3ojs_A : 3D-footprint complex

structure name	SNAPSHOTS OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS PROCESSING C5 MODIFIED THYMIDINES (DNA polymerase I, thermostable)
reference	Diederichs et al. Proc.Natl.Acad.Sci.USA 107 21327 2010
source	Thermus aquaticus
experiment	X-ray (resolution=1.90, R-factor=0.166)
structural superfamily	DNA/RNA polymerases;Ribonuclease H-like;
sequence family	DNA polymerase family A; Taq polymerase, exonuclease;
redundant complexes	3m8s 4ktq 3lwm 3ktq 1qsy 3m8r 1qss 1tau 3lwl 1qtm 2ktq 3oju
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 3ojs_A interface=247,251,280,287,290,461,491, leeapwpppegafvgfvlsrkepmwadllalaaarggrvhrapepykalrdlkeargllakdlsvlalreglglppgddpmllaylldpsnttpegvarryggewteeageraalserlfanlwgrlegeerllwlyreverplsavlahmeatgvrldvaylralslevaeeiarleaevfrlaghpfnlnsrdqlervlfdelglpaigktektgkrstsaavlealreahpivekilqyreltKlksTyidplpdlihprtgrlhtrfnqtatatgRlsssdpNlqNipvrtplgqrirrafiaeegwllvaldysqielrvlahlsgdenlirvfqegrdihtetaswmfgvpreavdplmrraaktinfgvlygmsahrlsqelaipyeeaqafieryfqsfpkvrawiektleegrrrgyvetlfgrrryvpdlearvksvreaaermafnmpvQgtaadlmklamvklfprleemgarmllqvHdelvleapkeraeavarlakevmegvyplavplevevgigedwlsake
interface signature	KTRNNQH

Estimated binding specificities ?

readout + contact

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

specificity:

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

scan!

Dendrogram of similar interfaces ?

matrix format

  
  ------------IASAAAVAAA--------KC--------RGNGNG--TAFA--YAMASAHARA--QAEA--EARANGQG--HG   L                        +--3ojs_A    
                                                                                                            +-----2 
  ----------------DT--KT--------KC--------RG--NTRGAAFA--YCIA------LAQTNANT------QC----                      !     ! +-2hhv_A    
                                                                                             +--------------3     +-1 
  LCNGKGYGMGEG----------------------SGHGVC--------------------------------------------       !              !       +-1kln_A    
                                                                                           --4              ! 
  --------------------------------KT------RTNG----------YA----------------------QA----       !              +--------1x9m_A    
                                                                                             ! 
  ----------------------ATYTDGKG----------------------TTYT------------------------HT--       +-----------------------1msw_D

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updated Mon Dec 16 21:37:28 2024