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structure nameCRYSTAL STRUCTURE OF HEPATOCYTE NUCLEAR FACTOR 4ALPHA IN COMPLEX WITH DNA: DIABETES GENE PRODUCT
(Hepatocyte Nuclear Factor 4-alpha, DNA binding domain)
referenceMelikishvili et al.
sourceHomo sapiens
experimentX-ray (resolution=2.00, R-factor=?)
structural superfamilyGlucocorticoid receptor-like DNA-binding domain;
sequence familyZinc finger, C4 type two domains;
multimeric complexes3cbb_AB
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureDKRR

Estimated binding specificities ?

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# IC=3.720 IC/col=0.744 n_of_columns=5 specificity:   
A |   0   8   8   0  72
C |   0  16  64  96   8
G |  88   8   8   0   8
T |   8  64  16   0   8
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: HNF-4
GGGTCAPubMed3cbb_AB(1.68e-03)
TGGACTTAGTTCAPubMed3cbb_A(1.80e-05)
AGTTCAPubMed3cbb_A(3.04e-03), 3cbb_AB(1.75e-04)
CCCTTTGGAPubMed3cbb_A(2.95e-03)
TGAACCCTTGACCPubMed3cbb_AB(3.85e-12)
TGTCCTPubMed3cbb_A(3.71e-04)

Dendrogram of similar interfaces ?

matrix format
  
  --ECKG--KGRG--   L               +--------2ff0_A    
                       +-----------6 
  ----KGVT--RG--       !           +--------5emp_A    
                       ! 
  --EAKG--RTRTRT       !                    +4umm_E    
                     --9               +----1 
  --EAKG--RTRTRT       !  +------------5    +2han_B    
                       !  !            ! 
  --ECKG--KGRG--       !  !            +----3dzy_A    
                       !  ! 
  --DGKG--RTRG--   L   +--8                +3cbb_A    
                          !             +--2 
  CAECKG--KGRG--   L      !     +-------4  +6l6q_B    
                          !     !       ! 
  --ECKG--RGRG--   L      +-----7       +---3dzy_D    
                                ! 
  ----KAVA--RA--   L            !          +5e69_A    
                                +----------3 
  --ETKGAT--RG--   L                       +1lat_A

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updated Tue Dec 19 07:12:55 2023