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structure nameKAISO (ZBTB33) K539A ZINC FINGER DNA BINDING DOMAIN IN COMPLEX WITH THE SPECIFIC KAISO BINDING SEQUENCE (KBS)
(Transcriptional regulator Kaiso)
referenceStanfield et al. Biochemistry ? ? 2020
sourceHomo sapiens
experimentX-ray (resolution=1.66, R-factor=0.181)
structural superfamilybeta-beta-alpha zinc fingers;
sequence familyZinc finger, C2H2 type;
redundant complexes6v8u 5vmu 5vmv 5vmw 5vmx 5vmy 5vmz 6df5 6df8 6df9 6dfa 6dfc 2lt7 4f6m 4f6n
reference complex2lt7_A
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureTSRLEYNYQRY

Estimated binding specificities ?

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# IC=8.247 IC/col=1.031 n_of_columns=8 specificity:   
A |  12   0   0   0   0   0   0  60
C |  12  96  96   0   0  96  84  12
G |  12   0   0   0  96   0   0  12
T |  60   0   0  96   0   0  12  12
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: KAISO
CTGCNAPubMed6dfb_A(1.88e-05), 6v8u_A(6.52e-03), 4f6m_A(2.01e-05), ... (total=9)
TCCTGCNAPubMed6dfb_A(2.83e-10), 5vmw_A(1.20e-05), 5vmx_A(9.93e-06), ... (total=12)
TNGCAGGAPubMed6dfb_A(2.83e-10), 5vmw_A(1.20e-05), 5vmx_A(9.93e-06), ... (total=12)
TCTCGCGAGAPubMed5vmw_A(1.18e-07), 5vmx_A(1.14e-07), 5vmy_A(1.14e-07)
NCTGCCAPubMed6dfb_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 Sat Aug 2 10:46:55 2025