4cn3_D : 3D-footprint complex

structure name	CRYSTAL STRUCTURE OF THE HUMAN RETINOID X RECEPTOR DNA-BINDING DOMAIN BOUND TO THE HUMAN GDE1SPA RESPONSE ELEMENT (RETINOIC ACID RECEPTOR RXR-ALPHA)
reference	Poussin-Courmontagne et al. Sci.Rep. 5 8216 2015
source	HOMO SAPIENS
experiment	X-ray (resolution=2.35, R-factor=0.183)
structural superfamily	Glucocorticoid receptor-like DNA-binding domain;
sequence family	Zinc finger, C4 type two domains;
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 4cn3_D interface=22,25,29,30,78, khicaicgdrssgkhygvyscEgcKgffKRtvrkdltytcrddkdclidkrqrnrcqycryqkclamgmkreavqeeR
interface signature	EKKRR

Estimated binding specificities ?

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# IC=4.638 IC/col=0.928 n_of_columns=5

specificity:

A |   0   0   0   0  48
C |   0   0  16  96  16
G |  96   0  16   0  16
T |   0  96  64   0  16

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Related DNA sequences reported in the literature ?

site	source	matches (E-value)
term: RXR-ALPHA
AGGTCA	PubMed	4cn3_D(2.64e-03), 4cn3_BC(1.86e-04)
TGATCCT	PubMed	4cn3_D(6.10e-03), 4cn3_BC(1.17e-02)

Dendrogram of similar interfaces ?

matrix format

  
  --EC--KG--KGRA--   L      +--5l0m_A    
                         +--6 
  HGECAGKGAAKGRT--   L   !  +--1lo1_A    
                         ! 
  --EA--KG--RTRTRT     --8 +---2han_B    
                         ! ! 
  --DG--KG--RTRG--   L   ! !     +3cbb_A    
                         ! !   +-3 
  --ET--KGAT--RG--   L   +-7   ! ! +1lat_A    
                           !   ! +-2 
  HC----KGVT--RG--         ! +-4   +3g9m_B    
                           ! ! ! 
  ------KAVA--RA--   L     ! ! ! +5e69_A    
                           +-5 +-1 
  ------KGVT--RG--   L       !   +5cbz_E    
                             ! 
  ------KGVT--RG--           +-5emc_A

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updated Mon Dec 18 09:55:43 2023