3ktq_A : 3D-footprint complex

structure name	CRYSTAL STRUCTURE OF AN ACTIVE TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS (PROTEIN LARGE FRAGMENT OF DNA POLYMERASE I)
reference	Waksman et al. 'EMBO 17 7514 1998
source	Thermus aquaticus
experiment	X-ray (resolution=2.30, R-factor=0.218)
structural superfamily	DNA/RNA polymerases;Ribonuclease H-like;
sequence family	DNA polymerase family A; Taq polymerase, exonuclease;
redundant complexes	4ktq 1qsy 1qss 1tau 1qtm 2ktq
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 3ktq_A interface=248,252,253,281,288,291,323,372,375,379,381,385,458,462,492, aleeapwpppegafvgfvlsrkepmwadllalaaarggrvhrapepykalrdlkeargllakdlsvlalreglglppgddpmllaylldpsnttpegvarryggewteeageraalserlfanlwgrlegeerllwlyreverplsavlahmeatgvrldvaylralslevaeeiarleaevfrlaghpfnlnsrdqlervlfdelglpaigktektgkrstsaavlealreahpivekilqyreltKlksTYidplpdlihprtgrlhtrfnqtatatgRlsssdpNlqNipvrtplgqrirrafiaeegwllvaldysqiElrvlahlsgdenlirvfqegrdihtetaswmfgvpreavdplmrraakTinFgvlYgMsahRlsqelaipyeeaqafieryfqsfpkvrawiektleegrrrgyvetlfgrrryvpdlearvksvreaaermafNmpvQgtaadlmklamvklfprleemgarmllqvHdelvleapkeraeavarlakevmegvyplavplevevgigedwlsak
interface signature	KTYRNNETFYMRNQH

Estimated binding specificities ?

readout + contact

# IC=3.143 IC/col=0.786 n_of_columns=4

specificity:

A |  19   9   0   0
C |  28  76   0  86
G |  38  11  96   0
T |  11   0   0  10

scan!

Dendrogram of similar interfaces ?

matrix format

  
  --------------------------KC--YG------RGNGNG--TGFG--YGMGRG--------KAEANGQG--HG   L                        +--3ktq_A    
                                                                                                      +-----2 
  --------------DTKT--------KC----------RG--NTRGAAFA--YCIA--LAQTNANT------QC----   L                  !     ! +-2hhv_A    
                                                                                       +--------------3     +-1 
  LCNGKGYGMGRCEG------------------SGHGVC----------------------------------------       !              !       +-1kln_A    
                                                                                     --4              ! 
  ----------------------------KT--------RTNG----------YA------------------QA----       !              +--------1x9m_A    
                                                                                       ! 
  ------------------ATYTDGKG------------------------TTYT--------------------HT--   L   +-----------------------1msw_D

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updated Mon Dec 16 21:15:16 2024