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structure nameTATA-BINDING PROTEIN/TRANSCRIPTION FACTOR (II)B/TATA-BOX COMPLEX FROM PYROCOCCUS WOESEI
(PROTEIN TATA-BINDING PROTEIN)
referenceDedecker et al. Proc.Natl.Acad.Sci.USA 94 6042 1997
sourcePYROCOCCUS WOESEI
experimentX-ray (resolution=2.10, R-factor=0.212)
structural superfamilyTATA-box binding protein-like;
sequence familyTranscription factor TFIID or TATAbinding;
multimeric complexes1ais_AB 1d3u_AB
redundant complexes1d3u_A
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureNVFPLFVTVFPLFVS

Estimated binding specificities ?

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# IC=5.339 IC/col=0.667 n_of_columns=8 specificity:   
A |   9   0   9  24  24  67  96  96
C |   9   0   9  24  24   9   0   0
G |   9   0  11  24  24   9   0   0
T |  69  96  67  24  24  11   0   0
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: TATA
TATAAAPubMed1ais_A(6.36e-03), 1ais_AB(1.71e-04), 1d3u_AB(2.29e-03)
TATAAAAGPubMed1ais_AB(1.23e-05)
TATAAAAPubMed1ais_AB(2.03e-06)
TATATATAPubMed1d3u_AB(3.61e-03)
TGTAAAPubMed1ais_A(6.36e-03), 1ais_AB(1.71e-04), 1d3u_AB(3.58e-04)
TTTATAPubMed1ais_A(6.36e-03), 1ais_AB(1.71e-04), 1d3u_AB(2.29e-03)
TATTTAAAPubMed1ais_A(3.12e-03), 1ais_AB(6.14e-09), 1d3u_AB(3.96e-11)
TATAAPubMed1ais_AB(9.96e-03)
CATAAAAPubMed1ais_AB(1.71e-04)
TCACTATATATAGPubMed1d3u_AB(1.14e-02)
CATAAAPubMed1ais_AB(6.50e-03)
TATATAAPubMed1ais_AB(5.33e-03), 1d3u_AB(9.51e-05)
TAAAAPubMed1ais_AB(1.69e-06), 1d3u_AB(1.25e-02)
AATAAAAGPubMed1ais_AB(6.29e-04)
TTATACATTPubMed1d3u_AB(9.45e-03)
CATAAAACPubMed1ais_AB(6.29e-04)
TATAAATPubMed1ais_AB(1.08e-03), 1d3u_AB(9.63e-05)
TAAAAGTPubMed1ais_AB(1.71e-04), 1d3u_AB(1.18e-02)
TAAATPubMed1ais_AB(1.82e-03), 1d3u_AB(3.01e-05)
TGTAAPubMed1ais_AB(9.96e-03), 1d3u_AB(1.25e-02)
TAAAAGCPubMed1ais_AB(1.71e-04)
TATTTAAPubMed1ais_AB(2.18e-06), 1d3u_AB(4.25e-09)
TAAATATAPubMed1ais_AB(3.32e-03), 1d3u_AB(1.34e-04)
TATAAGAGPubMed1ais_AB(1.28e-02)
TATAGATAPubMed1d3u_AB(3.61e-03)
CTTATTTATPubMed1ais_AB(6.95e-03), 1d3u_AB(8.60e-04)
TTAAGAPubMed1ais_AB(1.71e-04)
TTATATAPubMed1ais_AB(5.33e-03), 1d3u_AB(9.51e-05)
TAAATTPubMed1ais_AB(6.50e-03), 1d3u_AB(3.50e-04)
TATAAACGPubMed1ais_AB(3.18e-03)
CTTTTPubMed1ais_AB(1.82e-03)
TATTAPubMed1ais_AB(9.96e-03), 1d3u_AB(1.25e-02)
ATATAAPubMed1d3u_AB(2.27e-03)
CTATAAAAGPubMed1ais_AB(4.24e-05)
TATATAPubMed1d3u_AB(2.27e-03)
TACAAAAGPubMed1ais_AB(3.32e-03)
TATTATTTAPubMed1ais_AB(6.95e-03), 1d3u_AB(8.60e-04)
ATTATTATTPubMed1ais_AB(6.95e-03)
sitesourcematches (E-value)

Dendrogram of similar interfaces ?

matrix format
  
  NAVAFTPALTFAVATA----VAFTPALTFAVAST   L                         +1ais_A    
                                                  +--------------2 
  NTVTFA--LAFTVATT--NAVTFTPALTFAVTTA              !              +4roc_B    
                                           +------3 
  NTVAFC--LTFAVATT--NAVTFTPALTFTVATA   L   !      !               +4wzs_D    
                                         --4      +---------------1 
  NTVAFA--LAFT--TCQANTVAFAPALAFTVTTT   L   !                      +6cnb_R    
                                           ! 
  NAVTFT--LTFAVATA--NTVTFAPALAFTVATA   L   +----------------------1ytb_A

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updated Fri Sep 13 15:22:48 2024