1ytb_A : 3D-footprint complex

structure name	CRYSTAL STRUCTURE OF A YEAST TBP/TATA-BOX COMPLEX (PROTEIN TATA BINDING PROTEIN TBP)
reference	Geiger et al. Nature 365 512 1993
source	Saccharomyces cerevisiae
experiment	X-ray (resolution=1.80, R-factor=0.201)
structural superfamily	TATA-box binding protein-like;
sequence family	Transcription factor TFIID or TATAbinding;
multimeric complexes	1nh2_AC 1ytf_AC 4v1n_ABMO 4v1o_ABMO 5fmf_1AMPQUV
redundant complexes	1ngm_I 1ytf_A 4v1n_O 1nh2 4v1o 5fmf
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 1ytb_A interface=9,11,39,54,56,62,64,99,101,130,131,145,147,153,155, sgivptlqNiVatvtlgcrldlktvalharnaeynpkrFaavimrirepkttaLiFasgkmVvTgakseddsklasrkyariiqkigfaakftdfkiqNiVgscdvkfpirleglafshgtfssyepelFPgliyrmvkpkivlLiFvsgkiVlTgakqreeiyqafeaiypvlsefrkm
interface signature	NVFLFVTNVFPLFVT

Estimated binding specificities ?

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# IC=10.383 IC/col=0.865 n_of_columns=12

specificity:

A |   8   0  96   8  96   0  72  96  24  24   0   0
C |   8   0   0   8   0   0   8   0  24  24  96   0
G |  64   8   0  16   0   0   8   0  24  24   0  96
T |  16  88   0  64   0  96   8   0  24  24   0   0

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Related DNA sequences reported in the literature ?

site	source	matches (E-value)
term: TBP
TATAAAAG	PubMed	1ytb_A(3.11e-04), 1nh2_AC(1.18e-06), 1ytf_AC(8.20e-09), ... (total=8)
TATAAA	PubMed	1ytb_A(1.70e-04), 1nh2_AC(1.78e-05), 1ytf_AC(2.69e-08), ... (total=7)
TGTAAA	PubMed	1ytf_AC(5.53e-04), 1ngm_I(6.90e-05), 1ytf_A(5.45e-04)
TATATAA	PubMed	1ytb_A(1.40e-09), 1nh2_AC(1.07e-03), 1ytf_AC(2.42e-10), ... (total=7)
TATTTAAA	PubMed	1ytb_A(3.11e-04), 1ytf_AC(1.20e-07), 4v1n_ABMO(3.08e-03), ... (total=6)
AATAAAAG	PubMed	1nh2_AC(6.20e-04), 1ytf_AC(1.30e-05), 5fmf_1AMPQUV(6.20e-04), ... (total=5)
CTTTT	PubMed	1nh2_AC(1.79e-03), 1ytf_AC(4.19e-03), 5fmf_1AMPQUV(8.37e-05), ... (total=5)
CATAAA	PubMed	1nh2_AC(6.42e-03), 1ytf_AC(7.06e-05), 1ngm_I(6.36e-06), ... (total=4)
GGGTATAAAAGG	PubMed	1ytb_A(3.57e-04), 1nh2_AC(4.55e-05), 1ytf_AC(5.11e-06), ... (total=6)
TATAA	PubMed	1ytb_A(1.48e-05), 1nh2_AC(1.77e-03), 1ytf_AC(6.10e-06), ... (total=7)
TAAAAA	PubMed	1nh2_AC(1.78e-05), 1ytf_AC(7.06e-05), 5fmf_1AMPQUV(1.13e-03), ... (total=5)
TATATA	PubMed	1ytb_A(9.53e-08), 1ytf_AC(2.54e-08), 4v1n_ABMO(8.90e-07), ... (total=6)
site	source	matches (E-value)

Dendrogram of similar interfaces ?

matrix format

  
  NAVTFT--LTFAVATANTVTFAPALAFTVATA   L                         +1ytb_A    
                                                             +-1 
  NTVAFC--LTFAVATTNAVTFTPALTFTVATA   L   +-------------------2 +4wzs_D    
                                         !                   ! 
  NTVTFA--LAFTVATTNAVTFTPALTFAVTTA     --3                   +4roc_B    
                                         ! 
  NAVAFTPALTFAVATA--VAFTPALTFAVAST   L   +-------------------1ais_A

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updated Tue Dec 17 22:31:32 2024