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structure namePOU PROTEIN:DNA COMPLEX
(POU domain, class 5, transcription factor 1)
referenceVahokoski et al. 'Nat.Cell 15 295 2013
sourceMus musculus
experimentX-ray (resolution=2.80, R-factor=0.226)
structural superfamilylambda repressor-like DNA-binding domains;Homeodomain-like;
sequence familyPou domain Nterminal to homeobox domain;
multimeric complexes3l1p_AB 6ht5_DE
redundant complexes6ht5
reference complex8bx1_A
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureQSQTTSRLNRVNQ

Estimated binding specificities ?

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# IC=8.736 IC/col=0.971 n_of_columns=9 specificity:   
A |   6   0   6   0  96  78  96   6   6
C |   6   0   6  90   0   6   0   6   6
G |   6   0   6   6   0   6   0   0  78
T |  78  96  78   0   0   6   0  84   6
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: POU POU PROTEIN:DNA COMPLEX
AAACAAATPubMed3l1p_A(2.11e-03), 3l1p_AB(5.32e-03), 6ht5_DE(4.42e-03)
AAGCAAATPubMed3l1p_A(2.11e-03), 3l1p_AB(4.44e-06)
ATATGCAAPubMed3l1p_A(1.65e-04), 3l1p_AB(4.25e-03), 6ht5_DE(4.40e-03), ... (total=4)
ATGCAAANGAPubMed3l1p_A(4.17e-04), 3l1p_AB(2.09e-04), 6ht5_E(5.42e-03)
ATGCAAATPubMed3l1p_A(4.42e-05), 3l1p_AB(2.75e-06), 6ht5_E(2.42e-03)
ATGCAAATNNPubMed3l1p_A(4.18e-04), 3l1p_AB(2.08e-04), 6ht5_E(5.42e-03)
ATGCATATGCATPubMed3l1p_A(3.55e-03), 3l1p_AB(7.63e-03), 6ht5_DE(2.21e-03), ... (total=4)
ATTCAAATPubMed3l1p_A(3.95e-09), 3l1p_AB(3.66e-07)
ATTTGPubMed3l1p_A(6.46e-06), 3l1p_AB(3.57e-05)
ATTTGAAATGCAAATPubMed3l1p_A(2.56e-09), 6ht5_DE(2.44e-03)
ATTTGCATPubMed3l1p_A(4.42e-05), 3l1p_AB(2.75e-06), 6ht5_E(2.42e-03)
CAAATPubMed3l1p_A(6.46e-06), 3l1p_AB(3.57e-05)
TAATGAPubMed3l1p_A(1.06e-02)
TATGCAAATPubMed3l1p_A(1.72e-04), 3l1p_AB(3.41e-05), 6ht5_DE(1.22e-02), ... (total=4)
sitesourcematches (E-value)

Dendrogram of similar interfaces ?

matrix format
  
  QTSGQTTTTGSTRGLTNT----RG------VA--NAQA--   L          +----------------3l1p_A    
                                                 +------6 
  ------------------RT--RT------VAQTNA----   L   !      +----------------1fjl_B    
                                                 ! 
  ----------------------RT------VAQTNA----   L   !                         +5hod_A    
                                                 !                       +-1 
  --------------------KGRT------IAQCNAYA--   L   !                       ! +1nk2_P    
                                                 !             +---------3 
  ------------------RC--RT------ITQCNAACRG   L --9             !         ! +6a8r_A    
                                                 !    +--------5         +-2 
  --------------------RCRT------NT--NAITRG       !    !        !           +5zjt_B    
                                                 !    !        ! 
  --SGQATT--CTRGLTNT----------------------   L   ! +--7        +----------7xrc_C    
                                                 ! !  ! 
  --STQATT--CARGLTNT----------------------   L   ! !  !                +--1au7_A    
                                                 +-8  +----------------4 
  ----------------------RTSTVCKGDCRG------   L     !                   +--1w0t_A    
                                                   ! 
  ----------------------------RTVAITNAMCRG   L     +----------------------1yrn_A

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updated Thu Sep 12 17:32:22 2024