eF-site ID 1k83-ABCEFHIJKL
PDB Code 1k83
Chain A, B, C, E, F, H, I, J, K, L
Title Crystal Structure of Yeast RNA Polymerase II Complexed with the Inhibitor Alpha Amanitin
Classification TRANSCRIPTION/TOXIN
Compound DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT
Source ORGANISM_COMMON: BAKER'S YEAST; ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE;
Sequence A:  QYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPEKIGGL
NDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHV
GFIAKIKKVCECVCMHCGKLLLDEHNELMRQALAIKDSKK
RFAAIWTLCKTKMVCETDVPSEDDPTQLVSRGGCGNTQPT
IRKDGLKLVGSWKKEPELRVLSTEEILNIFKHISVKDFTS
LGFNEVFSRPEWMILTCLPVPPPPVRDDLTFKLADILKAN
ISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQSI
RARLKGKEGRIVDFSARTVISGDPNLELDQVGVPKSIAKT
LTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRI
DLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKM
SMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQ
SEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRK
LTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWS
GKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQII
FGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVV
NFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDV
TKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGRLA
EVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGK
RIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEF
FFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYD
NTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAF
EKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEY
KQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFHI
DHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRD
AVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQF
LRSVVHPGEMVGVLAAQSIGEPATQMTLKKVTSGVPRLKE
ILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTL
KSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSQQSPWLLR
LELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDE
KLIIRCRVVAEEDHMLKKIENTMLENITLRGVENIERVVM
MKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDP
TRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVN
YRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEE
TVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVM
IDEESL
B:  FEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDY
TLQDIICEDSTLIEISFGKIYVTKPMVNESDGVTHALYPQ
EARLRNLTYSSGLFVDVKKRTYKVFIGRLPIMLRSKNCYL
SEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGN
IVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGR
EGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHI
CYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRGTAL
GIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYM
INRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLF
KKLTKDIFRLAINAKTITSGLKYALATGNWGVSQVLNRYT
YSSTLSHLRRTNTPIAKPRQLHNTHWGLVCPAETPEGQAC
GLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQ
SPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEV
SMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKV
RKGHIAKLMATEYQDEYTWSSLLNEGLVEYIDAEEEESIL
IAMQPEDLEPDVDPAKRIRVSHHATTFTHCEIHPSMILGV
AASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDT
MANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYS
GYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSIT
ETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVI
IGKTTPSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKV
RVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGI
VPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASP
FTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIF
FGPTYYQRLRHMVDDKIHARARGPGLRFGEMERDCMIAHG
AASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFEC
KGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDRSR
DF
C:  EEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIP
TLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEY
SRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVS
NLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKG
IAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWP
QSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQ
VVVRGIDTLQKKVASILLALTQMDQD
E:  QENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDF
KAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVEF
CDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMK
LVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKR
ELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKS
ETSGRYASYRICM
F:  KAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDL
EGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEEL
IVDL
H:  SNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLD
INVELFPVAAQDSLTVTIASSLTRSWRPPQAGDRSLADDY
DYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYRNLN
NLKQENAYLLIRR
I:  MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGS
PLVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHS
RENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQ
FS
J:  MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLG
LKRYCCRRMILTHVDLIEKFLRYNP
K:  MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDH
TLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEG
YDPKDALKNACNSIINKLGALKTNFETEWNLQTL
L:  TLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLV
QFEAR
Description (1)  DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT (E.C.2.7.7.6), DNA-DIRECTED RNA POLYMERASE II 140KD POLYPEPTIDE (E.C.2.7.7.6), DNA-DIRECTED RNA POLYMERASE II 45KD POLYPEPTIDE (E.C.2.7.7.6), DNA-DIRECTED RNA POLYMERASE II 27KD POLYPEPTIDE (E.C.2.7.7.6), DNA-DIRECTED RNA POLYMERASE II 23KD POLYPEPTIDE (E.C.2.7.7.6), DNA-DIRECTED RNA POLYMERASE II 14.5KD POLYPEPTIDE (E.C.2.7.7.6), DNA-DIRECTED RNA POLYMERASE II 14.2KD POLYPEPTIDE (E.C.2.7.7.6), DNA-DIRECTED RNA POLYMERASE II 8.3KD POLYPEPTIDE (E.C.2.7.7.6), DNA-DIRECTED RNA POLYMERASE II 13.6KD POLYPEPTIDE (E.C.2.7.7.6), DNA-DIRECTED RNA POLYMERASE II 7.7KD POLYPEPTIDE (E.C.2.7.7.6), ALPHA AMANITIN


Functional site

1) chain J
residue 7
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN J3001
source : AC1

2) chain J
residue 10
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN J3001
source : AC1

3) chain J
residue 45
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN J3001
source : AC1

4) chain J
residue 46
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN J3001
source : AC1

5) chain C
residue 86
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN C3002
source : AC2

6) chain C
residue 88
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN C3002
source : AC2

7) chain C
residue 92
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN C3002
source : AC2

8) chain C
residue 95
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN C3002
source : AC2

9) chain I
residue 7
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN I3003
source : AC3

10) chain I
residue 10
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN I3003
source : AC3

11) chain I
residue 29
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN I3003
source : AC3

12) chain I
residue 32
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN I3003
source : AC3

13) chain I
residue 75
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN I3004
source : AC4

14) chain I
residue 78
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN I3004
source : AC4

15) chain I
residue 103
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN I3004
source : AC4

16) chain I
residue 106
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN I3004
source : AC4

17) chain L
residue 31
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN L3005
source : AC5

18) chain L
residue 34
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN L3005
source : AC5

19) chain L
residue 48
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN L3005
source : AC5

20) chain L
residue 51
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN L3005
source : AC5

21) chain A
residue 107
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN A3006
source : AC6

22) chain A
residue 110
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN A3006
source : AC6

23) chain A
residue 148
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN A3006
source : AC6

24) chain A
residue 167
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN A3006
source : AC6

25) chain B
residue 1163
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN B3007
source : AC7

26) chain B
residue 1166
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN B3007
source : AC7

27) chain B
residue 1182
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN B3007
source : AC7

28) chain B
residue 1185
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN B3007
source : AC7

29) chain A
residue 67
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN A3008
source : AC8

30) chain A
residue 70
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN A3008
source : AC8

31) chain A
residue 77
type
ligand
sequence C
description BINDING SITE FOR RESIDUE ZN A3008
source : AC8

32) chain A
residue 80
type
ligand
sequence H
description BINDING SITE FOR RESIDUE ZN A3008
source : AC8

33) chain A
residue 481
type
ligand
sequence D
description BINDING SITE FOR RESIDUE MN A3009
source : AC9

34) chain A
residue 483
type
ligand
sequence D
description BINDING SITE FOR RESIDUE MN A3009
source : AC9

35) chain A
residue 485
type
ligand
sequence D
description BINDING SITE FOR RESIDUE MN A3009
source : AC9

36) chain A
residue 719
type
ligand
sequence V
description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN
source : BC1

37) chain A
residue 723
type
ligand
sequence N
description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN
source : BC1

38) chain A
residue 726
type
ligand
sequence R
description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN
source : BC1

39) chain A
residue 756
type
ligand
sequence I
description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN
source : BC1

40) chain A
residue 759
type
ligand
sequence A
description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN
source : BC1

41) chain A
residue 760
type
ligand
sequence Q
description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN
source : BC1

42) chain A
residue 766
type
ligand
sequence G
description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN
source : BC1

43) chain A
residue 767
type
ligand
sequence Q
description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN
source : BC1

44) chain A
residue 768
type
ligand
sequence Q
description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN
source : BC1

45) chain A
residue 769
type
ligand
sequence S
description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN
source : BC1

46) chain A
residue 819
type
ligand
sequence G
description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN
source : BC1

47) chain A
residue 822
type
ligand
sequence E
description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN
source : BC1

48) chain A
residue 1081
type
ligand
sequence L
description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN
source : BC1

49) chain B
residue 763
type
ligand
sequence Q
description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN
source : BC1

50) chain B
residue 765
type
ligand
sequence P
description BINDING SITE FOR CHAIN M OF ALPHA AMANITIN
source : BC1

51) chain A
residue 481
type METAL
ligand
sequence D
description Magnesium 2; shared with RPB2
source Swiss-Prot : SWS_FT_FI1

52) chain A
residue 483
type METAL
ligand
sequence D
description Magnesium 2; shared with RPB2
source Swiss-Prot : SWS_FT_FI1

53) chain A
residue 481
type METAL
ligand
sequence D
description Magnesium 1; catalytic
source Swiss-Prot : SWS_FT_FI2

54) chain A
residue 483
type METAL
ligand
sequence D
description Magnesium 1; catalytic
source Swiss-Prot : SWS_FT_FI2

55) chain A
residue 485
type METAL
ligand
sequence D
description Magnesium 1; catalytic
source Swiss-Prot : SWS_FT_FI2

56) chain A
residue 107
type METAL
ligand
sequence C
description Zinc 2
source Swiss-Prot : SWS_FT_FI3

57) chain A
residue 110
type METAL
ligand
sequence C
description Zinc 2
source Swiss-Prot : SWS_FT_FI3

58) chain A
residue 148
type METAL
ligand
sequence C
description Zinc 2
source Swiss-Prot : SWS_FT_FI3

59) chain A
residue 167
type METAL
ligand
sequence C
description Zinc 2
source Swiss-Prot : SWS_FT_FI3

60) chain A
residue 67
type METAL
ligand
sequence C
description Zinc 1
source Swiss-Prot : SWS_FT_FI4

61) chain A
residue 70
type METAL
ligand
sequence C
description Zinc 1
source Swiss-Prot : SWS_FT_FI4

62) chain A
residue 77
type METAL
ligand
sequence C
description Zinc 1
source Swiss-Prot : SWS_FT_FI4

63) chain A
residue 80
type METAL
ligand
sequence H
description Zinc 1
source Swiss-Prot : SWS_FT_FI4

64) chain B
residue 1163
type METAL
ligand
sequence C
description Zinc
source Swiss-Prot : SWS_FT_FI5

65) chain B
residue 1166
type METAL
ligand
sequence C
description Zinc
source Swiss-Prot : SWS_FT_FI5

66) chain B
residue 1182
type METAL
ligand
sequence C
description Zinc
source Swiss-Prot : SWS_FT_FI5

67) chain B
residue 1185
type METAL
ligand
sequence C
description Zinc
source Swiss-Prot : SWS_FT_FI5

68) chain B
residue 837
type METAL
ligand
sequence D
description Magnesium; shared with RPB1
source Swiss-Prot : SWS_FT_FI6

69) chain C
residue 86
type METAL
ligand
sequence C
description Zinc
source Swiss-Prot : SWS_FT_FI7

70) chain C
residue 88
type METAL
ligand
sequence C
description Zinc
source Swiss-Prot : SWS_FT_FI7

71) chain C
residue 92
type METAL
ligand
sequence C
description Zinc
source Swiss-Prot : SWS_FT_FI7

72) chain C
residue 95
type METAL
ligand
sequence C
description Zinc
source Swiss-Prot : SWS_FT_FI7

73) chain I
residue 75
type METAL
ligand
sequence C
description Zinc 2
source Swiss-Prot : SWS_FT_FI8

74) chain I
residue 78
type METAL
ligand
sequence C
description Zinc 2
source Swiss-Prot : SWS_FT_FI8

75) chain I
residue 103
type METAL
ligand
sequence C
description Zinc 2
source Swiss-Prot : SWS_FT_FI8

76) chain I
residue 106
type METAL
ligand
sequence C
description Zinc 2
source Swiss-Prot : SWS_FT_FI8

77) chain I
residue 7
type METAL
ligand
sequence C
description Zinc 1
source Swiss-Prot : SWS_FT_FI9

78) chain I
residue 10
type METAL
ligand
sequence C
description Zinc 1
source Swiss-Prot : SWS_FT_FI9

79) chain I
residue 29
type METAL
ligand
sequence C
description Zinc 1
source Swiss-Prot : SWS_FT_FI9

80) chain I
residue 32
type METAL
ligand
sequence C
description Zinc 1
source Swiss-Prot : SWS_FT_FI9

81) chain J
residue 7
type METAL
ligand
sequence C
description Zinc (By similarity)
source Swiss-Prot : SWS_FT_FI10

82) chain J
residue 10
type METAL
ligand
sequence C
description Zinc (By similarity)
source Swiss-Prot : SWS_FT_FI10

83) chain J
residue 44
type METAL
ligand
sequence Y
description Zinc (By similarity)
source Swiss-Prot : SWS_FT_FI10

84) chain J
residue 45
type METAL
ligand
sequence C
description Zinc (By similarity)
source Swiss-Prot : SWS_FT_FI10

85) chain L
residue 31
type METAL
ligand
sequence C
description Zinc
source Swiss-Prot : SWS_FT_FI11

86) chain L
residue 34
type METAL
ligand
sequence C
description Zinc
source Swiss-Prot : SWS_FT_FI11

87) chain L
residue 48
type METAL
ligand
sequence C
description Zinc
source Swiss-Prot : SWS_FT_FI11

88) chain L
residue 51
type METAL
ligand
sequence C
description Zinc
source Swiss-Prot : SWS_FT_FI11


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