interface graph thumbnail
legend  pdf

structure nameMITF/CLEARBOX STRUCTURE
(Microphthalmia-associated transcription factor)
referencePogenberg et al. 'Sci 9 1055 2019
sourceMus musculus
experimentX-ray (resolution=2.40, R-factor=0.216)
structural superfamilyHLH, helix-loop-helix DNA-binding domain;
sequence familyHelixloophelix DNAbinding domain;
multimeric complexes4ati_AB 4atk_AB
redundant complexes4ati_B 4atk_A
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureHNER

Estimated binding specificities ?

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# IC=4.475 IC/col=0.895 n_of_columns=5 specificity:   
A |   0  13   0   0  57
C |  96  13   0   0  13
G |   0  54   0  96  13
T |   0  16  96   0  13
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: M-box
CATGTGPubMed4ati_AB(1.18e-08), 4atk_AB(3.30e-04), 4ati_B(1.14e-03)
CACGTGPubMed6g1l_A(3.54e-04), 4ati_AB(3.30e-04), 4atk_AB(1.18e-08)
GTCATGTGCTPubMed4ati_AB(7.77e-16), 4atk_AB(1.07e-06), 4atk_A(7.59e-06), ... (total=4)
GTGTGAPubMed6g1l_A(3.59e-04), 4ati_AB(1.02e-02), 4ati_B(1.14e-03)
term: MITF
CANNTGPubMed4ati_AB(1.02e-02), 4atk_AB(1.02e-02)
CATGTGPubMed4ati_AB(1.18e-08), 4atk_AB(3.30e-04), 4ati_B(1.14e-03)
CTTGAGPubMed6g1l_A(2.64e-03)
CACCTGPubMed4ati_AB(3.30e-04), 4atk_AB(3.30e-04)
TGTGGTCPubMed4ati_AB(2.28e-03), 4atk_A(7.11e-03), 4ati_B(7.00e-05)

Dendrogram of similar interfaces ?

matrix format
  
  ------HGNT----EC--RCRG   L             +-----------------------7d8t_A    
                                     +---5 
  ------HGNT--IAEC--YCRG   L         !   !                       +1am9_A    
                                     !   +-----------------------1 
  ------HGNT--MTEA--RCRG             !                           +1nlw_D    
                                   +-6 
  --RT----NT--RGEC--RCQT           ! !                    +------2ypa_A    
                                   ! !        +-----------3 
  ------HG------ET--RTRG           ! !        !           +------5v0l_A    
                                 +-7 +--------4 
  ------RTNT----EC--RCRG   L     ! !          !                 +4h10_B    
                                 ! !          +-----------------2 
  NTNGRTECRG--RC--------   L   +-8 !                            +6od3_F    
                               ! ! ! 
  RG----TT--RAEC--RC----       ! ! +-----------------------------1mdy_C    
                             --9 ! 
  ------HG------EC--RGRG   L   ! +-----------------------------4zpk_A    
                               ! 
  ------HG----ITEC--RCRG   L   +-----------------------------5nj8_D

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updated Sun Aug 3 11:25:31 2025