7om3_A : 3D-footprint complex

structure name	CRYSTAL STRUCTURE OF KOD DNA POLYMERASE IN A BINARY COMPLEX WITH HYPOXANTHINE CONTAINING TEMPLATE (DNA POLYMERASE,DNA POLYMERASE,DNA POLYMERASE)
reference	Diederichs et al. Chembiochem 22 3060 2021
source	THERMOCOCCUS KODAKARENSIS KOD1
experiment	X-ray (resolution=1.92, R-factor=0.184)
structural superfamily	DNA/RNA polymerases;Ribonuclease H-like;
sequence family	DNA polymerase family B; DNA polymerase family B, exonuclease do;
redundant complexes	4k8z_A 5omf_A 5vu6_A 5vu7_A 5vu8_A 5vu9_A 6q4t_A 6wya_A 6wyb_A 7omb_A 7omg_A 7rsr_A 7rss_A 7rsu_A 7tqw_A
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 7om3_A interface=409,494,592,612, mildtdyitedgkpvirifkkengefkieydrtfepyfyallkddsaieevkkitaerhgtvvtvkrvekvqkkflgrpvevwklyfthpqdvpairdkirehpavidiyeydipfakrylidkglvpmegdeelkmlafaiatlyhegeefaegpilmisyadeegarvitwknvdlpyvdvvsteremikrflrvvkekdpdvlityngdnfdfaylkkrceklginfalgrdgsepkiqrmgdrfavevkgrihfdlypvirrtinlptytleavyeavfgqpkekvyaeeittawetgenlervarysmedakvtyelgkeflpmeaqlsrligqslwdvsrsstgnlvewfllrkayernelapnkpdekelarrrqsyeggyvkeperglwenivyldfrslYpsiiithnvspdtlnregckeydvapqvghrfckdfpgfipsllgdlleerqkikkkmkatidpierklldyrqraikilansyYgyygyararwyckecaesvtawgreyitmtikeieekygfkviysdtdgffatipgadaetvkkkameflkyinaklpgaleleyegfykrgffvtkKkyavideegkittrgleivRrdwseiaketqarvleallkdgdvekavrivkevteklskyevppeklviheqitrdlkdykatgphvavakrlaargvkirpgtvisyivlkgsgrigdraipfdefdptkhkydaeyyienqvlpaverilrafgyrkedlryqk
interface signature	YYKR

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 |   7  73  73   7
G |  73   7   9   7
T |   9   9   7   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 Wed Dec 18 10:07:30 2024