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structure nameDNA-BINDING MECHANISM OF THE MONOMERIC ORPHAN NUCLEAR RECEPTOR NGFI-B
(PROTEIN ORPHAN NUCLEAR RECEPTOR NGFI-B)
referenceSigler et al. Nat.Struct.Biol. 6 471 1999
sourceRattus norvegicus
experimentX-ray (resolution=2.70, R-factor=?)
structural superfamilyGlucocorticoid receptor-like DNA-binding domain;
sequence familyZinc finger, C4 type two domains;
multimeric complexes6lc1_AD
redundant complexes6lc1_D
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureCEKKRRR

Estimated binding specificities ?

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# IC=7.625 IC/col=0.847 n_of_columns=9 specificity:   
A |   7   7  73   0   0   0  24   7   0
C |   7   7   7  96  96   0  24   7   0
G |   9  73   7   0   0   0  24   7   0
T |  73   9   9   0   0  96  24  75  96
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: NGFI-B
AGGTCAPubMed1cit_A(1.19e-08)
AAAGGTCAPubMed1cit_A(2.06e-09)
CAAGGTCAPubMed1cit_A(4.87e-06)
CCAAGGTCAPubMed1cit_A(2.40e-05)
NNAGGTCAPubMed1cit_A(4.87e-06)

Dendrogram of similar interfaces ?

matrix format
  
  CAECKG--KGRG--RTRT   L                         +----1cit_A    
                                          +------3 
  --EAKG--KTRG------   L                  !      !    +4umm_A    
                                          !      +----1 
  ----KGVG--RG------   L     +------------4           +4tnt_B    
                             !            ! 
  ----KGVT--RG------   L     !            !          +5emc_A    
                           +-5            +----------2 
  --ECKGAG--KTRG----   L   ! !                       +4aa6_B    
                         --6 ! 
  ----KGVT--RG------   L   ! +------------------------2c7a_B    
                           ! 
  --ECKGAG--RG------   L   +-------------------------4ond_A

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updated Mon Jun 29 14:05:31 2026