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structure nameCRYSTAL STRUCTURE OF A POU/HMG/DNA TERNARY COMPLEX
(OCTAMER-BINDING TRANSCRIPTION FACTOR 1)
referenceWilmanns et al. 'Genes 17 2048 2003
sourceHOMO SAPIENS
experimentX-ray (resolution=2.60, R-factor=0.232)
structural superfamilylambda repressor-like DNA-binding domains;Homeodomain-like;
sequence familyPou domain Nterminal to homeobox domain;
multimeric complexes1cqt_AI 1cqt_BJ 1gt0_CD 1hf0_AB 1o4x_AB
redundant complexes1cqt 1hf0 1o4x 1oct
reference complex1o4x_A
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureSQTSRRVSNQ

Estimated binding specificities ?

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# IC=9.306 IC/col=1.034 n_of_columns=9 specificity:   
A |   9  96   0   0   0   0  67  96   9
C |   9   0   0   0  96   9   9   0   9
G |  69   0   0  96   0   1   9   0   0
T |   9   0  96   0   0  86  11   0  78
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: HMG
AACAAAGPubMed1gt0_CD(1.89e-05), 1o4x_AB(1.45e-05)
CCAATPubMed1gt0_C(1.00e-02), 1cqt_AI(5.43e-03)
CCTTTGAAPubMed1cqt_AI(3.27e-03), 1cqt_BJ(1.15e-02), 1hf0_AB(3.85e-06), ... (total=5)
CGCAAAAAAGGCPubMed1cqt_BJ(3.67e-03), 1oct_C(6.36e-03)
TCAAAGPubMed1gt0_CD(5.19e-04), 1hf0_AB(4.97e-04), 1o4x_AB(3.68e-04), ... (total=5)
CTTTGPubMed1cqt_AI(4.96e-03), 1cqt_BJ(4.06e-03), 1gt0_CD(4.48e-05), ... (total=6)
CGCAAATTTGCGPubMed1cqt_BJ(9.15e-04), 1oct_C(6.36e-03)
GGAAAPubMed1hf0_B(2.92e-03), 1oct_C(9.72e-03)
TTCAAAGPubMed1cqt_AI(8.18e-04), 1cqt_BJ(3.67e-03), 1gt0_CD(4.97e-03), ... (total=7)
GCCTTTTTTGCGPubMed1cqt_BJ(3.67e-03), 1oct_C(6.36e-03)
term: POU
ATGCAAATPubMed1gt0_C(4.78e-08), 1cqt_AI(1.07e-08), 1cqt_BJ(6.46e-13), ... (total=8)
AAATAATGCPubMed1cqt_AI(8.66e-03), 1cqt_BJ(7.45e-03)
ATTTGCATPubMed1gt0_C(4.78e-08), 1cqt_AI(1.07e-08), 1cqt_BJ(6.46e-13), ... (total=8)
TATGCPubMed1gt0_C(2.91e-03), 1cqt_BJ(5.86e-06), 1oct_C(1.70e-06)
TATGCAAATPubMed1gt0_C(3.78e-07), 1cqt_AI(1.32e-07), 1cqt_BJ(7.77e-16), ... (total=7)
AAGCAAATPubMed1gt0_C(3.46e-04), 1cqt_AI(1.17e-04), 1cqt_BJ(1.28e-07), ... (total=7)
ATGCATATGCATPubMed1gt0_C(6.12e-03), 1cqt_AI(4.26e-03), 1cqt_BJ(3.36e-05), ... (total=6)
CCAATPubMed1gt0_C(1.00e-02), 1cqt_AI(5.43e-03)
CAATATGCTAATPubMed1gt0_C(3.48e-10), 1cqt_AI(5.94e-03), 1cqt_BJ(6.10e-08), ... (total=6)
AAACAAATPubMed1cqt_AI(1.17e-04), 1cqt_BJ(6.59e-04), 1hf0_AB(4.69e-03)
TAATTAPubMed1gt0_C(1.04e-02)
ATGCAAANGAPubMed1gt0_C(4.80e-04), 1cqt_AI(2.53e-04), 1cqt_BJ(5.36e-07), ... (total=7)
GCATAAPubMed1gt0_C(1.02e-02), 1cqt_BJ(6.78e-05), 1o4x_AB(1.97e-03), ... (total=4)
ATTTGAAATGCAAATPubMed1gt0_C(3.45e-05), 1cqt_AI(3.20e-05), 1cqt_BJ(4.68e-08), ... (total=7)
CCCCATGCAATPubMed1cqt_BJ(4.94e-04), 1o4x_AB(9.75e-03), 1oct_C(2.61e-05)
ATGCAAATNNPubMed1gt0_C(1.41e-06), 1cqt_AI(6.97e-07), 1cqt_BJ(2.40e-10), ... (total=7)
ATTCAAATPubMed1gt0_C(3.46e-04), 1cqt_AI(1.07e-08), 1cqt_BJ(1.28e-07), ... (total=8)
TCAGTAAATAPubMed1cqt_BJ(2.25e-04)
CAAATPubMed1cqt_AI(7.95e-06), 1cqt_BJ(5.81e-06), 1hf0_AB(3.57e-05), ... (total=5)
TATACPubMed1oct_C(1.00e-02)
TGTTTPubMed1hf0_B(3.00e-03)
ATATGCAAPubMed1gt0_C(7.70e-03), 1cqt_AI(3.27e-03), 1cqt_BJ(7.79e-09), ... (total=5)
TAATGAPubMed1gt0_C(1.04e-02)
ATTTGPubMed1cqt_AI(7.95e-06), 1cqt_BJ(5.81e-06), 1hf0_AB(3.57e-05), ... (total=5)
sitesourcematches (E-value)

Dendrogram of similar interfaces ?

matrix format
  
  SGQATTSTRG----------RT----------VASCNAQA--   L   +----------------1gt0_C    
                                                   !  
  --------------RA----RT----------VASGNA----   L   !                        +3cmy_A    
                                                   !                      +-1 
  --------------------RT----------VAQTNA----   L   !                    +-2 +5hod_A    
                                                   !                    ! ! 
  ----------------KG--RC----------IAQCNAYA--   L   !                  +-3 +1nk3_P    
                                                   !                  ! ! 
  --------------RA----RA----------IAQTNAMC--   L   !              +---9 +1puf_A    
                                                   !              !   ! 
  --------------RT----RT----------VAQTNA----   L   !              !   ! +1fjl_B    
                                                   !              !   +-4 
  --------------RC--RT------------NCICNARGRG   L   !           +-13     +6fqp_B    
                                                   !           !  !  
  --------------------RA----------ITQTNAMG--   L   !           !  !      +5zjt_E    
                                                 -18           !  !  +---5 
  ------------------YARA----------IAQTNA----   L   !        +-14  +-12   +5lux_L    
                                                   !        !  !     !  
  --------------------RT----STVCKGDCRG------   L   !        !  !     +---1w0t_A    
                                                   !     +-15  !  
  --------------------RT----------IAQCNAMG--   L   !     !  !  +--------1b72_A    
                                                   !     !  !  
  --------------RC----RT----------ITQCNAACRG   L   !     !  !         +-6a8r_A    
                                                   !     !  +--------10  
  ------------------------------RTVAIANAMCRG   L   !     !            ! +1le8_A    
                                                   !  +-16            +-7 
  ------------------YARA----------IAQTNA----   L   !  !  !              +6es3_K    
                                                   !  !  !  
  ----------------------HTRT------NCSTNARG--   L   !  !  !            +1k61_B    
                                                   !  !  !         +--6 
  --------------------RT----------NT--NAIARG   L   +-17  !         !  +1puf_B    
                                                      !  +--------11  
  ----------------------RT--------NT--NAIARG   L      !            !  +4cyc_B    
                                                      !            +--8 
  --------------------------------NCITNARGRG   L      !               +6fqq_E    
                                                      !  
  STQATTCARGLTNT----------------------------   L      +-------------1au7_A

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updated Mon Dec 18 05:07:44 2023