5omv_A : 3D-footprint complex

structure name	TERNARY COMPLEX OF 9N DNA POLYMERASE IN THE REPLICATIVE STATE WITH TWO METAL IONS IN THE ACTIVE SITE (DNA polymerase)
reference	Diederichs et al. 'PLoS 12 e0188005 2017
source	Thermococcus sp. 9oN-7
experiment	X-ray (resolution=2.00, R-factor=0.192)
structural superfamily	DNA/RNA polymerases;Ribonuclease H-like;
sequence family	DNA polymerase family B; DNA polymerase family B, exonuclease do;
redundant complexes	4k8x_A 5omq_A 6isf_A 6isg_A 6ish_A 6isi_A
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 5omv_A interface=409,494,541,592,612, mildtdyitengkpvirvfkkengefkieydrtfepyfyallkddsaiedvkkvtakrhgtvvkvkraekvqkkflgrpievwklyfnhpqdvpairdrirahpavvdiyeydipfakrylidkglipmegdeeltmlafaiatlyhegeefgtgpilmisyadgsearvitwkkidlpyvdvvstekemikrflrvvrekdpdvlityngdnfdfaylkkrceelgikftlgrdgsepkiqrmgdrfavevkgrihfdlypvirrtinlptytleavyeavfgkpkekvyaeeiaqawesgeglervarysmedakvtyelgreffpmeaqlsrligqslwdvsrsstgnlvewfllrkaykrnelapnkpderelarrrggyaggyvkeperglwdnivyldfrslYpsiiithnvspdtlnregckeydvapevghkfckdfpgfipsllgdlleerqkikrkmkatvdplekklldyrqraikilansfYgyygyakarwyckecaesvtawgreyiemvireleekfgfkvlyadTdglhatipgadaetvkkkakeflkyinpklpglleleyegfyvrgffvtkKkyavideegkittrgleivRrdwseiaketqarvleailkhgdveeavrivkevteklskyevppeklviheqitrdlrdykatgphvavakrlaargvkirpgtvisyivlkgsgrigdraipadefdptkhrydaeyyienqvlpaverilkafgyrkedlryq
interface signature	YYTKR

Estimated binding specificities ?

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# IC=2.250 IC/col=0.562 n_of_columns=4

specificity:

A |   7   7   7  73
C |   9  73  73   7
G |  73   9   7   7
T |   7   7   9   9

scan!

Dendrogram of similar interfaces ?

matrix format

  
  ------IT------------------------------------QGQAVT--FTITSAQTIGNGSGYGFT--VAKTLTKARGRCNC   L              +------------3iay_A    
                                                                                               +----------1 
  --------------------------------DG--FA----FG----------------------------WC----KT------       !          +------------2dtu_A    
                                                                                             --3 
  PIPIVIIIPGFIKGRINTNTFCQGMGDARAYT--RG--WGDG--------WG----------------------------------   L   ! +---------------------2xhb_A    
                                                                                               +-2 
  --------------------------RT----------------RC--------------LC--SCYG--FAYA----KA--RG--   L     +---------------------8g9l_A

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updated Sun Aug 3 09:50:28 2025