSCSC----   L   !        +--------6ml4_A    
                                         ! 
  --------RGST--YGYC----QCTGSTRAYT   L   +-----------------3uk3_C

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updated Thu Sep 12 23:06:24 2024