2rgr_A : 3D-footprint complex

structure name	TOPOISOMERASE IIA BOUND TO G-SEGMENT DNA (DNA topoisomerase 2)
reference	Berger et al. Nature 450 1201 2007
source	Saccharomyces cerevisiae
experiment	X-ray (resolution=3.00, R-factor=0.231)
structural superfamily	Type II DNA topoisomerase;
sequence family	DNA gyrase/topoisomerase IV, subunit A;
reference complex	3l4j_A
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 2rgr_A interface=57,59,269,273,415,420, rksritnypkledankagtkegykctlvltegdsalslavaglavvgrdyygcyplRgKmlnvreasadqilknaeiqaikkimglqhrkkyedtkslryghlmimtdqdhdgshikgliinflessflglldiqgfllefitpiikvsitkptkntiafynmpdyekwreeeshkftwkqkyykglgtslaqevreyfsnldrhlkifhslqgndkdyidlafskkkaddrkewlrqyepgtvldptlkeipisdfinkelilfslaDnirSipnvldgfkpgqrkvlygcfkknlkselkvaqlapyvsectayhhgeqslaqtiiglaqnfvgsnniylllpngafgtratggkdaaaaryiytelnkltrkifhpaddplykyiqedektvepewylpilpmilvngaegIgtgwStyippfnpleiiknirhlmndeeleqmhpwfrgwtgtieeieplryrmygrieqigdnvleitelpartwtstikeylllglsgndkikpwikdmeeqhddnikfiitlspeemaktrkigfyerfklispislmnmvafdphgkikkynsvneilsefyyvrleyyqkrkdhmserlqwevekysfqvkfikmiiekeltvtnkprnaiiqelenlgfprfnkegkpyygslygtyeyllgmriwsltkeryqkllkqkqeketelenllklsakdiwntdlkafevgyqeflqrdaear
interface signature	RKDSIS

Estimated binding specificities ?

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# IC=3.242 IC/col=0.648 n_of_columns=5

specificity:

A |   0   0  24  18  10
C |  96   0  24  18   8
G |   0  96  24  18  70
T |   0   0  24  42   8

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Dendrogram of similar interfaces ?

matrix format

  
  RGKA--SG------------------------ICSG------------   L                      +-----------2rgr_A    
                                                               +------------4 
  ----RC------STSA--------------RGIC--------------         +---8            +-----------3k9f_B    
                                                           !   ! 
  --KT--------------------------------------------         !   +------------------------3k9f_C    
                                                           ! 
  ----------------NASTRGHT------KA----------------   L     !                      +-----2c6y_A    
                                                         +-9               +------3 
  ------------------NA--RA----LT------------------   L   ! !    +----------5      +-----2a07_K    
                                                         ! !    !          ! 
  --------DTRTRGTT--KT----------------------------   L   ! !    !          +------------2o8k_A    
                                                         ! +----7 
  ------------RGRGYC------------------------------   L   !      !                   +---1cf7_A    
                                                       -10      !   +---------------2 
  ----------------------YG------------------------       !      +---6               +---2heo_D    
                                                         !          ! 
  ------HT----------NC--STNARG--------------------   L   !          +-------------------1k61_B    
                                                         !  
  ------------------------------------NCAAAT--RT--   L   !                          +--1a02_F    
                                                         +--------------------------1 
  --------------------------------------NCTTAT--RG   L                              +--2dgc_A

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updated Mon Dec 18 07:14:42 2023