eF-site ID 4q5s-ABCDEFGHI
PDB Code 4q5s
Chain A, B, C, D, E, F, G, H, I
Title Thermus thermophilus RNA polymerase initially transcribing complex containing 6-mer RNA
Classification transcription/DNA/rna
Compound DNA-directed RNA polymerase subunit alpha
Source ORGANISM_SCIENTIFIC: Thermus thermophilus;
Sequence A:  SKLKAPVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRI
LLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLK
ELVVRFLNPSLQTVTLLLKAEGPKEVKARDFLPVADVEIM
NPDLHIATLEEGGRLNMEVRVDRGVGYVPAEKHGIKDRIN
AIPVDAVFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDG
SVTPLEALNQAVEILREHLTYFSNPQ
B:  KAPVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRILLS
SIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKELV
VRFLNPSLQTVTLLLKAEGPKEVKARDFLPVADVEIMNPD
LHIATLEEGGRLNMEVRVDRGVGYVPAEKHGIKDRINAIP
VDAVFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVT
PLEALNQAVEILREHLTYFSNP
C:  MEIKRFGRIREVIPLPPLTEIQVESYRRALQADVPPEKRE
NVGIQAAFRETFPIEELVLDFLEYRLGEPPFPQDECREKD
LTYQAPLYARLQLIHKDTGLIKEDEVFLGHIPLMTEDGSF
IINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLPK
RGPWIDLEVEPNGVVSMKVNKRKFPLVLLLRVLGYDQETL
ARELGAYGELVQGLMDESVFAMRPEEALIRLFTLLRPGDP
PKRDKAVAYVYGLIADPRRYDLGEAGRYKAEEKLGIRLSG
RTLARFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDH
LGNRRIRTVGELMTDQFRVGLARLARGVRERMLMGSEDSL
TPAKLVNSRPLEAAIREFFSRSQLSQFKDETNPLSSLRHK
RRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGA
NIGLITSLAAYARVDELGFIRTPYRRVVGGVVTDEVVYMT
ATEEDRYTIAQANTPLEGNRIAAERVVARRKGEPVIVSPE
EVEFMDVSPKQVFSVNTNLIPFLEHDDANRALMGSNMQTQ
AVPLIRAQAPVVMTGLEERVVRDSLAALYAEEDGEVAKVD
GNRIVVRYEDGRLVEYPLRRFYRSNQGTALDQRPRVVVGQ
RVRKGDLLADGPASENGFLALGQNVLVAIMPFDGYNFEDA
IVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRDIP
HLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEP
TPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLR
RGDPGVELKPGVREVVRVYVAQKRKLQVGDKLANRHGNKG
VVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILE
THLGLAGYFLGQRYISPIFDGAKEPEIKELLAQAFEVYFG
KRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPEEQLKELF
LQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHA
RSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAH
TLQEMLTLKSDDIEGRNAAYEAIIKGEDVPEPSVPESFRV
LVKELQALALDVQTLDEKDNPVDIFEGLASK
D:  EVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDG
LFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVTKS
IVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATEL
EQVLYFSKYIVLDPKGAILNGVPVEKRQLLTDEEYRELRY
GKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDGVA
LYRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGEILA
ELPEPYLFRAEEEGVVELKELEEGAFLVLRREDEPVATYF
LPVGMTPLVVHGEIVEKGQPLAEAKGLLRMPRQVRAAQVE
AEEEGETVYLTLFLEWTEPKDYRVQPHMNVVVPEGARVEA
GDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYPF
EDDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEVDLVRNV
VRVVESYDIDARMGAEAIQQLLKELDLEALEKELLEEMKH
PSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPD
LRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAP
EIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRSL
TDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCG
LPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQRDI
KDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEG
QSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQM
LSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAG
LEFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYVF
ANPDEALLAVAHGIVDLQDVVTVRYMGKRLETSPGRILFA
RIVAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFLRLG
MEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKKQY
LEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEKV
TQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRG
LMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGAD
TALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISVPLF
QPDEVTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLEEG
RYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQK
CYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMQGLPR
VIELFEARRPKAKAVISEIDGVVRIEETEEKLSVFVESEG
FSKEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPHQLLEA
KGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKY
VEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAWK
PLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDE
LIGLKENVILGRLIPAGTGSDFVRFTQVVDQKTLKAIEEA
RKEA
E:  AEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFKNTVLE
PEERPKMQTLEGLFDDPNAVTWAMKELLTGRLVFGENLVP
EDRLQKEMERLYPV
F:  SDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLS
EITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTVE
EIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVS
IAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFST
YATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQ
LQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSL
ETPFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSER
EAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKA
LRKLKYHESRTRKLRDFL
G:  TGCATCCGTGAGTG
H:  TATAATGGGGGATGCA
I:  CUCAC
Description


Functional site

1) chain D
residue 739
type
sequence D
description BINDING SITE FOR RESIDUE MG D 2001
source : AC1

2) chain D
residue 741
type
sequence D
description BINDING SITE FOR RESIDUE MG D 2001
source : AC1

3) chain D
residue 743
type
sequence D
description BINDING SITE FOR RESIDUE MG D 2001
source : AC1

4) chain I
residue 5
type
sequence A
description BINDING SITE FOR RESIDUE MG D 2001
source : AC1

5) chain I
residue 6
type
sequence C
description BINDING SITE FOR RESIDUE MG D 2001
source : AC1

6) chain D
residue 58
type
sequence C
description BINDING SITE FOR RESIDUE ZN D 2002
source : AC2

7) chain D
residue 60
type
sequence C
description BINDING SITE FOR RESIDUE ZN D 2002
source : AC2

8) chain D
residue 73
type
sequence C
description BINDING SITE FOR RESIDUE ZN D 2002
source : AC2

9) chain D
residue 76
type
sequence C
description BINDING SITE FOR RESIDUE ZN D 2002
source : AC2

10) chain D
residue 1112
type
sequence C
description BINDING SITE FOR RESIDUE ZN D 2003
source : AC3

11) chain D
residue 1194
type
sequence C
description BINDING SITE FOR RESIDUE ZN D 2003
source : AC3

12) chain D
residue 1201
type
sequence C
description BINDING SITE FOR RESIDUE ZN D 2003
source : AC3

13) chain D
residue 1204
type
sequence C
description BINDING SITE FOR RESIDUE ZN D 2003
source : AC3

14) chain C
residue 390
type
sequence Q
description BINDING SITE FOR RESIDUE ATP I 101
source : AC4

15) chain C
residue 420
type
sequence R
description BINDING SITE FOR RESIDUE ATP I 101
source : AC4

16) chain G
residue 14
type
sequence G
description BINDING SITE FOR RESIDUE ATP I 101
source : AC4

17) chain G
residue 15
type
sequence T
description BINDING SITE FOR RESIDUE ATP I 101
source : AC4

18) chain I
residue 2
type
sequence C
description BINDING SITE FOR RESIDUE ATP I 101
source : AC4

19) chain F
residue 382-408
type prosite
sequence TLEEVGAFFGVTRERIRQIENKALRKL
description SIGMA70_2 Sigma-70 factors family signature 2. TleEVGaffgVTrerIrQIEnkaLrkL
source prosite : PS00716

20) chain F
residue 187-194
type prosite
sequence LIEANLRL
description CPSASE_2 Carbamoyl-phosphate synthase subdomain signature 2. LIEANLRL
source prosite : PS00867

21) chain C
residue 836-848
type prosite
sequence GDKLANRHGNKGV
description RNA_POL_BETA RNA polymerases beta chain signature. GdKLANrHGNKGV
source prosite : PS01166

22) chain D
residue 58
type BINDING
sequence C
description BINDING => ECO:0000255|HAMAP-Rule:MF_01322
source Swiss-Prot : SWS_FT_FI1

23) chain D
residue 1201
type BINDING
sequence C
description BINDING => ECO:0000255|HAMAP-Rule:MF_01322
source Swiss-Prot : SWS_FT_FI1

24) chain D
residue 1204
type BINDING
sequence C
description BINDING => ECO:0000255|HAMAP-Rule:MF_01322
source Swiss-Prot : SWS_FT_FI1

25) chain D
residue 60
type BINDING
sequence C
description BINDING => ECO:0000255|HAMAP-Rule:MF_01322
source Swiss-Prot : SWS_FT_FI1

26) chain D
residue 73
type BINDING
sequence C
description BINDING => ECO:0000255|HAMAP-Rule:MF_01322
source Swiss-Prot : SWS_FT_FI1

27) chain D
residue 76
type BINDING
sequence C
description BINDING => ECO:0000255|HAMAP-Rule:MF_01322
source Swiss-Prot : SWS_FT_FI1

28) chain D
residue 739
type BINDING
sequence D
description BINDING => ECO:0000255|HAMAP-Rule:MF_01322
source Swiss-Prot : SWS_FT_FI1

29) chain D
residue 741
type BINDING
sequence D
description BINDING => ECO:0000255|HAMAP-Rule:MF_01322
source Swiss-Prot : SWS_FT_FI1

30) chain D
residue 743
type BINDING
sequence D
description BINDING => ECO:0000255|HAMAP-Rule:MF_01322
source Swiss-Prot : SWS_FT_FI1

31) chain D
residue 1112
type BINDING
sequence C
description BINDING => ECO:0000255|HAMAP-Rule:MF_01322
source Swiss-Prot : SWS_FT_FI1

32) chain D
residue 1194
type BINDING
sequence C
description BINDING => ECO:0000255|HAMAP-Rule:MF_01322
source Swiss-Prot : SWS_FT_FI1


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