4rul_A : 3D-footprint complex

structure name	CRYSTAL STRUCTURE OF FULL-LENGTH E.COLI TOPOISOMERASE I IN COMPLEX WITH SSDNA (DNA topoisomerase 1)
reference	Tse-Dinh et al. 'Nucleic 43 11031 2015
source	Escherichia coli DH1
experiment	X-ray (resolution=2.90, R-factor=0.212)
structural superfamily	Prokaryotic type I DNA topoisomerase;Zinc beta-ribbon;
sequence family	DNA topoisomerase; Toprim domain; Topoisomerase I zincribbonlike; Topoisomerase DNA binding C4 zinc fing;
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 4rul_A interface=584,586,588,591,597,606,608,610,699,700,703,714,748,752,755,757,761,762,765,767,799,805,807,813, gkalvivespakaktinkylgsdyvvkssvghirdlptkdergalvnrmgvdpwhnweahyevlpgkekvvselkqlaekadhiylatdldregeaiawhlreviggddarysrvvfneitknairqafnkpgelnidrvnaqqarrfmdrvvgymvspllwkkiarglsagrvqsvavrlvverereikafvpeefwevdastttpsgealalqvthqndkpfrpvnkeqtqaavsllekarysvleredkpttskpgapfitstlqqaastrlgfgvkktmmmaqrlyeagyitymrtdstnlsqdavnmvrgyisdnfgkkylpespnqyaskqeaheairpsdvnvmaeslkdmeadaqklyqliwrqfvacqmtpakydsttltvgagdfrlkargrilrfdgwtkvmpalrkgdedrilpavnkgdaltlveltpaqhftkpparfseaslvkelekrgigrpstyasiistiqdrgyvrvenrrfyaekmgeivtdrleenfrelmnydftaqmensldqvanheaewkavldhffsdftqqldkaekdpeeggmrpnqmvltsidcptcgrkmgiRtAsTgvFlgcsgYalppkercKtTiNlvpenevlnvlegedaetnalrakrrcpkcgtamdsylidpkrklhvcgnnptcdgyeieegefrikgydgpivecekcgsemhlkmgRFgkYmactneecknTrkilrngevappkedpvplpelpceksdayfvlRdgaAgvFlAantFPksReTraplveefrdrlpeklryladapnktmvrfsRktkqqYvSsekgwSafyvdgkwve
interface signature	RATFYKTNRFYTRAFAFPRTRYSS

Estimated binding specificities ?

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# IC=12.867 IC/col=1.170 n_of_columns=11

specificity:

A |   4  21   0   0  96   0   0   0   0   0   0
C |   4  21  96   0   0   0   0   0   0   0   0
G |   4  33   0  96   0   0   0   0  96  96  96
T |  84  21   0   0   0  96  96  96   0   0   0

scan!

Dendrogram of similar interfaces ?

matrix format

  
  ------------------------------------------------RGAGTGFGYGKGTGNGRTFTYTTTRAAGFGAAFAPTRATGRCYTSTST   L                 +----------4rul_A    
                                                                                                              +--------1 
  ------HCDC--KT--RCRC--RCYTSTPT--WT--PTKTQTRTSTTG------------------------------------------------   L   +----2        +----------6cqi_A    
                                                                                                         !    ! 
  ----RTHCDGRT----RCRC--RCYTSTPT--WTKAPAKT--RTSTTG------------------------------------------------     --3    +-------------------6pcm_B    
                                                                                                         ! 
  ECKC----------DC----DCWCIG--RGRC------VC--RC--TT------------------------------------------------   L   +------------------------2o5c_B

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updated Fri Sep 13 18:45:46 2024