1cdw_A : 3D-footprint complex

structure name	HUMAN TBP CORE DOMAIN COMPLEXED WITH DNA (PROTEIN TATA BINDING PROTEIN TBP)
reference	Nikolov et al. Proc.Natl.Acad.Sci.USA 93 4862 1996
source	Homo sapiens
experiment	X-ray (resolution=1.90, R-factor=0.189)
structural superfamily	TATA-box binding protein-like;
sequence family	Transcription factor TFIID or TATAbinding;
multimeric complexes	1c9b_AEIM 1c9b_QR 1jfi_ABC 1nvp_AC 4roc_AB 4rod_AB 4roe_AB
redundant complexes	4roc_B 1c9b 1jfi 1nvp 4rod 4roe
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 1cdw_A interface=9,11,39,54,56,62,64,99,101,130,131,145,147,153,155, sgivpqlqNiVstvnlgckldlktialrarnaeynpkrFaavimrireprttaLiFssgkmVcTgakseensrlaarkyarvvqklgfpakfldfkiqNmVgscdvkfpirleglvlthqqfssyepelFPgliyrmikprivlLiFvsgkvVlTgakvraeiyeafeniypilkgfrk
interface signature	NVFLFVTNVFPLFVT

Estimated binding specificities ?

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# IC=8.472 IC/col=1.059 n_of_columns=8

specificity:

A |  13   0  13   0   0  96   0  96
C |  54   0  13   0   0   0   0   0
G |  16   0  13   0   0   0   0   0
T |  13  96  57  96  96   0  96   0

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Related DNA sequences reported in the literature ?

site	source	matches (E-value)
term: TBP
TATAAAAG	PubMed	1cdw_A(2.64e-10), 1c9b_QR(2.63e-10), 1jfi_ABC(4.59e-08), ... (total=7)
TATAAA	PubMed	1cdw_A(3.74e-09), 1c9b_QR(3.73e-09), 1jfi_ABC(8.44e-08), ... (total=7)
TGTAAA	PubMed	1cdw_A(1.68e-04), 1c9b_QR(1.68e-04), 1jfi_ABC(1.13e-03), ... (total=4)
TATAA	PubMed	1cdw_A(1.62e-06), 1c9b_QR(1.64e-06), 1jfi_ABC(1.37e-05), ... (total=7)
CATAAA	PubMed	1cdw_A(1.78e-05), 1c9b_QR(1.76e-05), 1jfi_ABC(1.60e-04), ... (total=4)
TATATAA	PubMed	1cdw_A(1.99e-06), 1c9b_QR(1.68e-06), 1jfi_ABC(3.78e-05), ... (total=7)
TATTTAAA	PubMed	1cdw_A(3.14e-03), 1c9b_QR(3.14e-03), 4roc_AB(2.20e-06), ... (total=7)
CTTTT	PubMed	1cdw_A(1.79e-03), 1c9b_QR(1.77e-03), 1jfi_ABC(7.13e-03), ... (total=6)
TAAAAA	PubMed	1cdw_A(1.78e-05), 1c9b_QR(1.76e-05), 1jfi_ABC(1.60e-04), ... (total=7)
TATATA	PubMed	1cdw_A(1.68e-04), 1c9b_QR(1.46e-04), 1jfi_ABC(1.13e-03), ... (total=6)
AATAAAAG	PubMed	1cdw_A(1.18e-06), 1c9b_QR(1.16e-06), 1jfi_ABC(4.49e-05), ... (total=6)
GGGTATAAAAGG	PubMed	1cdw_A(4.68e-08), 1c9b_QR(4.67e-08), 1jfi_ABC(6.56e-05), ... (total=6)
TATCGATA	PubMed	1tgh_A(4.55e-04)
site	source	matches (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 Fri Sep 13 15:29:04 2024