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

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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 D:  RGWFDILDDWLKRDRFVFVGWSGILLFPCAYLALGGWLTG
TTFVTSWYTHGLASSYLEGCNFLTVAVSTPANSMGHSLLL
LWGPEAQGDFTRWCQLGGLWTFIALHGAFGLIGFMLRQFE
IARLVGVRPYNAIAFSAPIAVFVSVFLIYPLGQSSWFFAP
SFGVAAIFRFLLFFQGFHNWTLNPFHMMGVAGVLGGALLC
AIHGATVENTLFQDGEGASTFRAFNPTQAEETYSMVTANR
FWSQIFGIAFSNKRWLHFFMLFVPVTGLWMSAIGVVGLAL
NLRSYDFISQEIRAAEDPEFETFYTKNLLLNEGIRAWMAP
QDQPHENFVFPEEVLPRGNAL
Description


Functional site

1) chain D
residue 214
type
sequence H
description binding site for residue FE2 A 602
source : AC2

2) chain D
residue 268
type
sequence H
description binding site for residue FE2 A 602
source : AC2

3) chain D
residue 232
type
sequence F
description binding site for residue SQD A 603
source : AC3

4) chain D
residue 233
type
sequence R
description binding site for residue SQD A 603
source : AC3

5) chain D
residue 317
type
sequence K
description binding site for residue CL A 604
source : AC4

6) chain D
residue 157
type
sequence F
description binding site for residue CLA A 607
source : AC7

7) chain D
residue 175
type
sequence V
description binding site for residue CLA A 607
source : AC7

8) chain D
residue 178
type
sequence I
description binding site for residue CLA A 607
source : AC7

9) chain D
residue 179
type
sequence F
description binding site for residue CLA A 607
source : AC7

10) chain D
residue 182
type
sequence L
description binding site for residue CLA A 607
source : AC7

11) chain D
residue 208
type
sequence A
description binding site for residue PHO A 608
source : AC8

12) chain D
residue 209
type
sequence L
description binding site for residue PHO A 608
source : AC8

13) chain D
residue 213
type
sequence I
description binding site for residue PHO A 608
source : AC8

14) chain D
residue 253
type
sequence W
description binding site for residue PHO A 608
source : AC8

15) chain D
residue 45
type
sequence L
description binding site for residue PL9 A 611
source : AD2

16) chain D
residue 198
type
sequence M
description binding site for residue CLA A 615
source : AD5

17) chain D
residue 201
type
sequence V
description binding site for residue CLA A 615
source : AD5

18) chain D
residue 202
type
sequence A
description binding site for residue CLA A 615
source : AD5

19) chain D
residue 206
type
sequence G
description binding site for residue CLA A 615
source : AD5

20) chain D
residue 141
type
sequence Y
description binding site for residue LHG A 616
source : AD6

21) chain D
residue 266
type
sequence W
description binding site for residue LHG A 616
source : AD6

22) chain D
residue 269
type
sequence F
description binding site for residue LHG A 616
source : AD6

23) chain D
residue 219
type
sequence E
description binding site for residue LHG A 617
source : AD7

24) chain D
residue 220
type
sequence N
description binding site for residue LHG A 617
source : AD7

25) chain D
residue 229
type
sequence A
description binding site for residue LHG A 617
source : AD7

26) chain D
residue 230
type
sequence S
description binding site for residue LHG A 617
source : AD7

27) chain D
residue 231
type
sequence T
description binding site for residue LHG A 617
source : AD7

28) chain D
residue 232
type
sequence F
description binding site for residue LHG A 617
source : AD7

29) chain D
residue 27
type
sequence F
description binding site for residue LHG A 618
source : AD8

30) chain D
residue 214
type
sequence H
description binding site for residue BCT A 620
source : AE1

31) chain D
residue 244
type
sequence Y
description binding site for residue BCT A 620
source : AE1

32) chain D
residue 264
type
sequence K
description binding site for residue BCT A 620
source : AE1

33) chain D
residue 268
type
sequence H
description binding site for residue BCT A 620
source : AE1

34) chain D
residue 158
type
sequence L
description binding site for residue CLA B 602
source : AE3

35) chain D
residue 120
type
sequence F
description binding site for residue CLA B 608
source : AE9

36) chain D
residue 123
type
sequence I
description binding site for residue CLA B 608
source : AE9

37) chain D
residue 126
type
sequence M
description binding site for residue CLA B 608
source : AE9

38) chain D
residue 41
type
sequence A
description binding site for residue PHO D 401
source : AJ1

39) chain D
residue 44
type
sequence A
description binding site for residue PHO D 401
source : AJ1

40) chain D
residue 48
type
sequence W
description binding site for residue PHO D 401
source : AJ1

41) chain D
residue 114
type
sequence I
description binding site for residue PHO D 401
source : AJ1

42) chain D
residue 121
type
sequence G
description binding site for residue PHO D 401
source : AJ1

43) chain D
residue 122
type
sequence L
description binding site for residue PHO D 401
source : AJ1

44) chain D
residue 125
type
sequence F
description binding site for residue PHO D 401
source : AJ1

45) chain D
residue 129
type
sequence Q
description binding site for residue PHO D 401
source : AJ1

46) chain D
residue 142
type
sequence N
description binding site for residue PHO D 401
source : AJ1

47) chain D
residue 146
type
sequence F
description binding site for residue PHO D 401
source : AJ1

48) chain D
residue 149
type
sequence P
description binding site for residue PHO D 401
source : AJ1

49) chain D
residue 153
type
sequence F
description binding site for residue PHO D 401
source : AJ1

50) chain D
residue 174
type
sequence G
description binding site for residue PHO D 401
source : AJ1

51) chain D
residue 275
type
sequence P
description binding site for residue PHO D 401
source : AJ1

52) chain D
residue 279
type
sequence L
description binding site for residue PHO D 401
source : AJ1

53) chain D
residue 48
type
sequence W
description binding site for residue CLA D 402
source : AJ2

54) chain D
residue 149
type
sequence P
description binding site for residue CLA D 402
source : AJ2

55) chain D
residue 152
type
sequence V
description binding site for residue CLA D 402
source : AJ2

56) chain D
residue 156
type
sequence V
description binding site for residue CLA D 402
source : AJ2

57) chain D
residue 182
type
sequence L
description binding site for residue CLA D 402
source : AJ2

58) chain D
residue 185
type
sequence F
description binding site for residue CLA D 402
source : AJ2

59) chain D
residue 186
type
sequence Q
description binding site for residue CLA D 402
source : AJ2

60) chain D
residue 191
type
sequence W
description binding site for residue CLA D 402
source : AJ2

61) chain D
residue 192
type
sequence T
description binding site for residue CLA D 402
source : AJ2

62) chain D
residue 197
type
sequence H
description binding site for residue CLA D 402
source : AJ2

63) chain D
residue 200
type
sequence G
description binding site for residue CLA D 402
source : AJ2

64) chain D
residue 201
type
sequence V
description binding site for residue CLA D 402
source : AJ2

65) chain D
residue 204
type
sequence V
description binding site for residue CLA D 402
source : AJ2

66) chain D
residue 282
type
sequence S
description binding site for residue CLA D 402
source : AJ2

67) chain D
residue 283
type
sequence A
description binding site for residue CLA D 402
source : AJ2

68) chain D
residue 35
type
sequence I
description binding site for residue CLA D 403
source : AJ3

69) chain D
residue 39
type
sequence P
description binding site for residue CLA D 403
source : AJ3

70) chain D
residue 43
type
sequence L
description binding site for residue CLA D 403
source : AJ3

71) chain D
residue 89
type
sequence L
description binding site for residue CLA D 403
source : AJ3

72) chain D
residue 90
type
sequence L
description binding site for residue CLA D 403
source : AJ3

73) chain D
residue 91
type
sequence L
description binding site for residue CLA D 403
source : AJ3

74) chain D
residue 92
type
sequence L
description binding site for residue CLA D 403
source : AJ3

75) chain D
residue 93
type
sequence W
description binding site for residue CLA D 403
source : AJ3

76) chain D
residue 112
type
sequence T
description binding site for residue CLA D 403
source : AJ3

77) chain D
residue 113
type
sequence F
description binding site for residue CLA D 403
source : AJ3

78) chain D
residue 116
type
sequence L
description binding site for residue CLA D 403
source : AJ3

79) chain D
residue 117
type
sequence H
description binding site for residue CLA D 403
source : AJ3

80) chain D
residue 42
type
sequence Y
description binding site for residue BCR D 404
source : AJ4

81) chain D
residue 43
type
sequence L
description binding site for residue BCR D 404
source : AJ4

82) chain D
residue 46
type
sequence G
description binding site for residue BCR D 404
source : AJ4

83) chain D
residue 47
type
sequence G
description binding site for residue BCR D 404
source : AJ4

84) chain D
residue 49
type
sequence L
description binding site for residue BCR D 404
source : AJ4

85) chain D
residue 50
type
sequence T
description binding site for residue BCR D 404
source : AJ4

86) chain D
residue 101
type
sequence F
description binding site for residue BCR D 404
source : AJ4

87) chain D
residue 67
type
sequence Y
description binding site for residue LMG D 405
source : AJ5

88) chain D
residue 71
type
sequence C
description binding site for residue LMG D 405
source : AJ5

89) chain D
residue 72
type
sequence N
description binding site for residue LMG D 405
source : AJ5

90) chain D
residue 73
type
sequence F
description binding site for residue LMG D 405
source : AJ5

91) chain D
residue 257
type
sequence F
description binding site for residue LHG D 406
source : AJ6

92) chain D
residue 259
type
sequence I
description binding site for residue LHG D 406
source : AJ6

93) chain D
residue 260
type
sequence A
description binding site for residue LHG D 406
source : AJ6

94) chain D
residue 261
type
sequence F
description binding site for residue LHG D 406
source : AJ6

95) chain D
residue 262
type
sequence S
description binding site for residue LHG D 406
source : AJ6

96) chain D
residue 263
type
sequence N
description binding site for residue LHG D 406
source : AJ6

97) chain D
residue 266
type
sequence W
description binding site for residue LHG D 406
source : AJ6

98) chain D
residue 199
type
sequence M
description binding site for residue PL9 D 407
source : AJ7

99) chain D
residue 210
type
sequence L
description binding site for residue PL9 D 407
source : AJ7

100) chain D
residue 213
type
sequence I
description binding site for residue PL9 D 407
source : AJ7

101) chain D
residue 214
type
sequence H
description binding site for residue PL9 D 407
source : AJ7

102) chain D
residue 217
type
sequence T
description binding site for residue PL9 D 407
source : AJ7

103) chain D
residue 253
type
sequence W
description binding site for residue PL9 D 407
source : AJ7

104) chain D
residue 259
type
sequence I
description binding site for residue PL9 D 407
source : AJ7

105) chain D
residue 260
type
sequence A
description binding site for residue PL9 D 407
source : AJ7

106) chain D
residue 261
type
sequence F
description binding site for residue PL9 D 407
source : AJ7

107) chain D
residue 267
type
sequence L
description binding site for residue PL9 D 407
source : AJ7

108) chain D
residue 274
type
sequence V
description binding site for residue PL9 D 407
source : AJ7

109) chain D
residue 19
type
sequence D
description binding site for residue SQD D 408
source : AJ8

110) chain D
residue 23
type
sequence K
description binding site for residue SQD D 408
source : AJ8

111) chain D
residue 32
type
sequence W
description binding site for residue SQD D 408
source : AJ8

112) chain D
residue 134
type
sequence R
description binding site for residue SQD D 408
source : AJ8

113) chain D
residue 135
type
sequence L
description binding site for residue SQD D 408
source : AJ8

114) chain D
residue 24
type
sequence R
description binding site for residue SQD D 409
source : AJ9

115) chain D
residue 26
type
sequence R
description binding site for residue SQD D 409
source : AJ9

116) chain D
residue 87
type
sequence H
description binding site for residue DGD H 103
source : AK3

117) chain D
residue 162
type
sequence L
description binding site for residue DGD H 103
source : AK3

118) chain D
residue 266
type
sequence W
description binding site for residue LHG L 101
source : AK6

119) chain D
residue 273
type
sequence F
description binding site for residue LHG L 101
source : AK6

120) chain D
residue 214
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

121) chain D
residue 261
type BINDING
sequence F
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:25006873, ECO:0000303|PubMed:25043005
source Swiss-Prot : SWS_FT_FI9

122) chain D
residue 268
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:25006873, ECO:0000303|PubMed:25043005, ECO:0000303|DOI:10.1039/B406989G
source Swiss-Prot : SWS_FT_FI10

123) chain D
residue 289-352
type TOPO_DOM
sequence LALNLRSYDFISQEIRAAEDPEFETFYTKNLLLNEGIRAW
MAPQDQPHENFVFPEEVLPRGNAL
description Lumenal => ECO:0000269|PubMed:33846594, ECO:0007744|PDB:7NHQ
source Swiss-Prot : SWS_FT_FI3

124) chain D
residue 142
type BINDING
sequence N
description BINDING => ECO:0000255|HAMAP-Rule:MF_01383, ECO:0000269|PubMed:16355230, ECO:0000269|PubMed:19219048, ECO:0000303|PubMed:20558739, ECO:0000303|PubMed:21367867, ECO:0000303|PubMed:25043005
source Swiss-Prot : SWS_FT_FI6

125) chain D
residue 197
type BINDING
sequence H
description axial binding residue => 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_FI7

126) chain D
residue 218-265
type TRANSMEM
sequence VENTLFQDGEGASTFRAFNPTQAEETYSMVTANRFWSQIF
GIAFSNKR
description Helical => ECO:0000269|PubMed:33846594, ECO:0007744|PDB:7NHQ
source Swiss-Prot : SWS_FT_FI1

127) chain D
residue 141-160
type TOPO_DOM
sequence YNAIAFSAPIAVFVSVFLIY
description Cytoplasmic => ECO:0000269|PubMed:33846594, ECO:0007744|PDB:7NHQ
source Swiss-Prot : SWS_FT_FI2

128) chain D
residue 194-217
type TOPO_DOM
sequence NPFHMMGVAGVLGGALLCAIHGAT
description Cytoplasmic => ECO:0000269|PubMed:33846594, ECO:0007744|PDB:7NHQ
source Swiss-Prot : SWS_FT_FI2

129) chain D
residue 266-288
type TOPO_DOM
sequence WLHFFMLFVPVTGLWMSAIGVVG
description Cytoplasmic => ECO:0000269|PubMed:33846594, ECO:0007744|PDB:7NHQ
source Swiss-Prot : SWS_FT_FI2

130) chain D
residue 190-216
type prosite
sequence NWTLNPFHMMGVAGVLGGALLCAIHGA
description REACTION_CENTER Photosynthetic reaction center proteins signature. NilmhPfHqlGvagvfggalfcAmHGS
source prosite : PS00244


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