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 : AL2

2) chain d
residue 268
type
sequence H
description binding site for residue FE2 a 602
source : AL2

3) chain d
residue 317
type
sequence K
description binding site for residue CL a 603
source : AL3

4) chain d
residue 214
type
sequence H
description binding site for residue BCT a 605
source : AL5

5) chain d
residue 244
type
sequence Y
description binding site for residue BCT a 605
source : AL5

6) chain d
residue 268
type
sequence H
description binding site for residue BCT a 605
source : AL5

7) chain d
residue 157
type
sequence F
description binding site for residue CLA a 607
source : AL7

8) chain d
residue 175
type
sequence V
description binding site for residue CLA a 607
source : AL7

9) chain d
residue 178
type
sequence I
description binding site for residue CLA a 607
source : AL7

10) chain d
residue 179
type
sequence F
description binding site for residue CLA a 607
source : AL7

11) chain d
residue 182
type
sequence L
description binding site for residue CLA a 607
source : AL7

12) chain d
residue 208
type
sequence A
description binding site for residue PHO a 608
source : AL8

13) chain d
residue 209
type
sequence L
description binding site for residue PHO a 608
source : AL8

14) chain d
residue 213
type
sequence I
description binding site for residue PHO a 608
source : AL8

15) chain d
residue 253
type
sequence W
description binding site for residue PHO a 608
source : AL8

16) chain d
residue 257
type
sequence F
description binding site for residue PHO a 608
source : AL8

17) chain d
residue 38
type
sequence F
description binding site for residue PL9 a 611
source : AM2

18) chain d
residue 198
type
sequence M
description binding site for residue CLA a 612
source : AM3

19) chain d
residue 201
type
sequence V
description binding site for residue CLA a 612
source : AM3

20) chain d
residue 202
type
sequence A
description binding site for residue CLA a 612
source : AM3

21) chain d
residue 206
type
sequence G
description binding site for residue CLA a 612
source : AM3

22) chain d
residue 141
type
sequence Y
description binding site for residue LHG a 613
source : AM4

23) chain d
residue 266
type
sequence W
description binding site for residue LHG a 613
source : AM4

24) chain d
residue 269
type
sequence F
description binding site for residue LHG a 613
source : AM4

25) chain d
residue 219
type
sequence E
description binding site for residue LHG a 614
source : AM5

26) chain d
residue 220
type
sequence N
description binding site for residue LHG a 614
source : AM5

27) chain d
residue 229
type
sequence A
description binding site for residue LHG a 614
source : AM5

28) chain d
residue 231
type
sequence T
description binding site for residue LHG a 614
source : AM5

29) chain d
residue 232
type
sequence F
description binding site for residue LHG a 614
source : AM5

30) chain d
residue 27
type
sequence F
description binding site for residue LHG a 615
source : AM6

31) chain d
residue 28
type
sequence V
description binding site for residue LHG a 615
source : AM6

32) chain d
residue 158
type
sequence L
description binding site for residue CLA b 605
source : AM9

33) chain d
residue 120
type
sequence F
description binding site for residue CLA b 611
source : AN6

34) chain d
residue 123
type
sequence I
description binding site for residue CLA b 611
source : AN6

35) chain d
residue 126
type
sequence M
description binding site for residue CLA b 611
source : AN6

36) chain d
residue 232
type
sequence F
description binding site for residue SQD c 501
source : AP3

37) chain d
residue 233
type
sequence R
description binding site for residue SQD c 501
source : AP3

38) chain d
residue 41
type
sequence A
description binding site for residue PHO d 401
source : AR7

39) chain d
residue 44
type
sequence A
description binding site for residue PHO d 401
source : AR7

40) chain d
residue 48
type
sequence W
description binding site for residue PHO d 401
source : AR7

41) chain d
residue 121
type
sequence G
description binding site for residue PHO d 401
source : AR7

42) chain d
residue 122
type
sequence L
description binding site for residue PHO d 401
source : AR7

43) chain d
residue 125
type
sequence F
description binding site for residue PHO d 401
source : AR7

44) chain d
residue 129
type
sequence Q
description binding site for residue PHO d 401
source : AR7

45) chain d
residue 142
type
sequence N
description binding site for residue PHO d 401
source : AR7

46) chain d
residue 146
type
sequence F
description binding site for residue PHO d 401
source : AR7

47) chain d
residue 153
type
sequence F
description binding site for residue PHO d 401
source : AR7

48) chain d
residue 174
type
sequence G
description binding site for residue PHO d 401
source : AR7

49) chain d
residue 275
type
sequence P
description binding site for residue PHO d 401
source : AR7

50) chain d
residue 279
type
sequence L
description binding site for residue PHO d 401
source : AR7

51) chain d
residue 149
type
sequence P
description binding site for residue CLA d 403
source : AR8

52) chain d
residue 152
type
sequence V
description binding site for residue CLA d 403
source : AR8

53) chain d
residue 156
type
sequence V
description binding site for residue CLA d 403
source : AR8

54) chain d
residue 182
type
sequence L
description binding site for residue CLA d 403
source : AR8

55) chain d
residue 185
type
sequence F
description binding site for residue CLA d 403
source : AR8

56) chain d
residue 186
type
sequence Q
description binding site for residue CLA d 403
source : AR8

57) chain d
residue 191
type
sequence W
description binding site for residue CLA d 403
source : AR8

58) chain d
residue 192
type
sequence T
description binding site for residue CLA d 403
source : AR8

59) chain d
residue 197
type
sequence H
description binding site for residue CLA d 403
source : AR8

60) chain d
residue 200
type
sequence G
description binding site for residue CLA d 403
source : AR8

61) chain d
residue 201
type
sequence V
description binding site for residue CLA d 403
source : AR8

62) chain d
residue 204
type
sequence V
description binding site for residue CLA d 403
source : AR8

63) chain d
residue 282
type
sequence S
description binding site for residue CLA d 403
source : AR8

64) chain d
residue 283
type
sequence A
description binding site for residue CLA d 403
source : AR8

65) chain d
residue 35
type
sequence I
description binding site for residue CLA d 404
source : AR9

66) chain d
residue 39
type
sequence P
description binding site for residue CLA d 404
source : AR9

67) chain d
residue 40
type
sequence C
description binding site for residue CLA d 404
source : AR9

68) chain d
residue 43
type
sequence L
description binding site for residue CLA d 404
source : AR9

69) chain d
residue 89
type
sequence L
description binding site for residue CLA d 404
source : AR9

70) chain d
residue 90
type
sequence L
description binding site for residue CLA d 404
source : AR9

71) chain d
residue 91
type
sequence L
description binding site for residue CLA d 404
source : AR9

72) chain d
residue 92
type
sequence L
description binding site for residue CLA d 404
source : AR9

73) chain d
residue 93
type
sequence W
description binding site for residue CLA d 404
source : AR9

74) chain d
residue 112
type
sequence T
description binding site for residue CLA d 404
source : AR9

75) chain d
residue 113
type
sequence F
description binding site for residue CLA d 404
source : AR9

76) chain d
residue 117
type
sequence H
description binding site for residue CLA d 404
source : AR9

77) chain d
residue 42
type
sequence Y
description binding site for residue BCR d 405
source : AS1

78) chain d
residue 43
type
sequence L
description binding site for residue BCR d 405
source : AS1

79) chain d
residue 46
type
sequence G
description binding site for residue BCR d 405
source : AS1

80) chain d
residue 49
type
sequence L
description binding site for residue BCR d 405
source : AS1

81) chain d
residue 67
type
sequence Y
description binding site for residue LMG d 406
source : AS2

82) chain d
residue 71
type
sequence C
description binding site for residue LMG d 406
source : AS2

83) chain d
residue 72
type
sequence N
description binding site for residue LMG d 406
source : AS2

84) chain d
residue 73
type
sequence F
description binding site for residue LMG d 406
source : AS2

85) chain d
residue 257
type
sequence F
description binding site for residue LHG d 407
source : AS3

86) chain d
residue 259
type
sequence I
description binding site for residue LHG d 407
source : AS3

87) chain d
residue 260
type
sequence A
description binding site for residue LHG d 407
source : AS3

88) chain d
residue 261
type
sequence F
description binding site for residue LHG d 407
source : AS3

89) chain d
residue 262
type
sequence S
description binding site for residue LHG d 407
source : AS3

90) chain d
residue 263
type
sequence N
description binding site for residue LHG d 407
source : AS3

91) chain d
residue 266
type
sequence W
description binding site for residue LHG d 407
source : AS3

92) chain d
residue 199
type
sequence M
description binding site for residue PL9 d 408
source : AS4

93) chain d
residue 210
type
sequence L
description binding site for residue PL9 d 408
source : AS4

94) chain d
residue 213
type
sequence I
description binding site for residue PL9 d 408
source : AS4

95) chain d
residue 214
type
sequence H
description binding site for residue PL9 d 408
source : AS4

96) chain d
residue 217
type
sequence T
description binding site for residue PL9 d 408
source : AS4

97) chain d
residue 253
type
sequence W
description binding site for residue PL9 d 408
source : AS4

98) chain d
residue 260
type
sequence A
description binding site for residue PL9 d 408
source : AS4

99) chain d
residue 261
type
sequence F
description binding site for residue PL9 d 408
source : AS4

100) chain d
residue 274
type
sequence V
description binding site for residue PL9 d 408
source : AS4

101) chain d
residue 19
type
sequence D
description binding site for residue LMG d 409
source : AS5

102) chain d
residue 23
type
sequence K
description binding site for residue LMG d 409
source : AS5

103) chain d
residue 32
type
sequence W
description binding site for residue LMG d 409
source : AS5

104) chain d
residue 134
type
sequence R
description binding site for residue LMG d 409
source : AS5

105) chain d
residue 24
type
sequence R
description binding site for residue SQD f 101
source : AS7

106) chain d
residue 26
type
sequence R
description binding site for residue SQD f 101
source : AS7

107) chain d
residue 87
type
sequence H
description binding site for residue DGD h 102
source : AS9

108) chain d
residue 162
type
sequence L
description binding site for residue DGD h 102
source : AS9

109) chain d
residue 163
type
sequence G
description binding site for residue DGD h 102
source : AS9

110) chain d
residue 266
type
sequence W
description binding site for residue LHG l 101
source : AT2

111) chain d
residue 273
type
sequence F
description binding site for residue LHG l 101
source : AT2

112) chain d
residue 132-140
type TRANSMEM
sequence IARLVGVRP
description Helical => ECO:0000269|PubMed:33846594, ECO:0007744|PDB:7NHQ
source Swiss-Prot : SWS_FT_FI1

113) 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

114) 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

115) 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

116) chain d
residue 32-53
type TOPO_DOM
sequence WSGILLFPCAYLALGGWLTGTT
description Cytoplasmic => ECO:0000269|PubMed:33846594, ECO:0007744|PDB:7NHQ
source Swiss-Prot : SWS_FT_FI2

117) chain d
residue 109-131
type TOPO_DOM
sequence GLWTFIALHGAFGLIGFMLRQFE
description Cytoplasmic => ECO:0000269|PubMed:33846594, ECO:0007744|PDB:7NHQ
source Swiss-Prot : SWS_FT_FI2

118) 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

119) 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

120) chain d
residue 54-108
type TOPO_DOM
sequence FVTSWYTHGLASSYLEGCNFLTVAVSTPANSMGHSLLLLW
GPEAQGDFTRWCQLG
description Lumenal => ECO:0000269|PubMed:33846594, ECO:0007744|PDB:7NHQ
source Swiss-Prot : SWS_FT_FI3

121) chain d
residue 161-193
type TOPO_DOM
sequence PLGQSSWFFAPSFGVAAIFRFLLFFQGFHNWTL
description Lumenal => ECO:0000269|PubMed:33846594, ECO:0007744|PDB:7NHQ
source Swiss-Prot : SWS_FT_FI3

122) 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

123) 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

124) 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

125) 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

126) 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


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