5krb_G : 3D-footprint complex

structure name	GCNF DNA BINDING DOMAIN - OCT4 DR0 COMPLEX (Nuclear receptor subfamily 6 group A member 1)
reference	Ortlund et al. 'J. 428 4981 2016
source	Mus musculus
experiment	X-ray (resolution=2.10, R-factor=0.218)
structural superfamily	Glucocorticoid receptor-like DNA-binding domain;
sequence family	Zinc finger, C4 type two domains;
multimeric complexes	5krb_BG
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 5krb_G interface=20,23,28,78,81, tclicgdratglhygiiscEgcKgffkRsisnkrvyrcsrdkncvmsrkqrnrcqycrllkclqmgmnrkairedgmPggRn
interface signature	EKRPR

Estimated binding specificities ?

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# IC=6.209 IC/col=0.690 n_of_columns=9

specificity:

A |   0  16  24  64   0   0  24   0  80
C |   8  64  24   8   0   0  24  80   0
G |   0   8  24   8  96  96  24   0   8
T |  88   8  24  16   0   0  24  16   8

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Related DNA sequences reported in the literature ?

site	source	matches (E-value)
term: GCNF
AGGTCA	PubMed	5krb_G(4.54e-05), 5krb_BG(1.13e-04)
TCAAGGTCA	PubMed	5krb_G(2.83e-08), 5krb_BG(3.81e-07)
AGGTCAAGGTCA	PubMed	5krb_G(8.93e-07), 5krb_BG(2.47e-11)
TCAAG	PubMed	5krb_G(3.14e-03), 5krb_BG(5.75e-03)

Dendrogram of similar interfaces ?

matrix format

  
  CAECKG--KGRG--RTRT   L                          +---1cit_A    
                                    +-------------2 
  --EAKG--KTRG------   L        +---3             +---4umm_A    
                                !   ! 
  ----KGVT--RG------   L   +----4   +-----------------2c7a_B    
                           !    ! 
  --ECKGAG--RG------   L --5    +---------------------4ond_A    
                           ! 
  --ECKGAGKGRG------   L   !                         +1hcq_E    
                           +-------------------------1 
  --ECKGAG--KTRG----   L                             +4aa6_B

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updated Sat Jan 10 08:26:02 2026