3py8_A : 3D-footprint complex

structure name	CRYSTAL STRUCTURE OF A MUTANT OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS IN A CLOSED TERNARY COMPLEX WITH DNA AND DDCTP (DNA polymerase I)
reference	Diederichs et al. Chembiochem 12 1574 2011
source	Thermus aquaticus
experiment	X-ray (resolution=1.74, R-factor=0.171)
structural superfamily	DNA/RNA polymerases;Ribonuclease H-like;
sequence family	DNA polymerase family A; Taq polymerase, exonuclease;
redundant complexes	3rrh 3m8s 4ktq 3t3f 3ojs 3lwm 3ktq 1qsy 3rrg 3m8r 1qss 3po5 1tau 3lwl 1qtm 3po4 3rr8 3rr7 2ktq 3oju
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 3py8_A interface=247,251,280,287,290,371,374,378,380,461,491, leeapwpppegafvgfvlsrkepmwadllalaaarggrvhrapepykalrdlkeargllakdlsvlalreglglppgddpmllaylldpsnttpegvarryggewteeageraalserlfanlwgrlegeerllwlyreverplsavlahmeatgvrldvaylralslevaeeiarleaevfrlaghpfnlnsrdqlervlfdelglpaigktektgkrstsaavlealreahpivekilqyreltKlksTyidplpdlihprtgrlhtrfnqtatatgRlsssdpNlqNipvrtplgqrirrafiaeegwllvaldysqkelrvlahlsgdenlirvfqegrdihtetaswmfgvpreavdplmrraakTinFgvlYgMsahrlsqelaipyeeaqafieryfqsfpkvrawiektleegrrrgyvetlfgrrryvpdlearvksvreaaerkafnmpvQgtaadlmklamvklfprleemgarmllqvHdelvleapkeraeavarlakevmegvyplavplevevgigedwlsake
interface signature	KTRNNTFYMQH

Estimated binding specificities ?

readout + contact

# IC=2.849 IC/col=0.712 n_of_columns=4

specificity:

A |  16   8   0   8
C |  24  80   0  72
G |  48   0  96   8
T |   8   8   0   8

scan!

Dendrogram of similar interfaces ?

matrix format

  
  ----------------------KC----------RG--NGNGTGFG--YGMGSA----------QG--HG   L                         +-3py8_A    
                                                                                                   +-1 
  ----------------------KT----------RG--NGNTAAYA--YAIASTYTNARTFANAQA--HG   L                 +-----2 +-3pv8_D    
                                                                                             !     ! 
  LCNGKGYGMGRCEG------------SGHGVC--------------------------------------       +-------------3     +---1kln_A    
                                                                               !             ! 
  ------------------------KT--------RT--NG--------YA--------------QA----     --4             +---------1x9m_A    
                                                                               ! 
  --------------ATYTDGKG----------RCRCYC--------TTYT----------------HT--       +-----------------------1msw_D

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updated Mon Dec 16 21:44:57 2024