3oqm_C : 3D-footprint complex

structure name	STRUCTURE OF CCPA-HPR-SER46P-ACKA2 COMPLEX (CATABOLITE CONTROL PROTEIN A)
reference	Schumacher et al. 'Nucleic 39 2931 2011
source	BACILLUS SUBTILIS
experiment	X-ray (resolution=2.96, R-factor=0.216)
structural superfamily	Periplasmic binding protein-like I;lambda repressor-like DNA-binding domains;
sequence family	Bacterial regulatory proteins, lacI fami; Periplasmic binding proteins and sugar b;
multimeric complexes	3oqm_AC 3oqn_AC 3oqo_AC
redundant complexes	3oqn_A 3oqo_C
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 3oqm_C interface=5,6,15,16,17,20,21,28,52,55,56, mnitIYdvareanvSMAtvSRvvngnpNvkpttrkkvleaierlgyrpnavArgLAskktttvgviipdissifyselargiediatmykyniilsnsdqnmekelhllntmlgkqvdgivfmggnitdehvaefkrspvpivlaasveeqeetpsvaidyeqaiydavkllvdkghtdiafvsgpmaepinrskklqgykraleeanlpfneqfvaegdytydsglealqhlmsldkkptailsatdemalgiihaaqdqglsipedldiigfdntrlslmvrpqlstvvqptydigavamrlltklmnkepveehivelphrielrkstk
interface signature	IYSMASRNALA

Estimated binding specificities ?

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# IC=7.099 IC/col=1.014 n_of_columns=7

specificity:

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

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Related DNA sequences reported in the literature ?

site	source	matches (E-value)
term: CCPA
ATAAAGCGTTTACA	PubMed	3oqm_AC(9.55e-03), 3oqn_AC(7.76e-08), 3oqo_AC(6.22e-04), ... (total=4)
ATAATTAATATAACAACAAA	PubMed	3oqm_C(7.60e-03)
TGTAAGCCCTAACA	PubMed	3oqm_AC(1.36e-03), 3oqn_AC(3.65e-13), 3oqo_AC(2.21e-04), ... (total=4)

Dendrogram of similar interfaces ?

matrix format

  
  IT--ST--ATTTSTRG----VTAGLCAC       +-----------------------------1rzr_C    
                                     ! 
  ITYTSGMTAA--STRG--NT--AGLCAT   L --3                             +3oqm_C    
                                     !            +----------------1 
  ----SG--TC------RG------LCKA   L   +------------2                +1jft_A    
                                                  ! 
  LT----ITTGTTST----DCIT--LCRT   L                +----------------7ce1_D

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updated Fri Sep 13 17:32:30 2024