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legend  pdf

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=8.004 IC/col=0.889 n_of_columns=9 specificity:   
A |  96  67  24  96   0   0   9   9  96
C |   0  11  24   0   0   0  11  69   0
G |   0   9  24   0  96  96   9   9   0
T |   0   9  24   0   0   0  67   9   0
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    
                                  +------------1 
  --EAKG--KTRG------   L     +----2            +---4umm_A    
                             !    ! 
  ----KGVT--RG------   L   +-3    +----------------2c7a_B    
                           ! ! 
  --ECKGAG--RG------   L --4 +---------------------4ond_A    
                           ! 
  --ECKGAG--KTRG----   L   +-----------------------4aa6_B

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updated Sat Jan 10 04:31:21 2026