eF-site ID 4mq9-ABCDEF
PDB Code 4mq9
Chain A, B, C, D, E, F

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Title Crystal structure of Thermus thermophilus RNA polymerase holoenzyme in complex with GE23077
Classification TRANSCRIPTION, TRANSFERASE/ANTIBIOTIC
Compound DNA-directed RNA polymerase subunit alpha
Source ORGANISM_SCIENTIFIC: Thermus thermophilus;
Sequence A:  LKAPVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRILL
SSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKEL
VVRFLNPSLQTVTLLLKAEGPKEVKARDFLPVADVEIMNP
DLHIATLEEGGRLNMEVRVDRGVGYVPAEKHGIKDRINAI
PVDAVFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSV
TPLEALNQAVEILREHLTYFSNPQAA
B:  KAPVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRILLS
SIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKELV
VRFLNPSLQTVTLLLKAEGPKEVKARDFLPVADVEIMNPD
LHIATLEEGGRLNMEVRVDRGVGYVPAERINAIPVDAVFS
PVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALN
QAVEILREHLTYFSNPQAAAVAAP
C:  MEIKRFGRIREVIPLPPLTEIQVESYRRALQADVPPEKRE
NVGIQAAFRETFPILDFLEYRLGEPPFPQDECREKDLTYQ
APLYARLQLIHKDTGLIKEDEVFLGHIPLMTEDGSFIING
ADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLPKRGPW
IDLEVEPNGVVSMKVNKRKFPLVLLLRVLGYDQETLAREL
GAYGELVQGLMDESVFAMRPEEALIRLFTLLRPGDPPKRD
KAVAYVYGLIADPRRYDLGEAGRYKAEEKLGIRLSGRTLA
DEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGEL
MTDQFRVGLARLARGVRERMLMGSEDSLTPAKLVNSRPLE
AAIREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLT
RERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYA
RVDELGFIRTPYRRVVGGVVTDEVVYMTATEEDRYTIAQA
NTPLEGNRIAAERVVARRKGEPVIVSPEEVEFMDVSPKQV
FSVNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVV
MTGLEERVVRDSLAALYAEEDGEVAKVDGNRIVVRYEDGR
LVEYPLRRFYRSNQGTALDQRPRVVVGQRVRKGDLLADGP
ASENGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDF
YTSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDE
EGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRSIFG
EKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGV
REVVRVYVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMP
HLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQ
RYISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKR
EVEVLRRAEKLGLVTPGKTPEEQLKELFLQGKVVLYDGRT
GEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQ
PLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLKSDD
IEGRNAAYEAIIKGEDVPEPSVPESFRVLVKELQALALDV
QTLDEKDNPVDIFEGLASKR
D:  KKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPER
DGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVT
KSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSAT
ELEQVLYFSKYIVLDPKGAILNGVPVEKRQLLTDEEYREL
RYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDG
VALYRFPRRVRVEYWTEPKDYRVQPHMNVVVPEGARVEAG
DKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYPFE
DDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEVDLVRNVV
RVVESYDIDARMGAEAIQQLLKELDLEALEKELLEEMKHP
SRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDL
RPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPE
IIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRSLT
DILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGL
PKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQRDIK
DEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQ
SIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQML
SAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGL
EFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYVFA
NPDEALLAVAHGIVDLQDVVTVRYMGKRLETSPGRILFAR
IVAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFLRLGM
EKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKKQYL
EEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEKVT
QAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGL
MQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADT
ALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISVPLFQ
PDEVTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLEEGR
YLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQKC
YGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTDITQ
GLPRVIELFEARRPKAKAVISEIDGVVRIEETEEKLSVFV
ESEGFSKEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPHQ
LLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQ
MMKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTP
VAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAG
KKDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQKTLKA
IEEAR
E:  AEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFKNTVLE
PEERPKMQTLEGLFDDPNAVTWAMKELLTGRLVFGENLVP
EDRLQKEMERLYP
F:  SDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLS
EITGLDPDLIREVVRAKILGSARVRHTLDPKTVEEIDQKL
KSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYT
GRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWI
RQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELG
REPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGD
EKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSE
REAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENK
ALRKLKYHESRTRKLRDFL
Description


Functional site

1) chain D
residue 58
type
sequence C
description BINDING SITE FOR RESIDUE ZN D 1601
source : AC1

2) chain D
residue 60
type
sequence C
description BINDING SITE FOR RESIDUE ZN D 1601
source : AC1

3) chain D
residue 73
type
sequence C
description BINDING SITE FOR RESIDUE ZN D 1601
source : AC1

4) chain D
residue 76
type
sequence C
description BINDING SITE FOR RESIDUE ZN D 1601
source : AC1

5) chain D
residue 1112
type
sequence C
description BINDING SITE FOR RESIDUE ZN D 1602
source : AC2

6) chain D
residue 1194
type
sequence C
description BINDING SITE FOR RESIDUE ZN D 1602
source : AC2

7) chain D
residue 1201
type
sequence C
description BINDING SITE FOR RESIDUE ZN D 1602
source : AC2

8) chain D
residue 1204
type
sequence C
description BINDING SITE FOR RESIDUE ZN D 1602
source : AC2

9) chain D
residue 739
type
sequence D
description BINDING SITE FOR RESIDUE MG D 1603
source : AC3

10) chain D
residue 741
type
sequence D
description BINDING SITE FOR RESIDUE MG D 1603
source : AC3

11) chain D
residue 743
type
sequence D
description BINDING SITE FOR RESIDUE MG D 1603
source : AC3

12) chain C
residue 444
type
sequence P
description BINDING SITE FOR CHAIN I OF GE23077
source : AC4

13) chain C
residue 445
type
sequence E
description BINDING SITE FOR CHAIN I OF GE23077
source : AC4

14) chain C
residue 446
type
sequence G
description BINDING SITE FOR CHAIN I OF GE23077
source : AC4

15) chain C
residue 448
type
sequence N
description BINDING SITE FOR CHAIN I OF GE23077
source : AC4

16) chain C
residue 557
type
sequence R
description BINDING SITE FOR CHAIN I OF GE23077
source : AC4

17) chain C
residue 560
type
sequence M
description BINDING SITE FOR CHAIN I OF GE23077
source : AC4

18) chain C
residue 563
type
sequence N
description BINDING SITE FOR CHAIN I OF GE23077
source : AC4

19) chain C
residue 567
type
sequence Q
description BINDING SITE FOR CHAIN I OF GE23077
source : AC4

20) chain C
residue 838
type
sequence K
description BINDING SITE FOR CHAIN I OF GE23077
source : AC4

21) chain C
residue 846
type
sequence K
description BINDING SITE FOR CHAIN I OF GE23077
source : AC4

22) chain D
residue 1088
type
sequence T
description BINDING SITE FOR CHAIN I OF GE23077
source : AC4

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

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

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

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

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

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

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

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

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

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

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

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

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

36) 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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