3s14_A : 3D-footprint complex

3D-footprint cannot reliably estimate the specificity of 'beta and beta-prime subunits of DNA dependent RNA-polymerases', as these often contain single-stranded DNA molecules which accumulate many base contacts which distort the calculations.

Dendrogram of similar interfaces ?

matrix format

structure name	RNA POLYMERASE II INITIATION COMPLEX WITH A 6-NT RNA (DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1)
reference	Bushnell et al. Science 333 633 2011
source	SACCHAROMYCES CEREVISIAE S288C
experiment	X-ray (resolution=2.85, R-factor=0.190)
structural superfamily	beta and beta-prime subunits of DNA dependent RNA-polymerase;
sequence family	RNA polymerase Rpb1, domain 5; RNA polymerase Rpb1, domain 1; RNA polymerase Rpb1, domain 2; RNA polymerase Rpb1, domain 6; RNA polymerase Rpb1, domain 3; RNA polymerase Rpb1, domain 7; RNA polymerase Rpb1, domain 4;
redundant complexes	2nvz 2e2h 5oqj 2yu9 2ja6 3gtm 3how 5fyw 7ml0 3po2 3po3 7ml2 6gyk 4v1n 3hou 3hov 5c4x 2r7z 3hox 4a93 5ot2 4v1o 4a3b 3hoz 3gtg 4a3c 3gtj 4a3d 3gtk 7mei 4a3f 3gtl 6blo 4a3g 6blp 4a3i 4a3k 3gtp 2ja5 4a3l 3gtq 4a3m 6bm2 1r9s 6bm4 1r9t 5c4j 7nky 5c44 3s1q 4y52 6bqf 5sva 7ked 5oqm 7kee 7kef 6upx 2ja8 6upy 7nkx 6upz 3s1r 6uq0 5vvs 4y7n 6uq1 3s16 6uq2 6i84 6uq3 1y77 7o4i 4x67 7ml4 7o4j 4x6a 5c3e 3m3y 7o72 4bxx 5c4a 3gto 7o73 7mka 4by1 4a3e 2nvq 2vum 4v1m 7o75 3rzd 4by7 2nvt 3rzo 3hoy 1y1w 5w4u 5w51 3s15 5fz5 3s17 3s1m 3s1n 3s2d 3s2h 2e2i 6gym 7rim 6gyl 7rip 7riq 4bbs 3i4m 7riw 3i4n 7rix 2nvx 7riy 1sfo 5vvr 2e2j 7mk9 4a3j 5fmf 6o6c 1i6h 3h3v 3m4o
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 3s14_A interface=427,428,811,812,1346,1347, gqqyssaplrtvkevqfglfspeevraisvakirfpetmdetqtrakigglndprlgsidrnlkcqtcqegmnecpghfghidlakpvfhvgfiakikkvcecvcmhcgkllldehnelmrqalaikdskkrfaaiwtlcktkmvcetdvpslvsrggcgntqptirkdglklvgswklrvlsteeilnifkhisvkdftslgfnevfsrpewmiltclpvppppvrpsisfnesqrgeddltfkladilkanisletlehngaphhaieeaesllqfhvatymdndiagqpqalqksgrpvksirarlkgkegrirgnlmgkrvdfsartvisgdpnleldqvgvpksiaktltypevvtpynidrltqlvrngpnehpgakyvirdsgdridlryskragdiqlqygwkverhimdndpvlfnrQPslhkmsmmahrvkvipystfrlnlsvtspynadfdgdemnlhvpqseetraelsqlcavplqivspqsnkpcmgivqdtlcgirkltlrdtfieldqvlnmlywvpdwdgviptpaiikpkplwsgkqilsvaipngihlqrfdegttllspkdngmliidgqiifgvvekktvgssngglihvvtrekgpqvcaklfgniqkvvnfwllhngfstgigdtiadgptmreitetiaeakkkvldvtkeaqanlltakhgmtlresfednvvrflneardkagrlaevnlkdlnnvkqmvmagskgsfiniaqmsacvgqqsvegkriafgfvdrtlphfskddyspeskgfvensylrgltpqefffhamggreglidtavkTAetgyiqrrlvkaledimvhydnttrnslgnviqfiygedgmdaahiekqsldtiggsdaafekryrvdllntdhtldpsllesgseilgdlklqvlldeeykqlvkdrkflrevfvdgeanwplpvnirriiqnaqqtfhidhtkpsdltikdivlgvkdlqenllvlrgkneiiqnaqrdavtlfccllrsrlatrrvlqeyrltkqafdwvlsnieaqflrsvvhpgemvgvlaaqsigepatqmtlntfhfagvaskkvtsgvprlkeilnvaknmktpsltvylepghaadqeqaklirsaiehttlksvtiaseiyydpdprstvipedeeiiqlhfslqqspwllrleldraamndkdltmgqvgerikqtfkndlfviwsedndekliircrvvaeedhmlkkientmlenitlrgveniervvmmkydrkvpsptgeyvkepewvletdgvnlsevmtvpgidptriytnsfidimevlgieagraalykevynviasdgsyvnyrhmallvdvmttqggltsvtRHgfnrsntgalmrcsfeetveilfeagasaelddcrgvsenvilgqmapigtgafdvmi

  
  TAAA----------------------           +-----------------------------6kf9_A    
                                     +-1 
  ------------------------RT       +-2 +-----------------------------6kf9_C    
                                   ! ! 
  --------------VCNTICECRC--   L --3 +-----------------------------2axy_C    
                                   ! 
  ----NCKGCAYTRC------------   L   +-----------------------------1jj4_B

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updated Mon Dec 18 09:04:35 2023