interface graph thumbnail
legend  pdf

structure nameGCN4 BASIC DOMAIN, LEUCINE ZIPPER COMPLEXED WITH ATF/CREB SITE DNA
referenceRichmond et al.
experimentX-ray (resolution=2.20, R-factor=0.214)
structural superfamilyLeucine zipper domain;
sequence familybZIP transcription factor; Basic region leucine zipper;
multimeric complexes1ysa_CD
redundant complexes1dgc_A 1ysa_C
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureNTAR

Estimated binding specificities ?

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# IC=3.157 IC/col=0.631 n_of_columns=5 specificity:   
A |   2   4   4   9  45
C |  88   4   7  67  19
G |   2  84   4   9  16
T |   4   4  81  11  16
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: GCN4
ATGACTCATPubMed2dgc_A(3.01e-03), 1ysa_CD(7.73e-11), 1dgc_A(2.94e-03), ... (total=4)
ATGACGTCATPubMed2dgc_A(6.12e-06), 1dgc_A(5.90e-06)
TGACTCAPubMed2dgc_A(1.04e-03), 1ysa_CD(1.06e-12), 1dgc_A(1.01e-03), ... (total=4)
TGACTCPubMed2dgc_A(3.68e-04), 1ysa_CD(8.33e-10), 1dgc_A(3.58e-04), ... (total=4)
ATGACTCTTPubMed2dgc_A(3.01e-03), 1ysa_CD(5.22e-07), 1dgc_A(2.94e-03), ... (total=4)
TTGCGTGAPubMed2dgc_A(1.07e-02), 1ysa_CD(5.59e-03), 1dgc_A(9.80e-03)
ACTCATPubMed1ysa_CD(6.27e-06), 1ysa_C(1.52e-06)
GTCACPubMed2dgc_A(1.40e-04), 1ysa_CD(1.01e-03), 1dgc_A(1.35e-04)
TGAGCAAPubMed1ysa_CD(1.97e-03)
ATGACPubMed2dgc_A(1.40e-04), 1ysa_CD(1.01e-03), 1dgc_A(1.35e-04), ... (total=4)
ATGATTCAPubMed1ysa_CD(1.97e-06), 1ysa_C(2.78e-05)
TTGACTCAAPubMed2dgc_A(3.01e-03), 1ysa_CD(7.73e-11), 1dgc_A(2.94e-03)
GAGATGACTCATCTCPubMed2dgc_A(1.28e-02), 1ysa_CD(4.21e-09), 1dgc_A(1.25e-02), ... (total=4)
TGAGTCAPubMed2dgc_A(1.04e-03), 1ysa_CD(1.06e-12), 1dgc_A(1.01e-03), ... (total=4)
ATGAGPubMed1ysa_CD(1.01e-03), 1ysa_C(3.61e-04)
GTGACTCACPubMed2dgc_A(3.01e-03), 1ysa_CD(7.73e-11), 1dgc_A(2.94e-03)
GTGAGTCATPubMed2dgc_A(3.01e-03), 1ysa_CD(7.73e-11), 1dgc_A(2.94e-03), ... (total=4)
TGACGTCAPubMed2dgc_A(1.71e-06), 1dgc_A(1.64e-06)
TGAGCCAPubMed1ysa_CD(4.12e-07)
TGACATCAPubMed2dgc_A(1.83e-03), 1dgc_A(1.79e-03)
TGACTAPubMed2dgc_A(3.68e-04), 1ysa_CD(6.27e-06), 1dgc_A(3.58e-04), ... (total=4)
GAGATGAGTCATCTCPubMed2dgc_A(1.28e-02), 1ysa_CD(4.21e-09), 1dgc_A(1.25e-02), ... (total=4)
CTGACTAATPubMed2dgc_A(3.01e-03), 1ysa_CD(6.04e-06), 1dgc_A(2.94e-03)
CATGACGTCATGPubMed2dgc_A(1.44e-05), 1dgc_A(1.39e-05)
GTCATPubMed2dgc_A(1.40e-04), 1ysa_CD(1.01e-03), 1dgc_A(1.35e-04), ... (total=4)
sitesourcematches (E-value)

Dendrogram of similar interfaces ?

matrix format
  
  ------NCTT--AT--RG----   L                           +2dgc_A    
                                        +--------------1 
  ------NG--AT--STRG----             +--7              +5szx_B    
                                     !  ! 
  RG----NC--YGATCTRG----   L         !  +--------------2wt7_B    
                                     ! 
  RC----NC--AAATCTRC----   L      +--8                 +2wt7_A    
                                  !  !    +------------2 
  --RA--NA--AAVTSTRG----   L      !  !    !            +1h89_A    
                                  !  !    ! 
  ------NT--ATATSTRG----   L      !  +----6            +1dh3_C    
                                  !       !         +--3 
  RG----NC--YGAT--RC----   L   +--9       !         !  +4eot_A    
                               !  !       +---------5 
  NC--AT----STRA--------       !  !                 !  +1a02_J    
                               !  !                 +--4 
  --------RA--NTAAVTSTRG   L -10  !                    +1hjb_A    
                               !  ! 
  --RA--NT--ATVTSTRG----       !  +--------------------6mg1_B    
                               !  
  ------NCRTATATSTRG----       +-----------------------1t2k_D

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updated Fri Sep 13 16:14:29 2024