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.

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updated Thu Jul 31 16:19:33 2025

structure name	RNA POLYMERASE II PRE-INITIATION COMPLEX WITH CLOSED PROMOTER DNA IN PROXIMAL POSITION
source	HOMO SAPIENS / SUS SCROFA
experiment	NMR
structural superfamily	Cyclin-like;Zinc beta-ribbon;Transcription factor IIA TFIIA, beta-barrel domain;Transcription factor IIA TFIIA, alpha-helical domain;TATA-box binding protein-like;Rap30/74 interaction domains;"Winged helix" DNA-binding domain;beta and beta-prime subunits of DNA dependent RNA-polymerase;Eukaryotic RPB5 N-terminal domain;RPB5-like RNA polymerase subunit;
reference complex	5iy6_M 5iy6_N 5iy6_P 5iy6_T 7nvy_B 7nvy_E
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 7nvy_7 interface=494,514, tkvdeygakdyrlqmplkddhtsrplwvapdghifleafspvykyaqdflvaiaepvcrpthvheykltayslyaavsvglqtsditeylrklsktgvpdgimqfiklctvsygkvklvlkhnryfveschpdviqhllqdpvirecrlrqtvsfevkqemieelqkrcihleypllaeydfrndsvnpdinidlkptavlrpyqekslrkmfgngrarsgvivlpcgagkslvgvtaactvrkrclvlgnsavsveqwkaqfkmwstiddsqicrftsdakdkpigcsvaistysmlghttkrsweaervmewlktqewglmildevhtipakmfrrvltivqahcklgltatlvreddkivdlnfligpklyeanwmelqnngyiakvqcaevwcpmspefyreyvaiktkkrillytmnpnkfracqflikfherrndkiivfadnvfalkeyairlnkpyiygptsqgermqilqnfkhnpkintifisKvgdtsfdlpeanvliqissHggsrrqeaqrlgrvlrakkgmvaeeynaffyslvsqdtqemaystkrqrflvdqgysfkvitklagmeeedlafstkeeqqqllqkvlaat > 7nvy_A interface= sacplrtikrvqfgvlspdelkrmsvteggikypetteggrpklgglmdprqgviertgrcqtcagnmtecpghfghielakpvfhvgflvktmkvlrcvcffcskllvdsnnpkikdilakskgqpkkrlthvydlckgkniceggcgryqprirrsglelyaewkkillspervheifkrisdeecfvlgmepryarpewmivtvlpvpplsvrpavvmqgsarnqddlthkladivkinnqlrrneqngaaahviaedvkllqfhvatmvdnelpglpramqksgrplkslkqrlkgkegrvrgnlmgkrvdfsartvitpdpnlsidqvgvprsiaanmtfaeivtpfnidrlqelvrrgnsqypgakyiirdngdridlrfhpkpsdlhlqtgykverhmcdgdivifnrqptlhkmsmmghrvrilpwstfrlnlsvttpynadfdgdemnlhlpqsletraeiqelamvprmivtpqsnrpvmgivQdtltavrkftkrdvflergEvmnllmflstwdgkvpqpailkprplwtgkqifsliipghincirthsthpddedsgpykhispgdtkvvvengelimgilckkslgtsagslvhisylemghditrlfysniqtvinnwllieghtigigdsiadsktyqdiqntikkakqdvieviekahnneleptpgntlrqtfenqvnrilndardktgssaqkslseynnfksmvvsgakgskinisqviavvgqqnvegkripfgfkhrtlphfikddygpesrgfvensylagltptefffhamggreglidtavktaetgyiqrrliksmesvmvkydatvrnsinqvvqlrygedglagesvefqnlatlkpsnkafekkfrfdytneralrrtlqedlvkdvlsnahiqnelerefermredrevlrvifptgdskvvlpcnllrmiwnaqkifhinprlpsdlhpikvvegvkelskklvivngddplsrqaqenatllfnihlrstlcsrrmaeefrlsgeafdwllgeieskfnqaiahpgemvgalaaqslgepatqmtlnknvtlgvprlkeliniskkpktpsltvfllgqsardaerakdilcrlehttlrkvtantaiyydpnpqstvvaedqewvnvyyempdfdvarispwllrveldrkhmtdrkltmeqiaekinagfgddlncifnddnaeklvlririmnsdenkmdddvflrciesnmltdmtlqgieqiskvymhlpqtdnkkkiiitedgefkalqewiletdgvslmrvlsekdvdpvrttsndiveiftvlgieavrkalerelyhvisfdgsyvnyrhlallcdtmtcrghlmaitrhgvnrqdtgplmkcsfeetvdvlmeaaahgesdpmkgvsenimlgqlapagtgcfdllldaekckygmeip > 7nvy_M interface= tcpnhpdailvedyragdmicpecglvvgdrvidvgsewrttmsssdrammnafkeittmadrinlprnivdrtnnlfkqvyeqkslkgrandaiasaclyiacrqegvprtfkeicavsriskkeigrcfklilkaletsvdlittgdfmsrfcsnlclpkqvqmaathiarkaveldlvpgrspisvaaaaiymasqasaekrtqkeigdiagvadvtirqsyrliyprapdlfptdfkfdtpvdklpql > 7nvy_O interface=9,11,39,40,54,56,62,64,99,101,130,131,145,147,153,155, sgivpqlqNiVstvnlgckldlktialrarnaeynpkrFAavimrireprttaLiFssgkmVcTgakseeqsrlaarkyarvvqklgfpakfldfkiqNmVgscdvkfpirleglvlthqqfssyepelFPgliyrmikprivlLiFvsgkvVlTgakvraeiyeafeniypilkgfrk > 7nvy_R interface=158, aergeldltgakqntgvwlvkvpkylsqqwakasgrgevgklriaktqgrtevsftlnedlanehpfvlqsvggqtltvftesssdklslegivvqraecrpaasenymrlkrlqieesskpvrlsqqldkvvttnykpvanhqynieyerkkkedgKraradkqhvldmlfsafekhqyynlkdlvditkqpvvylkeilkeigvqnvkgihkntwelkpe > 7nvy_U interface= tvpklyrsviedvindvrdiflddgvdeqvlmelktlwenklmgqveeeplnseddvsdeegqelfdtenvvvcqydkihrsknkwkfhlkdgimnlngrdyifskaigdaew