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structure nameGCNF DNA BINDING DOMAIN - OCT4 DR0 COMPLEX
(Nuclear receptor subfamily 6 group A member 1)
referenceOrtlund et al. 'J. 428 4981 2016
sourceMus musculus
experimentX-ray (resolution=2.10, R-factor=0.218)
structural superfamilyGlucocorticoid receptor-like DNA-binding domain;
sequence familyZinc finger, C4 type two domains;
multimeric complexes5krb_BG
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureEKRPR

Estimated binding specificities ?

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# IC=4.944 IC/col=0.549 n_of_columns=9 specificity:   
A |   6  19  24   0   0  24  24  21  83
C |   6   6  24  96  96  24  24  12   6
G |   6  64  24   0   0  24  24  57   7
T |  78   7  24   0   0  24  24   6   0
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: GCNF
AGGTCAPubMed5krb_G(4.54e-05), 5krb_BG(1.13e-04)
TCAAGGTCAPubMed5krb_G(2.83e-08), 5krb_BG(3.81e-07)
AGGTCAAGGTCAPubMed5krb_G(8.93e-07), 5krb_BG(2.47e-11)
TCAAGPubMed5krb_G(3.14e-03), 5krb_BG(5.75e-03)

Dendrogram of similar interfaces ?

matrix format
  
  ----ECKG--KGRG----RCRC   L         +-------------------2ff0_A    
                                  +-13  
  --HC--KGVT--RG--------          !  !                +--3g9m_B    
                                  !  +----------------6 
  ------KGVT--RG--------          !                   +--5emp_A    
                                  !  
  ----ECKG--KGRA----RTRC   L      !              +------5l0m_A    
                                  !              !  
  CA--ECKG--KGRG--------   L   +-14              !   +---6l6q_B    
                               !  !    +--------10 +-7 
  ----DGKG--RTRG--------   L   !  !    !         ! ! !   +3cbb_A    
                               !  !    !         ! ! +---3 
  ----ECKG--KGRG--------       !  !    !         ! !     +3dzy_A    
                               !  !    !         +-9 
  ------KAVA--RA--------   L   !  !    !           !      +5e69_A    
                               !  !    !           !    +-4 
  ----ECKG--RGRG--------   L   !  +---12           +----5 +3dzy_D    
                               !       !                ! 
  ----ETKGAT--RG--------   L -15       !                +1lat_A    
                               !       !  
  ----EAKG--RTRTRT------       !       !                +2han_B    
                               !       !          +-----1 
  ----EAKG--RTRTRT------       !       +----------8     +4umm_E    
                               !                  ! 
  ----ECKG--RGRG--------   L   !                  +-----5uan_B    
                               !  
  ------KGVT--RG--------   L   !                       +6x6e_A    
                               !       +---------------2 
  ----DAKG--RGRG--RT----   L   +------11               +4iqr_B    
                                       !  
  ----ECKG--KGRG--------               +---------------4nqa_H    
                             

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updated Tue Dec 19 10:50:26 2023