1s40_A : 3D-footprint complex

3D-footprint cannot reliably estimate the specificity of 'Nucleic acid-binding proteins', as they bind to single-stranded DNA and thus accumulate more base contacts.

Related DNA sequences reported in the literature ?

structure name	SOLUTION STRUCTURE OF THE CDC13 DNA-BINDING DOMAIN COMPLEXED WITH A SINGLE-STRANDED TELOMERIC DNA 11-MER (CELL DIVISION CONTROL PROTEIN 13)
source	SACCHAROMYCES CEREVISIAE
experiment	NMR
structural superfamily	Nucleic acid-binding proteins;
sequence family	CDC13, ssDNA binding;
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 1s40_A interface=20,21,23,34,36,37,39,40,42,44,56,57,58,59,66,77,81,107,108,110,123,127,132,133,136, kmarkdptiefcqlgldtfETkYitmfgmlvscSfDKpAFiSfVfsdftkndivqNYLYdrylidYenklelnegfKaimYknqfetfdsklrkifnnglrdlqngRDeNlsqygivckmniKvkmYngklNAivRecepvphsqissiaspsqcehlrlfyqrafkrigesaisryfeeyrrffpi

site	source	matches (E-value)
term: CDC13
GTGTGGGTGTG	PubMed	1s40_A(3.22e-12)

Dendrogram of similar interfaces ?

matrix format

  
  ----EGTGYGSGDGKGATFTSGVGNGYTLGYG------YG------KG----YT------------RGDGNG------KT--YG----NGAG--RT----------   L                               +-1s40_A    
                                                                                                                          +--------------------1 
  KTFT----YT--------------NTYT--YADGFGSGFGRGET--HA--LTYT--NTRTITMTDT--NG----RG--KTQGFG--KANT--VTLT--EALATGRT   L       +--2                    +-6lbr_A    
                                                                                                                       !  ! 
  --------YT------------------------------------------YGDG--------------------------------------RT----------   L     +-3  +----------------------3kjp_A    
                                                                                                                     ! ! 
  --------QT----------------------------------------RT------------------------LTTTKTFTQT------ST--HT--------       +-4 +-------------------------4gnx_B    
                                                                                                                   ! ! 
  --------------------------------------------QC--HC----------------------------TGRAYC----------------------   L --5 +--------------------------1qzh_E    
                                                                                                                   ! 
  ----------------------------------------------WT--TTFT------------------MT--RTRT------RTRT----------------   L   +---------------------------6i52_C

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updated Tue Dec 17 22:21:55 2024