eF-site ID 5kaf-A
PDB Code 5kaf
Chain A

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Title RT XFEL structure of Photosystem II in the dark state at 3.0 A resolution
Classification ELECTRON TRANSPORT
Compound Photosystem II protein D1 1
Source ORGANISM_SCIENTIFIC: Thermosynechococcus elongatus (strain BP-1);
Sequence A:  ANLWERFCNWVTSTDNRLYVGWFGVIMIPTLLAATICFVI
AFIAAPPVDIDGIREPVSGSLLYGNNIITGAVVPSSNAIG
LHFYPIWEAASLDEWLYNGGPYQLIIFHFLLGASCYMGRQ
WELSYRLGMRPWICVAYSAPLASAFAVFLIYPIGQGSFSD
GMPLGISGTFNFMIVFQAEHNILMHPFHQLGVAGVFGGAL
FCAMHGSLVTSSLIRETTETESANYGYKFGQEEETYNIVA
AHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGVWFTALGI
STMAFNLNGFNFNHSVIDAKGNVINTWADIINRANLGMEV
MHERNAHNFPLDLA
Description


Functional site

1) chain A
residue 170
type
sequence D
description binding site for residue OEX A 601
source : AC1

2) chain A
residue 189
type
sequence E
description binding site for residue OEX A 601
source : AC1

3) chain A
residue 332
type
sequence H
description binding site for residue OEX A 601
source : AC1

4) chain A
residue 333
type
sequence E
description binding site for residue OEX A 601
source : AC1

5) chain A
residue 337
type
sequence H
description binding site for residue OEX A 601
source : AC1

6) chain A
residue 342
type
sequence D
description binding site for residue OEX A 601
source : AC1

7) chain A
residue 344
type
sequence A
description binding site for residue OEX A 601
source : AC1

8) chain A
residue 215
type
sequence H
description binding site for residue FE2 A 602
source : AC2

9) chain A
residue 272
type
sequence H
description binding site for residue FE2 A 602
source : AC2

10) chain A
residue 200
type
sequence L
description binding site for residue SQD A 603
source : AC3

11) chain A
residue 267
type
sequence N
description binding site for residue SQD A 603
source : AC3

12) chain A
residue 270
type
sequence S
description binding site for residue SQD A 603
source : AC3

13) chain A
residue 274
type
sequence F
description binding site for residue SQD A 603
source : AC3

14) chain A
residue 278
type
sequence W
description binding site for residue SQD A 603
source : AC3

15) chain A
residue 282
type
sequence G
description binding site for residue SQD A 603
source : AC3

16) chain A
residue 332
type
sequence H
description binding site for residue CL A 604
source : AC4

17) chain A
residue 333
type
sequence E
description binding site for residue CL A 604
source : AC4

18) chain A
residue 337
type
sequence H
description binding site for residue CL A 605
source : AC5

19) chain A
residue 338
type
sequence N
description binding site for residue CL A 605
source : AC5

20) chain A
residue 339
type
sequence F
description binding site for residue CL A 605
source : AC5

21) chain A
residue 147
type
sequence Y
description binding site for residue CLA A 606
source : AC6

22) chain A
residue 150
type
sequence P
description binding site for residue CLA A 606
source : AC6

23) chain A
residue 153
type
sequence S
description binding site for residue CLA A 606
source : AC6

24) chain A
residue 157
type
sequence V
description binding site for residue CLA A 606
source : AC6

25) chain A
residue 183
type
sequence M
description binding site for residue CLA A 606
source : AC6

26) chain A
residue 186
type
sequence F
description binding site for residue CLA A 606
source : AC6

27) chain A
residue 192
type
sequence I
description binding site for residue CLA A 606
source : AC6

28) chain A
residue 193
type
sequence L
description binding site for residue CLA A 606
source : AC6

29) chain A
residue 198
type
sequence H
description binding site for residue CLA A 606
source : AC6

30) chain A
residue 201
type
sequence G
description binding site for residue CLA A 606
source : AC6

31) chain A
residue 202
type
sequence V
description binding site for residue CLA A 606
source : AC6

32) chain A
residue 206
type
sequence F
description binding site for residue CLA A 606
source : AC6

33) chain A
residue 286
type
sequence T
description binding site for residue CLA A 606
source : AC6

34) chain A
residue 287
type
sequence A
description binding site for residue CLA A 606
source : AC6

35) chain A
residue 290
type
sequence I
description binding site for residue CLA A 606
source : AC6

36) chain A
residue 199
type
sequence Q
description binding site for residue CLA A 607
source : AC7

37) chain A
residue 202
type
sequence V
description binding site for residue CLA A 607
source : AC7

38) chain A
residue 203
type
sequence A
description binding site for residue CLA A 607
source : AC7

39) chain A
residue 207
type
sequence G
description binding site for residue CLA A 607
source : AC7

40) chain A
residue 278
type
sequence W
description binding site for residue CLA A 607
source : AC7

41) chain A
residue 41
type
sequence L
description binding site for residue PHO A 608
source : AC8

42) chain A
residue 45
type
sequence T
description binding site for residue PHO A 608
source : AC8

43) chain A
residue 126
type
sequence Y
description binding site for residue PHO A 608
source : AC8

44) chain A
residue 130
type
sequence Q
description binding site for residue PHO A 608
source : AC8

45) chain A
residue 147
type
sequence Y
description binding site for residue PHO A 608
source : AC8

46) chain A
residue 279
type
sequence P
description binding site for residue PHO A 608
source : AC8

47) chain A
residue 283
type
sequence V
description binding site for residue PHO A 608
source : AC8

48) chain A
residue 36
type
sequence I
description binding site for residue CLA A 609
source : AC9

49) chain A
residue 40
type
sequence T
description binding site for residue CLA A 609
source : AC9

50) chain A
residue 93
type
sequence F
description binding site for residue CLA A 609
source : AC9

51) chain A
residue 94
type
sequence Y
description binding site for residue CLA A 609
source : AC9

52) chain A
residue 95
type
sequence P
description binding site for residue CLA A 609
source : AC9

53) chain A
residue 96
type
sequence I
description binding site for residue CLA A 609
source : AC9

54) chain A
residue 97
type
sequence W
description binding site for residue CLA A 609
source : AC9

55) chain A
residue 114
type
sequence L
description binding site for residue CLA A 609
source : AC9

56) chain A
residue 118
type
sequence H
description binding site for residue CLA A 609
source : AC9

57) chain A
residue 38
type
sequence I
description binding site for residue BCR A 610
source : AD1

58) chain A
residue 42
type
sequence L
description binding site for residue BCR A 610
source : AD1

59) chain A
residue 43
type
sequence A
description binding site for residue BCR A 610
source : AD1

60) chain A
residue 211
type
sequence F
description binding site for residue PL9 A 611
source : AD2

61) chain A
residue 215
type
sequence H
description binding site for residue PL9 A 611
source : AD2

62) chain A
residue 218
type
sequence L
description binding site for residue PL9 A 611
source : AD2

63) chain A
residue 255
type
sequence F
description binding site for residue PL9 A 611
source : AD2

64) chain A
residue 263
type
sequence A
description binding site for residue PL9 A 611
source : AD2

65) chain A
residue 264
type
sequence S
description binding site for residue PL9 A 611
source : AD2

66) chain A
residue 265
type
sequence F
description binding site for residue PL9 A 611
source : AD2

67) chain A
residue 271
type
sequence L
description binding site for residue PL9 A 611
source : AD2

68) chain A
residue 97
type
sequence W
description binding site for residue LMG A 612
source : AD3

69) chain A
residue 98
type
sequence E
description binding site for residue LMG A 612
source : AD3

70) chain A
residue 117
type
sequence F
description binding site for residue LMG A 612
source : AD3

71) chain A
residue 26
type
sequence N
description binding site for residue LMG A 613
source : AD4

72) chain A
residue 27
type
sequence R
description binding site for residue LMG A 613
source : AD4

73) chain A
residue 28
type
sequence L
description binding site for residue LMG A 613
source : AD4

74) chain A
residue 42
type
sequence L
description binding site for residue LMG A 613
source : AD4

75) chain A
residue 48
type
sequence F
description binding site for residue CLA A 615
source : AD5

76) chain A
residue 158
type
sequence F
description binding site for residue CLA A 615
source : AD5

77) chain A
residue 172
type
sequence M
description binding site for residue CLA A 615
source : AD5

78) chain A
residue 176
type
sequence I
description binding site for residue CLA A 615
source : AD5

79) chain A
residue 179
type
sequence T
description binding site for residue CLA A 615
source : AD5

80) chain A
residue 180
type
sequence F
description binding site for residue CLA A 615
source : AD5

81) chain A
residue 183
type
sequence M
description binding site for residue CLA A 615
source : AD5

82) chain A
residue 232
type
sequence S
description binding site for residue LHG A 616
source : AD6

83) chain A
residue 234
type
sequence N
description binding site for residue LHG A 616
source : AD6

84) chain A
residue 140
type
sequence R
description binding site for residue LHG A 617
source : AD7

85) chain A
residue 142
type
sequence W
description binding site for residue LHG A 617
source : AD7

86) chain A
residue 273
type
sequence F
description binding site for residue LHG A 617
source : AD7

87) chain A
residue 285
type
sequence F
description binding site for residue LHG A 617
source : AD7

88) chain A
residue 258
type
sequence L
description binding site for residue LHG A 618
source : AD8

89) chain A
residue 262
type
sequence Y
description binding site for residue LHG A 618
source : AD8

90) chain A
residue 264
type
sequence S
description binding site for residue LHG A 618
source : AD8

91) chain A
residue 265
type
sequence F
description binding site for residue LHG A 618
source : AD8

92) chain A
residue 103
type
sequence D
description binding site for residue SQD A 619
source : AD9

93) chain A
residue 106
type
sequence L
description binding site for residue SQD A 619
source : AD9

94) chain A
residue 215
type
sequence H
description binding site for residue BCT A 620
source : AE1

95) chain A
residue 244
type
sequence E
description binding site for residue BCT A 620
source : AE1

96) chain A
residue 246
type
sequence Y
description binding site for residue BCT A 620
source : AE1

97) chain A
residue 272
type
sequence H
description binding site for residue BCT A 620
source : AE1

98) chain A
residue 33
type
sequence F
description binding site for residue CLA C 505
source : AH3

99) chain A
residue 121
type
sequence L
description binding site for residue CLA C 505
source : AH3

100) chain A
residue 131
type
sequence W
description binding site for residue CLA C 505
source : AH3

101) chain A
residue 91
type
sequence L
description binding site for residue DGD C 516
source : AI5

102) chain A
residue 155
type
sequence F
description binding site for residue DGD C 516
source : AI5

103) chain A
residue 163
type
sequence I
description binding site for residue DGD C 516
source : AI5

104) chain A
residue 197
type
sequence F
description binding site for residue DGD C 517
source : AI6

105) chain A
residue 196
type
sequence P
description binding site for residue DGD C 518
source : AI7

106) chain A
residue 199
type
sequence Q
description binding site for residue DGD C 518
source : AI7

107) chain A
residue 301
type
sequence N
description binding site for residue DGD C 518
source : AI7

108) chain A
residue 302
type
sequence F
description binding site for residue DGD C 518
source : AI7

109) chain A
residue 305
type
sequence S
description binding site for residue DGD C 518
source : AI7

110) chain A
residue 210
type
sequence L
description binding site for residue PHO D 401
source : AJ1

111) chain A
residue 214
type
sequence M
description binding site for residue PHO D 401
source : AJ1

112) chain A
residue 258
type
sequence L
description binding site for residue PHO D 401
source : AJ1

113) chain A
residue 183
type
sequence M
description binding site for residue CLA D 402
source : AJ2

114) chain A
residue 52
type
sequence F
description binding site for residue PL9 D 407
source : AJ7

115) chain A
residue 77
type
sequence I
description binding site for residue PL9 D 407
source : AJ7

116) chain A
residue 102
type
sequence L
description binding site for residue SQD I 101
source : AK4

117) chain A
residue 232
type
sequence S
description binding site for residue LHG L 101
source : AK6

118) chain A
residue 234
type
sequence N
description binding site for residue LHG L 101
source : AK6

119) chain A
residue 191-217
type prosite
sequence NILMHPFHQLGVAGVFGGALFCAMHGS
description REACTION_CENTER Photosynthetic reaction center proteins signature. NwtlnPfHmmGvagvlggallcAiHGA
source prosite : PS00244

120) chain A
residue 344
type BINDING
sequence A
description BINDING => ECO:0000255|HAMAP-Rule:MF_01379, ECO:0000269|PubMed:19219048, ECO:0000303|PubMed:14764885, ECO:0000303|PubMed:16355230, ECO:0000303|PubMed:20558739, ECO:0000303|PubMed:21367867, ECO:0000303|PubMed:23413188, ECO:0000303|PubMed:25043005
source Swiss-Prot : SWS_FT_FI11

121) chain A
residue 161
type SITE
sequence Y
description Tyrosine radical intermediate => ECO:0000255|HAMAP-Rule:MF_01379, ECO:0000303|PubMed:11217865, ECO:0000303|PubMed:14764885, ECO:0000303|PubMed:19219048, ECO:0000303|PubMed:21367867, ECO:0000303|DOI:10.1039/B406989G
source Swiss-Prot : SWS_FT_FI12

122) chain A
residue 190
type SITE
sequence H
description Stabilizes free radical intermediate => ECO:0000255|HAMAP-Rule:MF_01379
source Swiss-Prot : SWS_FT_FI13

123) chain A
residue 344
type SITE
sequence A
description Cleavage; by CtpA => ECO:0000255|HAMAP-Rule:MF_01379
source Swiss-Prot : SWS_FT_FI14

124) chain A
residue 272
type MOD_RES
sequence H
description N-acetylthreonine => ECO:0000269|PubMed:19219048, ECO:0000269|PubMed:20558739
source Swiss-Prot : SWS_FT_FI5

125) chain A
residue 332
type BINDING
sequence H
description BINDING => ECO:0000255|HAMAP-Rule:MF_01383, ECO:0000269|PubMed:16355230, ECO:0000269|PubMed:19219048, ECO:0000303|PubMed:14764885, ECO:0000303|PubMed:20558739, ECO:0000303|PubMed:21367867, ECO:0000303|PubMed:22665786, ECO:0000303|PubMed:23413188, ECO:0000303|PubMed:25043005, ECO:0000303|DOI:10.1039/B406989G
source Swiss-Prot : SWS_FT_FI8

126) chain A
residue 333
type BINDING
sequence E
description BINDING => ECO:0000255|HAMAP-Rule:MF_01383, ECO:0000269|PubMed:16355230, ECO:0000269|PubMed:19219048, ECO:0000303|PubMed:14764885, ECO:0000303|PubMed:20558739, ECO:0000303|PubMed:21367867, ECO:0000303|PubMed:22665786, ECO:0000303|PubMed:23413188, ECO:0000303|PubMed:25043005, ECO:0000303|DOI:10.1039/B406989G
source Swiss-Prot : SWS_FT_FI8


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