interface graph thumbnail
legend  pdf

structure nameGLUCOCORTICOID RECEPTOR DNA BINDING DOMAIN - IL8 NF-KB RESPONSE ELEMENT COMPLEX
(Glucocorticoid receptor)
referenceOrtlund et al. 'Nat 9 1337 2018
sourceHomo sapiens
experimentX-ray (resolution=1.85, R-factor=0.221)
structural superfamilyGlucocorticoid receptor-like DNA-binding domain;
sequence familyZinc finger, C4 type two domains;
multimeric complexes4hn6_AB 5cc1_AB 5cc1_WX 5e69_AB 5e6a_AB 5e6b_AB 5e6c_AB
redundant complexes4hn6_B 5cc1_A 5e6a_B 5e6b_A 5e6c_B 5e6d_B
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureKVR

Estimated binding specificities ?

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# IC=3.101 IC/col=0.620 n_of_columns=5 specificity:   
A |  54  24  54   0   0
C |  16  24  13   0   0
G |  13  24  16   0   0
T |  13  24  13  96  96
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: nGRE
TGTCCTPubMed5e6c_AB(7.58e-03), 5cby_A(1.50e-03), 5cbx_E(3.59e-04), ... (total=4)

Dendrogram of similar interfaces ?

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

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updated Fri Sep 13 19:29:23 2024