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structure nameHUMAN TBP CORE DOMAIN COMPLEXED WITH DNA
(PROTEIN TATA BINDING PROTEIN TBP)
referenceNikolov et al. Proc.Natl.Acad.Sci.USA 93 4862 1996
sourceHomo sapiens
experimentX-ray (resolution=1.90, R-factor=0.189)
structural superfamilyTATA-box binding protein-like;
sequence familyTranscription factor TFIID or TATAbinding;
multimeric complexes1c9b_AEIM 1c9b_QR 1jfi_ABC 1nvp_AC 4roc_AB 4rod_AB 4roe_AB
redundant complexes4roc_B 1c9b 1jfi 1nvp 4rod 4roe
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureNVFLFVTNVFPLFVT

Estimated binding specificities ?

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# IC=8.431 IC/col=1.054 n_of_columns=8 specificity:   
A |   0  96   0  96  96  54  96  16
C |   0   0   0   0   0  13   0  13
G |   0   0   0   0   0  13   0  54
T |  96   0  96   0   0  16   0  13
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: TBP
TATAAAAGPubMed1cdw_A(2.64e-10), 1c9b_QR(2.63e-10), 1jfi_ABC(4.59e-08), ... (total=7)
TATAAAPubMed1cdw_A(3.74e-09), 1c9b_QR(3.73e-09), 1jfi_ABC(8.44e-08), ... (total=7)
TGTAAAPubMed1cdw_A(1.68e-04), 1c9b_QR(1.68e-04), 1jfi_ABC(1.13e-03), ... (total=4)
TATAAPubMed1cdw_A(1.62e-06), 1c9b_QR(1.64e-06), 1jfi_ABC(1.37e-05), ... (total=7)
CATAAAPubMed1cdw_A(1.78e-05), 1c9b_QR(1.76e-05), 1jfi_ABC(1.60e-04), ... (total=4)
TATATAAPubMed1cdw_A(1.99e-06), 1c9b_QR(1.68e-06), 1jfi_ABC(3.78e-05), ... (total=7)
TATTTAAAPubMed1cdw_A(3.14e-03), 1c9b_QR(3.14e-03), 4roc_AB(2.20e-06), ... (total=7)
CTTTTPubMed1cdw_A(1.79e-03), 1c9b_QR(1.77e-03), 1jfi_ABC(7.13e-03), ... (total=6)
TAAAAAPubMed1cdw_A(1.78e-05), 1c9b_QR(1.76e-05), 1jfi_ABC(1.60e-04), ... (total=7)
TATATAPubMed1cdw_A(1.68e-04), 1c9b_QR(1.46e-04), 1jfi_ABC(1.13e-03), ... (total=6)
AATAAAAGPubMed1cdw_A(1.18e-06), 1c9b_QR(1.16e-06), 1jfi_ABC(4.49e-05), ... (total=6)
GGGTATAAAAGGPubMed1cdw_A(4.68e-08), 1c9b_QR(4.67e-08), 1jfi_ABC(6.56e-05), ... (total=6)
TATCGATAPubMed1tgh_A(4.55e-04)
sitesourcematches (E-value)

Dendrogram of similar interfaces ?

matrix format
  
  NTVAFTLTFAVATTNAVTFAPALAFTVATA   L         +1cdw_A    
                                           +-1 
  NAVTFTLTFAVATANTVTFAPALAFTVATA   L     +-2 +1ytb_A    
                                         ! ! 
  NTVAFTLTFAVATTNAVAFAPALTFTVATA   L   +-3 +1rm1_A    
                                       ! ! 
  NTVAFCLTFAVATTNAVTFTPALTFTVATA   L --4 +4wzs_D    
                                       ! 
  NTVTFALAFTVATTNAVTFTPALTFAVTTA   L   +5n9g_G    
                                     

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updated Tue Dec 19 05:28:59 2023