eF-site ID 5flm-ABCDEFGHIJKLNPT
PDB Code 5flm
Chain A, B, C, D, E, F, G, H, I, J, K, L, N, P, T
Title Structure of transcribing mammalian RNA polymerase II
Classification TRANSCRIPTION
Compound DNA-DIRECTED RNA POLYMERASE
Source ORGANISM_COMMON: BOVINE; ORGANISM_SCIENTIFIC: BOS TAURUS;
Sequence A:  SACPLRTIKRVQFGVLSPDELKRMSVTEGGIKYPETTEGG
RPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIEL
AKPVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDIL
AKSKGQPKKRLTHVYDLCKGKNICEHGGCGRYQPRIRRSG
LELYAEWKKILLSPERVHEIFKRISDEECFVLGMEPRYAR
PEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIV
KINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPG
LPRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSAR
TVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQE
LVRRGNSQYPGAKYIIRDNGDRIDLRFHPKPSDLHLQTGY
KVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRL
NLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRM
IVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLL
MFLSTWDGKVPQPAILKPRPLWTGKQIFSLIIPGHINCIR
THSTHPDDEDSGPYKHISPGDTKVVVENGELIMGILCKKS
LGTSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEG
HTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNE
LEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYN
NFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKH
RTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGR
EGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSIN
QVVQLRYGEDGLAGESVEFQNLATLKPSNKAFEKKFRFDY
TNERALRRTLQEDLVKDVLSNAHIQNELEREFERMREDRE
VLRVIFPTGDSKVVLPCNLLRMIWNAQKIFHINPRLPSDL
HPIKVVEGVKELSKKLVIVNGDDPLSRQAQENATLLFNIH
LRSTLCSRRMAEEFRLSGEAFDWLLGEIESKFNQAIAHPG
EMVGALAAQSLGEPATQMTLNTFHKNVTLGVPRLKELINI
SKKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVT
ANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVARISPW
LLRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDD
NAEKLVLRIRIMNSDENKMDDDVFLRCIESNMLTDMTLQG
IEQISKVYMHLPQTDNKKKIIITEDGEFKALQEWILETDG
VSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALER
ELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVN
RQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIML
GQLAPAGTGCFDLLLDAEKCKYGMEIP
B:  EITPDLWQEACWIVISSYFDEKGLVRQQLDSFDEFIQMSV
QRIVEDAPPIDLQPPRYLLKFEQIYLSKPTHWERDGAPSP
MMPNEARLRNLTYSAPLYVDITKTVIKEGEEQLQTQHQKT
FIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFII
NGSEKVLIAQEKMATNTVYVFAKKDSKYAYTGECRSCLEN
SSRPTSTIWVSMLARGGQGAKKSAIGQRIVATLPYIKQEV
PIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDE
AFVIQEQNVALNFIGSRGAKPGVTKEKRIKYAKEVLQKEM
LPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDH
YGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGK
DFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVS
QVLNRLTFASTLSHLRRLNSPIGRDGKLAKPRQLHNTLWG
MVCPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEE
WSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTL
RKLRRQMDIIVSEVSMIRDIREREIRIYTDAGRICRPLLI
VEKQKLLLKKRHIDQLKEREYNNYSWQDLVASGVVEYIDT
LEEETVMLAMTPDDLQEKEVAYCSTYTHCEIHPSMILGVC
ASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTL
AHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTG
YNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEE
VFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVII
GKTVTLPTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCK
IRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEG
ITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDAT
PFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQ
IFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSR
DGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCN
LCGIMAIANTRTHTYECRGCRNKTQISLVRMPYACKLLFQ
ELMSMSIAPRMMSV
C:  PYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAE
VPIIAIDWVQIDANSSVLHDEFIAHRLGLIPLTSDDIVDK
LQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDLI
SNSPRVIPVTSDDILIVKLRKGQELRLRAYAKKGFGKEHA
KWNPTAGVAFEYDPDNALRHTVYPKPEEWPKSEYSELDED
ESQAPYDPNGKPERFYYNVESCGSLRPETIVLSALSGLKK
KLSDLQTQLSHEIQSDV
D:  EEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAED
EQELSEVFMKTLNYTARFSRFKNRETIASVRSLLLQKKLH
KFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDD
IQTKRSFQ
E:  DDEEETYRLWKIRKTIMQLCHDRGYLVTQDGLDQTLEEFK
AQFGGKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFPEEPK
VGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDM
APKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLA
RYKLRENQLPRIQAGDPVARYFGIKRGQVVKIIRPSETAG
RYITYRLVQ
F:  QANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEG
ETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELII
TD
G:  MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTG
KYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPF
KGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFD
PNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAI
GSLMDDYLGLV
H:  AGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLIL
DVNIQIYPVDLGDKFRLVIASTLYEDGTLDDGEYNPTDDR
PSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGGL
LMRLQGDANNLHGFEVDSRVYLLMKKLA
I:  VGIRFCQECNNMLYPKEDKENRILLYACRNCDYQQEADNS
CIYVNKITHEVDELTQIIADVSQDPTLPRTEDHPCQKCGH
KEAVFFQSHSARAEDAMRLYYVCTAPHCGHRWTE
J:  MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGL
KRYCCRRMLLAHVDLIEKLLNYAPLEK
K:  MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDH
TLGNIIKSQLLKDPQVLFAGYKVPHPLEHKIIIRVQTTPD
YSPQEAFTNAITDLISELSLLEERFRVAIKDKQEG
L:  MIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVV
FDAR
N:  GGCAGTACTAGTAAAGTACTTGAGCTT
P:  CAUAAAGACCAGGC
T:  AAGCTCAAGTACTTAAGCCTGGTCATTACTAGTACTGCC
Description


Functional site

1) chain A
residue 71
type
sequence C
description BINDING SITE FOR RESIDUE ZN A 2488
source : AC1

2) chain A
residue 73
type
sequence T
description BINDING SITE FOR RESIDUE ZN A 2488
source : AC1

3) chain A
residue 74
type
sequence C
description BINDING SITE FOR RESIDUE ZN A 2488
source : AC1

4) chain A
residue 81
type
sequence C
description BINDING SITE FOR RESIDUE ZN A 2488
source : AC1

5) chain A
residue 84
type
sequence H
description BINDING SITE FOR RESIDUE ZN A 2488
source : AC1

6) chain A
residue 111
type
sequence C
description BINDING SITE FOR RESIDUE ZN A 2489
source : AC2

7) chain A
residue 114
type
sequence C
description BINDING SITE FOR RESIDUE ZN A 2489
source : AC2

8) chain A
residue 154
type
sequence C
description BINDING SITE FOR RESIDUE ZN A 2489
source : AC2

9) chain A
residue 183
type
sequence G
description BINDING SITE FOR RESIDUE ZN A 2489
source : AC2

10) chain A
residue 184
type
sequence C
description BINDING SITE FOR RESIDUE ZN A 2489
source : AC2

11) chain A
residue 495
type
sequence D
description BINDING SITE FOR RESIDUE MG A 2490
source : AC3

12) chain A
residue 497
type
sequence D
description BINDING SITE FOR RESIDUE MG A 2490
source : AC3

13) chain A
residue 499
type
sequence D
description BINDING SITE FOR RESIDUE MG A 2490
source : AC3

14) chain P
residue 20
type
sequence C
description BINDING SITE FOR RESIDUE MG A 2490
source : AC3

15) chain B
residue 1119
type
sequence C
description BINDING SITE FOR RESIDUE ZN B 2175
source : AC4

16) chain B
residue 1122
type
sequence C
description BINDING SITE FOR RESIDUE ZN B 2175
source : AC4

17) chain B
residue 1137
type
sequence C
description BINDING SITE FOR RESIDUE ZN B 2175
source : AC4

18) chain B
residue 1140
type
sequence C
description BINDING SITE FOR RESIDUE ZN B 2175
source : AC4

19) chain C
residue 88
type
sequence C
description BINDING SITE FOR RESIDUE ZN C 1272
source : AC5

20) chain C
residue 90
type
sequence C
description BINDING SITE FOR RESIDUE ZN C 1272
source : AC5

21) chain C
residue 94
type
sequence C
description BINDING SITE FOR RESIDUE ZN C 1272
source : AC5

22) chain C
residue 97
type
sequence C
description BINDING SITE FOR RESIDUE ZN C 1272
source : AC5

23) chain I
residue 17
type
sequence C
description BINDING SITE FOR RESIDUE ZN I 1126
source : AC6

24) chain I
residue 20
type
sequence C
description BINDING SITE FOR RESIDUE ZN I 1126
source : AC6

25) chain I
residue 39
type
sequence C
description BINDING SITE FOR RESIDUE ZN I 1126
source : AC6

26) chain I
residue 42
type
sequence C
description BINDING SITE FOR RESIDUE ZN I 1126
source : AC6

27) chain I
residue 86
type
sequence C
description BINDING SITE FOR RESIDUE ZN I 1127
source : AC7

28) chain I
residue 89
type
sequence C
description BINDING SITE FOR RESIDUE ZN I 1127
source : AC7

29) chain I
residue 114
type
sequence C
description BINDING SITE FOR RESIDUE ZN I 1127
source : AC7

30) chain I
residue 119
type
sequence C
description BINDING SITE FOR RESIDUE ZN I 1127
source : AC7

31) chain J
residue 7
type
sequence C
description BINDING SITE FOR RESIDUE ZN J 1068
source : AC8

32) chain J
residue 10
type
sequence C
description BINDING SITE FOR RESIDUE ZN J 1068
source : AC8

33) chain J
residue 44
type
sequence C
description BINDING SITE FOR RESIDUE ZN J 1068
source : AC8

34) chain J
residue 45
type
sequence C
description BINDING SITE FOR RESIDUE ZN J 1068
source : AC8

35) chain L
residue 19
type
sequence C
description BINDING SITE FOR RESIDUE ZN L 1059
source : AC9

36) chain L
residue 22
type
sequence C
description BINDING SITE FOR RESIDUE ZN L 1059
source : AC9

37) chain L
residue 24
type
sequence T
description BINDING SITE FOR RESIDUE ZN L 1059
source : AC9

38) chain L
residue 36
type
sequence C
description BINDING SITE FOR RESIDUE ZN L 1059
source : AC9

39) chain L
residue 39
type
sequence C
description BINDING SITE FOR RESIDUE ZN L 1059
source : AC9

40) chain I
residue 112-118
type prosite
sequence YVCTAPH
description IG_MHC Immunoglobulins and major histocompatibility complex proteins signature. YVCTAPH
source prosite : PS00290

41) chain C
residue 32-72
type prosite
sequence NSIRRVFIAEVPIIAIDWVQIDANSSVLHDEFIAHRLGLI
P
description RNA_POL_D_30KD RNA polymerases D / 30 to 40 Kd subunits signature. NSIRRvfiaevpiiAidwVqidaNsSvlhDEfIAhRLGLIP
source prosite : PS00446

42) chain I
residue 86-123
type prosite
sequence CQKCGHKEAVFFQSHSARAEDAMRLYYVCTAPHCGHRW
description ZF_TFIIS_1 Zinc finger TFIIS-type signature. CqkCghkeavffqSHSARaEDAmrlyyvCtaph.CghrW
source prosite : PS00466

43) chain I
residue 16-42
type prosite
sequence FCQECNNMLYPKEDKENRILLYACRNC
description RNA_POL_M_15KD RNA polymerases M / 15 Kd subunits signature. FCQECNNMLypkedkenrillyaCrnC
source prosite : PS01030

44) chain E
residue 142-155
type prosite
sequence HELVPEHVVMTKEE
description RNA_POL_H_23KD RNA polymerases H / 23 Kd subunits signature. HELVPEHvvMtkEE
source prosite : PS01110

45) chain F
residue 58-72
type prosite
sequence TKYERARVLGTRALQ
description RNA_POL_K_14KD RNA polymerases K / 14 to 18 Kd subunits signature. TkYErARvLGtRAlQ
source prosite : PS01111

46) chain J
residue 2-11
type prosite
sequence IIPVRCFTCG
description RNA_POL_N_8KD RNA polymerases N / 8 Kd subunits signature. IIPVrCFTCG
source prosite : PS01112

47) chain K
residue 35-66
type prosite
sequence INKEDHTLGNIIKSQLLKDPQVLFAGYKVPHP
description RNA_POL_L_13KD RNA polymerases L / 13 to 16 Kd subunits signature. InkEdHTLgNiIksqLlkdpqVlfagYkvpHP
source prosite : PS01154

48) chain B
residue 932-944
type prosite
sequence GDKFASRHGQKGT
description RNA_POL_BETA RNA polymerases beta chain signature. GdKFASrHGQKGT
source prosite : PS01166

49) chain A
residue 154
type MOD_RES
sequence C
description Phosphoserine; by CK2 => ECO:0000250|UniProtKB:O88828
source Swiss-Prot : SWS_FT_FI1

50) chain A
residue 1421
type MOD_RES
sequence R
description Phosphoserine; by CK2 => ECO:0000250|UniProtKB:O88828
source Swiss-Prot : SWS_FT_FI1

51) chain J
residue 45
type MOD_RES
sequence C
description Phosphoserine; by CK2 => ECO:0000250|UniProtKB:O88828
source Swiss-Prot : SWS_FT_FI1

52) chain A
residue 71
type BINDING
sequence C
description BINDING => ECO:0000269|PubMed:26789250, ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5FLM, ECO:0007744|PDB:5OIK
source Swiss-Prot : SWS_FT_FI2

53) chain A
residue 499
type BINDING
sequence D
description BINDING => ECO:0000269|PubMed:26789250, ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5FLM, ECO:0007744|PDB:5OIK
source Swiss-Prot : SWS_FT_FI2

54) chain A
residue 1416
type BINDING
sequence R
description BINDING => ECO:0000269|PubMed:26789250, ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5FLM, ECO:0007744|PDB:5OIK
source Swiss-Prot : SWS_FT_FI2

55) chain A
residue 74
type BINDING
sequence C
description BINDING => ECO:0000269|PubMed:26789250, ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5FLM, ECO:0007744|PDB:5OIK
source Swiss-Prot : SWS_FT_FI2

56) chain A
residue 81
type BINDING
sequence C
description BINDING => ECO:0000269|PubMed:26789250, ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5FLM, ECO:0007744|PDB:5OIK
source Swiss-Prot : SWS_FT_FI2

57) chain A
residue 84
type BINDING
sequence H
description BINDING => ECO:0000269|PubMed:26789250, ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5FLM, ECO:0007744|PDB:5OIK
source Swiss-Prot : SWS_FT_FI2

58) chain A
residue 111
type BINDING
sequence C
description BINDING => ECO:0000269|PubMed:26789250, ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5FLM, ECO:0007744|PDB:5OIK
source Swiss-Prot : SWS_FT_FI2

59) chain A
residue 114
type BINDING
sequence C
description BINDING => ECO:0000269|PubMed:26789250, ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5FLM, ECO:0007744|PDB:5OIK
source Swiss-Prot : SWS_FT_FI2

60) chain A
residue 184
type BINDING
sequence C
description BINDING => ECO:0000269|PubMed:26789250, ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5FLM, ECO:0007744|PDB:5OIK
source Swiss-Prot : SWS_FT_FI2

61) chain A
residue 346
type BINDING
sequence K
description BINDING => ECO:0000269|PubMed:26789250, ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5FLM, ECO:0007744|PDB:5OIK
source Swiss-Prot : SWS_FT_FI2

62) chain A
residue 460
type BINDING
sequence R
description BINDING => ECO:0000269|PubMed:26789250, ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5FLM, ECO:0007744|PDB:5OIK
source Swiss-Prot : SWS_FT_FI2

63) chain A
residue 358
type BINDING
sequence R
description BINDING => ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5OIK
source Swiss-Prot : SWS_FT_FI3

64) chain I
residue 20
type BINDING
sequence C
description BINDING => ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5OIK
source Swiss-Prot : SWS_FT_FI3

65) chain I
residue 39
type BINDING
sequence C
description BINDING => ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5OIK
source Swiss-Prot : SWS_FT_FI3

66) chain I
residue 42
type BINDING
sequence C
description BINDING => ECO:0000269|PubMed:28892040, ECO:0007744|PDB:5OIK
source Swiss-Prot : SWS_FT_FI3

67) chain A
residue 493
type BINDING
sequence N
description BINDING => ECO:0000250|UniProtKB:P24928
source Swiss-Prot : SWS_FT_FI4

68) chain A
residue 495
type BINDING
sequence D
description BINDING => ECO:0000250|UniProtKB:P24928
source Swiss-Prot : SWS_FT_FI4

69) chain I
residue 119
type BINDING
sequence C
description BINDING => ECO:0000250|UniProtKB:P24928
source Swiss-Prot : SWS_FT_FI4

70) chain B
residue 1085
type BINDING
sequence R
description BINDING => ECO:0000250|UniProtKB:P24928
source Swiss-Prot : SWS_FT_FI4

71) chain B
residue 1119
type BINDING
sequence C
description BINDING => ECO:0000250|UniProtKB:P24928
source Swiss-Prot : SWS_FT_FI4

72) chain B
residue 1122
type BINDING
sequence C
description BINDING => ECO:0000250|UniProtKB:P24928
source Swiss-Prot : SWS_FT_FI4

73) chain B
residue 1137
type BINDING
sequence C
description BINDING => ECO:0000250|UniProtKB:P24928
source Swiss-Prot : SWS_FT_FI4

74) chain B
residue 1140
type BINDING
sequence C
description BINDING => ECO:0000250|UniProtKB:P24928
source Swiss-Prot : SWS_FT_FI4

75) chain A
residue 497
type BINDING
sequence D
description BINDING => ECO:0000250|UniProtKB:P04050
source Swiss-Prot : SWS_FT_FI5

76) chain A
residue 27
type MOD_RES
sequence S
description Phosphoserine => ECO:0000250|UniProtKB:P24928
source Swiss-Prot : SWS_FT_FI7

77) chain A
residue 217
type MOD_RES
sequence S
description Phosphoserine => ECO:0000250|UniProtKB:P24928
source Swiss-Prot : SWS_FT_FI7


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