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.


Dendrogram of similar interfaces ?

matrix format
structure nameDNA SUBSTRATE SELECTION BY APOBEC3G
referenceBuzovetsky et al. 'PLoS 13 e0195048 2018
experimentX-ray (resolution=2.90, R-factor=0.237)
structural superfamilyNucleic acid-binding proteins;Cytidine deaminase-like;
sequence familyAPOBEClike Nterminal domain; Telomerebinding protein alpha subunit, cen; APOBEClike Cterminal domain;
links to other resourcesNAKB PDBSum PDIdb DNAproDB 
  
  NG--------STTTDT----------QC--HCFA----------TGRGYCRCQCLGSGKGDG----------------------------------------------                       +-------------6bwy_A    
                                                                                                                             +-------2 
  ------------------------------------------------------------------------------------------------YTPTKTKTYTLT           +---3       +-------------5w2m_D    
                                                                                                                         !   ! 
  --------------------------------------------------------------------RAHGTCHCACICWT------YCDTYT--YGPG--DG--QA           !   +---------------------5sww_C    
                                                                                                                       +-6 
  ----------STTTDT----------QC--HCFAKT--------TGRAYC--QCLG--KGDGQG--------------------------------------------   L     ! !                          +1qzh_E    
                                                                                                                       ! ! +------------------------1 
  ----------STTTDT----------QC--HCFTKT--------TGRCYC--QCLG--KGDG----------------------------------------------   L     ! +-5                        +7cuh_A    
                                                                                                                       !   ! 
  --KTNT----------TTAT----WT--RT------RTITYTET----------------------------------------------------------------   L   +-8   +------------------------6irq_A    
                                                                                                                     ! ! 
  ----------------------------------------------------------------RGWA----------------------------------------       ! !    +------------------------5w0u_B    
                                                                                                                     ! ! +--4 
  --------------------------------------------------------------------------------------NCKC------------------     --9 +-7  +------------------------6vpc_F    
                                                                                                                     !   ! 
  ----------------------------------------------------------------------------------LGSC----TG--YG------------       !   +---------------------------2pfj_A    
                                                                                                                     ! 
  ----RTTTKT------TT--ATNTFT--NT------------------------------------------------------------------------------   L   +----------------------------6bhx_B

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updated Fri Sep 13 21:22:01 2024