eF-site ID 4oiq-ABCDEF PDB Code 4oiq Chain A, B, C, D, E, F Title Crystal structure of Thermus thermophilus transcription initiation complex soaked with GE23077 and rifampicin Classification TRANSCRIPTION, TRANSFERASE/ANTIBIOTIC Compound DNA-directed RNA polymerase subunit alpha Source ORGANISM_SCIENTIFIC: Thermus thermophilus; Sequence A:  SKLKAPVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRI LLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLK ELVVRFLNPSLQTVTLLLKAEGPKEVKARDFLPVADVEIM NPDLHIATLEEGGRLNMEVRVDRGVGYVPAEKHGIKDRIN AIPVDAVFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDG SVTPLEALNQAVEILREHLTYFSNPQAAAVA B:  APVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRILLSS IPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKELVV RFLNPSLQTVTLLLKAEGPKEVKARDFLPVADVEIMNPDL HIATLEEGGRLNMEVRVDRGVGYVPAEKHGIKDRINAIPV DAVFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTP LEALNQAVEILREHLTYFSNP C:  MEIKRFGRIREVIPLPPLTEIQVESYRRALQADVPPEKRE NVGIQAAFRETFPIEEGLVLDFLEYRLGEPPFPQDECREK DLTYQAPLYARLQLIHKDTGLIKEDEVFLGHIPLMTEDGS FIINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLP KRGPWIDLEVEPNGVVSMKVNKRKFPLVLLLRVLGYDQET LARELGAYGELVQGLMDESVFAMRPEEALIRLFTLLRPGD PPKRDKAVAYVYGLIADPRRYDLGEAGRYKAEEKLGIRLS GRTLARFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDID HLGNRRIRTVGELMTDQFRVGLARLARGVRERMLMGSEDS LTPAKLVNSRPLEAAIREFFSRSQLSQFKDETNPLSSLRH KRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEG ANIGLITSLAAYARVDELGFIRTPYRRVVGGVVTDEVVYM TATEEDRYTIAQANTPLEGNRIAAERVVARRKGEPVIVSP EEVEFMDVSPKQVFSVNTNLIPFLEHDDANRALMGSNMQT QAVPLIRAQAPVVMTGLEERVVRDSLAALYAEEDGEVAKV DGNRIVVRYEDGRLVEYPLRRFYRSNQGTALDQRPRVVVG QRVRKGDLLADGPASENGFLALGQNVLVAIMPFDGYNFED AIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRDI PHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESE PTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRL RRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLANRHGNK GVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQIL ETHLGLAGYFLGQRYISPIFDGAKEPEIKELLAQAFEVYF GKRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPEEQLKEL FLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMH ARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAA HTLQEMLTLKSDDIEGRNAAYEAIIKGEDVPEPSVPESFR VLVKELQALALDVQTLDEKDNPVDIFEGLASK D:  KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERD GLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVTK SIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATE LEQVLYFSKYIVLDPKGAILNGVPVEKRQLLTDEEYRELR YGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDGV ALYRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGEIL AELPEPYLFRAEEEGVVELKELEEGAFLVLRREDEPVATY FLPVGMTPLVVHGEIVEKGQPLAEAKGLLRMPRQVRAAQV EAEEEGETVYLTLFLEWTEPKDYRVQPHMNVVVPEGARVE AGDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYP FEDDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEVDLVRN VVRVVESYDIDARMGAEAIQQLLKELDLEALEKELLEEMK HPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPP DLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGA PEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRS LTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQC GLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQRD IKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVE GQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQ MLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGA GLEFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYV FANPDEALLAVAHGIVDLQDVVTVRYMGKRLETSPGRILF ARIVAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFLRL GMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKKQ YLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEK VTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLR GLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGA DTALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISVPL FQPDEVTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLEE GRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQ KCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMITQG LPRVIELFEARRPKAKAVISEIDGVVRIEETEEKLSVFVE SEGFSKEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPHQL LEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQM MKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPV AWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGK KDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQKTLKAI EEARKEA E:  AEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFKNTVLE PEERPKMQTLEGLFDDPNAVTWAMKELLTGRLVFGENLVP EDRLQKEMERLYPV F:  SDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLS EITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTVE EIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVS IAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFST YATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQ LQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSL ETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKA LSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERI RQIENKALRKLKYHESRTRKLRDFLD Description Functional site 1) chain D residue 1112 type sequence C description BINDING SITE FOR RESIDUE ZN D 2001 source : AC1 2) chain D residue 1194 type sequence C description BINDING SITE FOR RESIDUE ZN D 2001 source : AC1 3) chain D residue 1201 type sequence C description BINDING SITE FOR RESIDUE ZN D 2001 source : AC1 4) chain D residue 1204 type sequence C description BINDING SITE FOR RESIDUE ZN D 2001 source : AC1 5) chain D residue 58 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : AC2 6) chain D residue 60 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : AC2 7) chain D residue 73 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : AC2 8) chain D residue 76 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : AC2 9) chain D residue 739 type sequence D description BINDING SITE FOR RESIDUE MG D 2003 source : AC3 10) chain D residue 741 type sequence D description BINDING SITE FOR RESIDUE MG D 2003 source : AC3 11) chain D residue 743 type sequence D description BINDING SITE FOR RESIDUE MG D 2003 source : AC3 12) chain B residue 154 type sequence E description BINDING SITE FOR RESIDUE MG D 2004 source : AC4 13) chain B residue 168 type sequence D description BINDING SITE FOR RESIDUE MG D 2004 source : AC4 14) chain D residue 840 type sequence K description BINDING SITE FOR RESIDUE MG D 2004 source : AC4 15) chain D residue 897 type sequence W description BINDING SITE FOR RESIDUE MG D 2005 source : AC5 16) chain D residue 900 type sequence I description BINDING SITE FOR RESIDUE MG D 2005 source : AC5 17) chain F residue 292 type sequence A description BINDING SITE FOR RESIDUE MG F 2001 source : AC6 18) chain F residue 293 type sequence E description BINDING SITE FOR RESIDUE MG F 2001 source : AC6 19) chain F residue 296 type sequence G description BINDING SITE FOR RESIDUE MG F 2001 source : AC6 20) chain F residue 299 type sequence W description BINDING SITE FOR RESIDUE MG F 2001 source : AC6 21) chain C residue 8 type sequence R description BINDING SITE FOR GE23077 source : AC7 22) chain C residue 9 type sequence I description BINDING SITE FOR GE23077 source : AC7 23) chain C residue 445 type sequence E description BINDING SITE FOR GE23077 source : AC7 24) chain C residue 446 type sequence G description BINDING SITE FOR GE23077 source : AC7 25) chain C residue 557 type sequence R description BINDING SITE FOR GE23077 source : AC7 26) chain C residue 560 type sequence M description BINDING SITE FOR GE23077 source : AC7 27) chain C residue 563 type sequence N description BINDING SITE FOR GE23077 source : AC7 28) chain C residue 567 type sequence Q description BINDING SITE FOR GE23077 source : AC7 29) chain C residue 838 type sequence K description BINDING SITE FOR GE23077 source : AC7 30) chain C residue 846 type sequence K description BINDING SITE FOR GE23077 source : AC7 31) chain C residue 898 type sequence G description BINDING SITE FOR GE23077 source : AC7 32) chain C residue 899 type sequence Q description BINDING SITE FOR GE23077 source : AC7 33) chain C residue 900 type sequence R description BINDING SITE FOR GE23077 source : AC7 34) chain C residue 901 type sequence Y description BINDING SITE FOR GE23077 source : AC7 35) chain C residue 902 type sequence I description BINDING SITE FOR GE23077 source : AC7 36) chain C residue 904 type sequence P description BINDING SITE FOR GE23077 source : AC7 37) chain C residue 907 type sequence D description BINDING SITE FOR GE23077 source : AC7 38) chain C residue 908 type sequence G description BINDING SITE FOR GE23077 source : AC7 39) chain C residue 909 type sequence A description BINDING SITE FOR GE23077 source : AC7 40) chain C residue 917 type sequence L description BINDING SITE FOR GE23077 source : AC7 41) chain D residue 741 type sequence D description BINDING SITE FOR GE23077 source : AC7 42) chain D residue 1201 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 43) chain D residue 1204 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 44) chain D residue 739 type BINDING sequence D description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 45) chain D residue 741 type BINDING sequence D description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 46) chain D residue 743 type BINDING sequence D description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 47) chain D residue 1112 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 48) chain D residue 1194 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 49) chain D residue 76 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 50) chain D residue 58 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 51) chain D residue 60 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 52) chain D residue 73 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 53) chain C residue 836-848 type prosite sequence GDKLANRHGNKGV description RNA_POL_BETA RNA polymerases beta chain signature. GdKLANrHGNKGV source prosite : PS01166 54) chain F residue 382-408 type prosite sequence TLEEVGAFFGVTRERIRQIENKALRKL description SIGMA70_2 Sigma-70 factors family signature 2. TleEVGaffgVTrerIrQIEnkaLrkL source prosite : PS00716 55) chain F residue 187-194 type prosite sequence LIEANLRL description CPSASE_2 Carbamoyl-phosphate synthase subdomain signature 2. LIEANLRL source prosite : PS00867

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