1msw_D : 3D-footprint complex

structure name	STRUCTURAL BASIS FOR THE TRANSITION FROM INITIATION TO ELONGATION TRANSCRIPTION IN T7 RNA POLYMERASE (DNA-directed RNA polymerase)
reference	Steitz et al. Science 298 1387 2002
source	Enterobacteria phage T7
experiment	X-ray (resolution=2.10, R-factor=0.241)
structural superfamily	DNA/RNA polymerases;
sequence family	DNAdependent RNA polymerase;
redundant complexes	1cez_A 1h38_C 1qln_A 1s76_D 1s77_D 2pi4_A 2pi5_A 3e2e_A 3e3j_C 8dh0_B 8dh1_L 8dh2_E 8dh3_M 8dh4_I 8dh5_M
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 1msw_D interface=163,164,168,171,172,177,362,365,403,405,407,582,616,619,624,627,629,636,639,640,764, ntiniakndfsdielaaipfntladhygerlareqlalehesyemgearfrkmferqlkagevadnaaakplittllpkmiarindwfeevkakrgkrptafqflqeikpeavayitikttlacltsadnttvqavasaigraiedearfgrirdleakhfkKNveeQlnKRvghvYkkafmqvveadmlskgllggeawsswhkedsihvgvrciemliestgmvslhrqsetielapeyaeaiatragalagispmfqpcvvppkpwtgitgggywangrrplalvrthskkalmryedvympevykainiaqntawkinkkvlavanvitkwkhcpvedipaiereelpmktawkraaAavYrkdkarksrrislefmleqankfanhkaiwfpynmdwRgRvYavsmfnpqgndmtkglltlakgkpigkegyywlkihgancagvdkvpfperikfieenhenimacaksplentwwaeqdspfcflafcfeyagvqhhglsyncslplafdgscsgiqhfsamlrdevggravnllpsetvqdiygivakkvneilqadaingtdnevvtvtdenTgeisekvklgtkalagqwlaygvtrsvtkrsvmTlaYgskeFgfRqQvledtiQpaIDsgkglmftqpnqaagymakliwesvsvtvvaaveamnwlksaakllaaevkdkktgeilrkrcavhwvtpdgfpvwqeykkpiqtrlnlmflgqfrlqptintnkdseidahkqesgiapnfvHsqdgshlrktvvwahekygiesfalihdsfgtipadaanlfkavretmvdtyescdvladfydqfadqlhesqldkmpalpakgnlnlrdilesdfafa
interface signature	KNQKRYAYRRYTTYFRQQIDH

Estimated binding specificities ?

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# IC=6.907 IC/col=1.151 n_of_columns=6

specificity:

A |   0  96  13   0   0   0
C |   0   0  56   0   0   0
G |   0   0  13  96   0   0
T |  96   0  14   0  96  96

scan!

Dendrogram of similar interfaces ?

matrix format

  
  RTKTNTQTKARAYTRGATYTDGKG--------RCRCYCTC----TTYT----FA--RTQT--QGIGDG----------------HT--                            +-------------1msw_D    
                                                                                                              +-------1 
  ------------------------SC--EG----------QG--TGYGVG--YT------QG------WGEG----RG----------   L           +----2       +-------------4boc_A    
                                                                                                         !    ! 
  ------------------------------------------------------------------------QAFTRG----------   L         +-3    +---------------------6ymv_A    
                                                                                                       ! ! 
  --------------------------------------------TCYC----------------------------------------           +-4 +--------------------------6dta_B    
                                                                                                     ! ! 
  --------------------------KT--YG----------YG--YAIG--SC----------------------------QA--HG         +-5 +--------------------------4yfu_D    
                                                                                                   ! ! 
  --------------------------KC------RT----------YCMCSA--HA----------------------NG--QG----       +-6 +---------------------------6fbc_A    
                                                                                                 ! ! 
  --------------------------RC------RA------YG--YT--SC--------------------------NT--QT----   L --7 +---------------------------6vdd_A    
                                                                                                 ! 
  --------------------------------------------------------------------------------QG----HT   L   +----------------------------6xbu_A

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updated Sat Jan 10 04:49:26 2026