3iay_A : 3D-footprint complex

structure name	TERNARY COMPLEX OF DNA POLYMERASE DELTA (DNA polymerase delta catalytic subunit)
reference	Aggarwal et al. Nat.Struct.Mol.Biol. 16 979 2009
source	Saccharomyces cerevisiae
experiment	X-ray (resolution=2.00, R-factor=0.195)
structural superfamily	DNA/RNA polymerases;Ribonuclease H-like;
sequence family	DNA polymerase family B; DNA polymerase family B, exonuclease do;
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 3iay_A interface=350,486,714,715,739,799,801, ssferkklptdfdpslydisfqqidaeqsvlngikdentstvvrffgvtseghsvlcnvtgfknylyvpapnssdandqeqinkfvhylnetfdhaidsievvskqsiwgysgdtklpfwkiyvtyphmvnklrtaferghlsfnswfsngtttydniaytlrlmvdcgivgmswitlpkgkysmiepnnrvsscqlevsinyrnliahpaegdwshtaplrimsfdiecagrigvfpepeydpviqianvvsiagakkpfirnvftlntcspitgsmifshateeemlsnwrnfiikvdpdviigynttnfdipyllnrakalkvndfpyfgrlktvkqeikesvfssKaygtretknvnidgrlqldllqfiqreyklrsytlnavsahflgeqsiisdlqngdsetrrrlavyclkdaylplrlmeklmalvnytemarvtgvpfsyllargqqikvvsqlfrkcleidtvipnmqsqasddQyegatviepirgyydvpiatldfnslypsimmahnlcyttlcnkatverlnlkidedyvitpngdyfvttkrrrgilpiildelisarkrakkdlrdekdpfkrdvlngrqlalkisansvygftgatvgklpclaisssvtaygrtmilktktavqekycikngykhdavvvygdtdsvmvkfgttdlkeamdlgteaakyvstlfkhpinlefekayfpyllinkKRyaglfwtnpdkfdkldqkglasvRrdscslvsivmnkvlkkiliernvdgalafvretindilhnrvdiskliisktlapnytNpQphavlaermkrregvgpnvgdrvdyviiggndklynraedplfvlenniqvdsryyltnqlqnpiisivapiigdkqangmfvv
interface signature	KQKRRNQ

Estimated binding specificities ?

readout + contact

# IC=4.007 IC/col=0.668 n_of_columns=6

specificity:

A |  11  96  11   0  24   9
C |   9   0   9   0  24   9
G |   9   0  67  96  24  69
T |  67   0   9   0  24   9

scan!

Dendrogram of similar interfaces ?

matrix format

  
  ------IT--------------SAKT------------------QGQAVT--FTITSAQTIGNGSGYGFT--VAKTLTKARGRCNC   L              +------------3iay_A    
                                                                                               +----------1 
  --------------------------------DG--FA----FG----------------------------------KT------       !          +------------2dtu_A    
                                                                                             --3 
  PIPIVIIIPGFIKGRINTNTFC----DARAYT--RG--WGDG--------WG----------------------------------   L   ! +---------------------2xhb_A    
                                                                                               +-2 
  --------------------------------------------RC--------------LC--SCYG--FAYA----KA--RG--   L     +---------------------8g9l_A

home
updated Tue Dec 17 23:26:24 2024