5fmf_1AMPQUV : 3D-footprint complex

structure name	THE P-LOBE OF RNA POLYMERASE II PRE-INITIATION COMPLEX
reference	Bushnell et al. Proc.Natl.Acad.Sci.USA 112 13543 2015
source	SACCHAROMYCES CEREVISIAE
experiment	X-ray (resolution=6.00, R-factor=?)
structural superfamily	TATA-box binding protein-like;Transcription factor IIA TFIIA, beta-barrel domain;Transcription factor IIA TFIIA, alpha-helical domain;Rap30/74 interaction domains;"Winged helix" DNA-binding domain;Cyclin-like;Zinc beta-ribbon;TFB5-like;
reference complex	1ytb_A 5fmf_M 5fmf_U 5fmf_V 5oqj_M 7k04_5
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 5fmf_1 interface=166,473, saviggdnereeedddidavhsfeianesvevvkkrcqeidypvleeydfrndhrnpdldidlkpstqirpyqekslskmfgngrarsgiivlpcgagktlvgitaactikksvivlctssvsvmqwrqqflqwctlqpencavftsdnkemfqtesglvvstysMvantrnrshdsqkvmdfltgrewgfiildevhvvpaamfrrvvstiaahaklgltatlvreddkigdlnfligpklyeaianvqcaevwcpmtaefyqeylretarkrmllyimnptkfqacqfliqyherrgdkiivfsdnvyalqeyalkmgkpfiygstpqqermnilqnfqyndqintiflskvgdtsidlpeatcliqisshygsrrqeaqrlgrilrakrrndegfnaffyslvskdtqemyystkrqaflvdqgyafkvithlhgmenpnlayasprerrellqevlagievdadnsvgR > 5fmf_A interface=193, gqqyssaplrtvkevqfglfspeevraisvakirfpetmdetqtrakigglndprlgsidrnlkcqtcqegmnecpghfghidlakpvfhvgfiakikkvcecvcmhcgkllldehnelmrqalaikdskkrfaaiwtlcktkmvcetdvpseddptqlvsrggcgntqptirkdglklvgswkkdratgdaDepelrvlsteeilnifkhisvkdftslgfnevfsrpewmiltclpvppppvrpsisfnesqrgeddltfkladilkanisletlehngaphhaieeaesllqfhvatymdndiagqpqalqksgrpvksirarlkgkegrirgnlmgkrvdfsartvisgdpnleldqvgvpksiaktltypevvtpynidrltqlvrngpnehpgakyvirdsgdridlryskragdiqlqygwkverhimdndpvlfnrqpslhkmsmmahrvkvipystfrlnlsvtspynadfdgdemnlhvpqseetraelsqlcavplqivspqsnkpcmgivqdtlcgirkltlrdtfieldqvlnmlywvpdwdgviptpaiikpkplwsgkqilsvaipngihlqrfdegttllspkdngmliidgqiifgvvekktvgssngglihvvtrekgpqvcaklfgniqkvvnfwllhngfstgigdtiadgptmreitetiaeakkkvldvtkeaqanlltakhgmtlresfednvvrflneardkagrlaevnlkdlnnvkqmvmagskgsfiniaqmsacvgqqsvegkriafgfvdrtlphfskddyspeskgfvensylrgltpqefffhamggreglidtavktaetgyiqrrlvkaledimvhydnttrnslgnviqfiygedgmdaahiekqsldtiggsdaafekryrvdllntdhtldpsllesgseilgdlklqvlldeeykqlvkdrkflrevfvdgeanwplpvnirriiqnaqqtfhidhtkpsdltikdivlgvkdlqenllvlrgkneiiqnaqrdavtlfccllrsrlatrrvlqeyrltkqafdwvlsnieaqflrsvvhpgemvgvlaaqsigepatqmtkkvtsgvprlkeilnvaknmktpsltvylepghaadqeqaklirsaiehttlksvtiaseiyydpdprstvipedeeiiqlhfslqqspwllrleldraamndkdltmgqvgerikqtfkndlfviwsedndekliircrvvaeedhmlkkientmlenitlrgveniervvmmkydrkvpsptgeyvkepewvletdgvnlsevmtvpgidptriytnsfidimevlgieagraalykevynviasdgsyvnyrhmallvdvmttqggltsvtrhgfnrsntgalmrcsfeetveilfeagasaelddcrgvsenvilgqmapigtgafdvmideeslvkymp > 5fmf_M interface= snaeasrvyeiivesvvnevredfenagideqtlqdlkniwqkkltetkvttfswdnqfndylisedgpdenlmlclydkvtrtkarwkcslkdgvvtinrndytfqkaqveaewv > 5fmf_P interface= nlnivltcpeckvyppkiverfsegdvvcalcglvlsdklvdtrsewrtfeasnplldgnnlstrigkgettdmrftkelnkaqgknvmdkkdnevqaafakitmlcdaaelpkivkdcakeayklchdektlkgksmesimaasiligcrraevartfkeiqslihvktkefgktlnimkngflkidtdnmSrfcshlglpmqvttsaeytakkckeikeiagkspitiavvsiylnillfqipitaakvgqtlqvtegtiksgykilyehrdklvdpqliangvvsldnlp > 5fmf_Q interface=9,11,39,40,41,43,54,56,62,64,99,101,130,131,145,155, sgivptlqNiVatvtlgcrldlktvalharnaeynpkrFAAvImrirepkttaLiFasgkmVvTgakseddsklasrkyariiqkigfaakftdfkiqNiVgscdvkfpirleglafshgtfssyepelFPgliyrmvkpkivlLifvsgkivlTgakqreeiyqafeaiypvlsefrkm > 5fmf_U interface= dpneynefPlRapkedlerthllkfqskkkinpvthlpVRLhRkdtrnlqfqlAdVagnlrRkTrqlkvlenakklrfefypwvmedfdgyntwvgsyEaGnsdsyvllsveddgsftmipadkvykftARnkyatltideaekRmdkks > 5fmf_V interface=106,107,109,110,138, eesldldlersnrqvwlvrlpmflaekwrdrnnlhgqelgkirinkdgskitlllnendndsipheydleltkkvveneyvfteqnlkktaivgtvchecqvmpsSIrMPkkeildylfklfdeydywslkglkertRqpeahlkecldkvatlvkkgpyafkytlrpeykklk
interface signature	MR/D//S/NVFAAILFVTNVFPLT/PRVRLRAVRTEGARR/SIMPR

Estimated binding specificities ?

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# IC=17.966 IC/col=0.561 n_of_columns=32

specificity:

A |   0  10  69  96  96  96   0  10   7   0   0  24  24   7  96  96  24  24  24  24  24  24  24  24  24  24  24  24  24  88   0   0
C |   0  10  10   0   0   0   0   9  14   0   0  24  24  69   0   0  24  24  24  24  24  24  24  24  24  24  24  24  24   2   0   0
G |   0  10  10   0   0   0  96  67  70  96   0  24  24  10   0   0  24  24  24  24  24  24  24  24  24  24  24  24  24   4  96  96
T |  96  66   7   0   0   0   0  10   5   0  96  24  24  10   0   0  24  24  24  24  24  24  24  24  24  24  24  24  24   2   0   0

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updated Mon Jan 5 16:26:55 2026