4dfk_A : 3D-footprint complex

structure name	LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS IN A CLOSED TERNARY COMPLEX WITH 5-(N-(10-HYDROXYDECANOYL)-AMINOPENTINYL)-2-DUTP (DNA polymerase I, thermostable)
reference	Diederichs et al. J.Am.Chem.Soc. 134 11840 2012
source	Thermus aquaticus
experiment	X-ray (resolution=1.65, R-factor=0.172)
structural superfamily	DNA/RNA polymerases;Ribonuclease H-like;
sequence family	DNA polymerase family A; Taq polymerase, exonuclease;
redundant complexes	3rrh 3m8s 4ktq 4dfm 4dfj 4elt 3t3f 3ojs 3lwm 3ktq 1qsy 3sz2 4df8 3rrg 3m8r 3py8 1qss 3po5 1tau 4dfp 3lwl 4dle 3syz 3sv3 1qtm 3rtv 3po4 3sv4 4df4 3rr8 3rr7 2ktq 4elv 3oju 4elu 4dlg
reference complex	6fbc_A
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 4dfk_A interface=247,251,280,287,290,491, leeapwpppegafvgfvlsrkepmwadllalaaarggrvhrapepykalrdlkeargllakdlsvlalreglglppgddpmllaylldpsnttpegvarryggewteeageraalserlfanlwgrlegeerllwlyreverplsavlahmeatgvrldvaylralslevaeeiarleaevfrlaghpfnlnsrdqlervlfdelglpaigktektgkrstsaavlealreahpivekilqyreltKlksTyidplpdlihprtgrlhtrfnqtatatgRlsssdpNlqNipvrtplgqrirrafiaeegwllvaldysqielrvlahlsgdenlirvfqegrdihtetaswmfgvpreavdplmrraaktinfgvlygmsahrlsqelaipyeeaqafieryfqsfpkvrawiektleegrrrgyvetlfgrrryvpdlearvksvreaaermafnmpvqgtaadlmklamvklfprleemgarmllqvHdelvleapkeraeavarlakevmegvyplavplevevgigedwlsake
interface signature	KTRNNH

Estimated binding specificities ?

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# IC=2.628 IC/col=0.657 n_of_columns=4

specificity:

A |  11   0  11   8
C |   8  96   8  61
G |  69   0  69  10
T |   8   0   8  17

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Dendrogram of similar interfaces ?

matrix format

  
  ------------IASAAAVAAA--------KC--------RGNGNGTAFA--YAMASAHARAQAEA----NGQG--HG   L                          +4dfk_A    
                                                                                                            +-1 
  ------------------------------KT--------RGNGNTAAYA--YAIASTYT----NARTFANAQA--HG   L                 +------2 +3pv8_D    
                                                                                                     !      ! 
  LCNGKGYGMGEG----------------------SGHGVC--------------------------------------       +-------------3      +--1kln_A    
                                                                                       !             ! 
  --------------------------------KT------RTNG--------YA------------------QA----     --4             +---------1x9m_A    
                                                                                       ! 
  ----------------------ATYTDGKG--------------------TTYT--------------------HT--       +-----------------------1msw_D

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updated Mon Dec 18 09:57:31 2023