eF-site ID 6dhe-d
PDB Code 6dhe
Chain d

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Title RT XFEL structure of the dark-stable state of Photosystem II (0F, S1-rich) at 2.05 Angstrom resolution
Classification PHOTOSYNTHESIS
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 401
source : AK6

2) chain d
residue 268
type
sequence H
description binding site for residue FE2 a 401
source : AK6

3) chain d
residue 317
type
sequence K
description binding site for residue CL a 402
source : AK7

4) chain d
residue 214
type
sequence H
description binding site for residue BCT a 404
source : AK9

5) chain d
residue 244
type
sequence Y
description binding site for residue BCT a 404
source : AK9

6) chain d
residue 264
type
sequence K
description binding site for residue BCT a 404
source : AK9

7) chain d
residue 268
type
sequence H
description binding site for residue BCT a 404
source : AK9

8) chain d
residue 205
type
sequence L
description binding site for residue CLA a 405
source : AL1

9) chain d
residue 157
type
sequence F
description binding site for residue CLA a 406
source : AL2

10) chain d
residue 175
type
sequence V
description binding site for residue CLA a 406
source : AL2

11) chain d
residue 178
type
sequence I
description binding site for residue CLA a 406
source : AL2

12) chain d
residue 179
type
sequence F
description binding site for residue CLA a 406
source : AL2

13) chain d
residue 182
type
sequence L
description binding site for residue CLA a 406
source : AL2

14) chain d
residue 208
type
sequence A
description binding site for residue PHO a 407
source : AL3

15) chain d
residue 209
type
sequence L
description binding site for residue PHO a 407
source : AL3

16) chain d
residue 213
type
sequence I
description binding site for residue PHO a 407
source : AL3

17) chain d
residue 253
type
sequence W
description binding site for residue PHO a 407
source : AL3

18) chain d
residue 257
type
sequence F
description binding site for residue PHO a 407
source : AL3

19) chain d
residue 38
type
sequence F
description binding site for residue PL9 a 410
source : AL6

20) chain d
residue 39
type
sequence P
description binding site for residue PL9 a 410
source : AL6

21) chain d
residue 45
type
sequence L
description binding site for residue PL9 a 410
source : AL6

22) chain d
residue 230
type
sequence S
description binding site for residue SQD a 411
source : AL7

23) chain d
residue 232
type
sequence F
description binding site for residue SQD a 411
source : AL7

24) chain d
residue 233
type
sequence R
description binding site for residue SQD a 411
source : AL7

25) chain d
residue 159
type
sequence I
description binding site for residue CLA b 603
source : AM3

26) chain d
residue 162
type
sequence L
description binding site for residue CLA b 603
source : AM3

27) chain d
residue 281
type
sequence M
description binding site for residue CLA b 608
source : AM8

28) chain d
residue 120
type
sequence F
description binding site for residue CLA b 609
source : AM9

29) chain d
residue 123
type
sequence I
description binding site for residue CLA b 609
source : AM9

30) chain d
residue 127
type
sequence L
description binding site for residue CLA b 609
source : AM9

31) chain d
residue 284
type
sequence I
description binding site for residue LMG b 621
source : AO3

32) chain d
residue 32
type
sequence W
description binding site for residue LMG b 624
source : AO5

33) chain d
residue 41
type
sequence A
description binding site for residue PHO d 401
source : AR1

34) chain d
residue 48
type
sequence W
description binding site for residue PHO d 401
source : AR1

35) chain d
residue 114
type
sequence I
description binding site for residue PHO d 401
source : AR1

36) chain d
residue 121
type
sequence G
description binding site for residue PHO d 401
source : AR1

37) chain d
residue 122
type
sequence L
description binding site for residue PHO d 401
source : AR1

38) chain d
residue 125
type
sequence F
description binding site for residue PHO d 401
source : AR1

39) chain d
residue 129
type
sequence Q
description binding site for residue PHO d 401
source : AR1

40) chain d
residue 142
type
sequence N
description binding site for residue PHO d 401
source : AR1

41) chain d
residue 145
type
sequence A
description binding site for residue PHO d 401
source : AR1

42) chain d
residue 146
type
sequence F
description binding site for residue PHO d 401
source : AR1

43) chain d
residue 153
type
sequence F
description binding site for residue PHO d 401
source : AR1

44) chain d
residue 198
type
sequence M
description binding site for residue CLA d 402
source : AR2

45) chain d
residue 201
type
sequence V
description binding site for residue CLA d 402
source : AR2

46) chain d
residue 202
type
sequence A
description binding site for residue CLA d 402
source : AR2

47) chain d
residue 149
type
sequence P
description binding site for residue CLA d 403
source : AR3

48) chain d
residue 152
type
sequence V
description binding site for residue CLA d 403
source : AR3

49) chain d
residue 156
type
sequence V
description binding site for residue CLA d 403
source : AR3

50) chain d
residue 182
type
sequence L
description binding site for residue CLA d 403
source : AR3

51) chain d
residue 185
type
sequence F
description binding site for residue CLA d 403
source : AR3

52) chain d
residue 186
type
sequence Q
description binding site for residue CLA d 403
source : AR3

53) chain d
residue 191
type
sequence W
description binding site for residue CLA d 403
source : AR3

54) chain d
residue 192
type
sequence T
description binding site for residue CLA d 403
source : AR3

55) chain d
residue 197
type
sequence H
description binding site for residue CLA d 403
source : AR3

56) chain d
residue 200
type
sequence G
description binding site for residue CLA d 403
source : AR3

57) chain d
residue 282
type
sequence S
description binding site for residue CLA d 403
source : AR3

58) chain d
residue 283
type
sequence A
description binding site for residue CLA d 403
source : AR3

59) chain d
residue 286
type
sequence V
description binding site for residue CLA d 403
source : AR3

60) chain d
residue 35
type
sequence I
description binding site for residue CLA d 404
source : AR4

61) chain d
residue 40
type
sequence C
description binding site for residue CLA d 404
source : AR4

62) chain d
residue 43
type
sequence L
description binding site for residue CLA d 404
source : AR4

63) chain d
residue 89
type
sequence L
description binding site for residue CLA d 404
source : AR4

64) chain d
residue 90
type
sequence L
description binding site for residue CLA d 404
source : AR4

65) chain d
residue 91
type
sequence L
description binding site for residue CLA d 404
source : AR4

66) chain d
residue 92
type
sequence L
description binding site for residue CLA d 404
source : AR4

67) chain d
residue 93
type
sequence W
description binding site for residue CLA d 404
source : AR4

68) chain d
residue 104
type
sequence W
description binding site for residue CLA d 404
source : AR4

69) chain d
residue 112
type
sequence T
description binding site for residue CLA d 404
source : AR4

70) chain d
residue 113
type
sequence F
description binding site for residue CLA d 404
source : AR4

71) chain d
residue 116
type
sequence L
description binding site for residue CLA d 404
source : AR4

72) chain d
residue 117
type
sequence H
description binding site for residue CLA d 404
source : AR4

73) chain d
residue 42
type
sequence Y
description binding site for residue 8CT d 405
source : AR5

74) chain d
residue 46
type
sequence G
description binding site for residue 8CT d 405
source : AR5

75) chain d
residue 47
type
sequence G
description binding site for residue 8CT d 405
source : AR5

76) chain d
residue 49
type
sequence L
description binding site for residue 8CT d 405
source : AR5

77) chain d
residue 50
type
sequence T
description binding site for residue 8CT d 405
source : AR5

78) chain d
residue 199
type
sequence M
description binding site for residue PL9 d 406
source : AR6

79) chain d
residue 202
type
sequence A
description binding site for residue PL9 d 406
source : AR6

80) chain d
residue 214
type
sequence H
description binding site for residue PL9 d 406
source : AR6

81) chain d
residue 217
type
sequence T
description binding site for residue PL9 d 406
source : AR6

82) chain d
residue 246
type
sequence M
description binding site for residue PL9 d 406
source : AR6

83) chain d
residue 253
type
sequence W
description binding site for residue PL9 d 406
source : AR6

84) chain d
residue 260
type
sequence A
description binding site for residue PL9 d 406
source : AR6

85) chain d
residue 261
type
sequence F
description binding site for residue PL9 d 406
source : AR6

86) chain d
residue 274
type
sequence V
description binding site for residue PL9 d 406
source : AR6

87) chain d
residue 141
type
sequence Y
description binding site for residue LHG d 407
source : AR7

88) chain d
residue 144
type
sequence I
description binding site for residue LHG d 407
source : AR7

89) chain d
residue 266
type
sequence W
description binding site for residue LHG d 407
source : AR7

90) chain d
residue 269
type
sequence F
description binding site for residue LHG d 407
source : AR7

91) chain d
residue 276
type
sequence V
description binding site for residue LHG d 407
source : AR7

92) chain d
residue 277
type
sequence T
description binding site for residue LHG d 407
source : AR7

93) chain d
residue 257
type
sequence F
description binding site for residue LHG d 408
source : AR8

94) chain d
residue 259
type
sequence I
description binding site for residue LHG d 408
source : AR8

95) chain d
residue 260
type
sequence A
description binding site for residue LHG d 408
source : AR8

96) chain d
residue 261
type
sequence F
description binding site for residue LHG d 408
source : AR8

97) chain d
residue 262
type
sequence S
description binding site for residue LHG d 408
source : AR8

98) chain d
residue 263
type
sequence N
description binding site for residue LHG d 408
source : AR8

99) chain d
residue 266
type
sequence W
description binding site for residue LHG d 408
source : AR8

100) chain d
residue 219
type
sequence E
description binding site for residue LHG d 409
source : AR9

101) chain d
residue 220
type
sequence N
description binding site for residue LHG d 409
source : AR9

102) chain d
residue 229
type
sequence A
description binding site for residue LHG d 409
source : AR9

103) chain d
residue 230
type
sequence S
description binding site for residue LHG d 409
source : AR9

104) chain d
residue 231
type
sequence T
description binding site for residue LHG d 409
source : AR9

105) chain d
residue 232
type
sequence F
description binding site for residue LHG d 409
source : AR9

106) chain d
residue 67
type
sequence Y
description binding site for residue LMG d 410
source : AS1

107) chain d
residue 70
type
sequence G
description binding site for residue LMG d 410
source : AS1

108) chain d
residue 71
type
sequence C
description binding site for residue LMG d 410
source : AS1

109) chain d
residue 72
type
sequence N
description binding site for residue LMG d 410
source : AS1

110) chain d
residue 73
type
sequence F
description binding site for residue LMG d 410
source : AS1

111) chain d
residue 27
type
sequence F
description binding site for residue LHG e 101
source : AS2

112) chain d
residue 26
type
sequence R
description binding site for residue SQD f 101
source : AS4

113) chain d
residue 86
type
sequence G
description binding site for residue DGD h 102
source : AS6

114) chain d
residue 87
type
sequence H
description binding site for residue DGD h 102
source : AS6

115) chain d
residue 162
type
sequence L
description binding site for residue DGD h 102
source : AS6

116) chain d
residue 163
type
sequence G
description binding site for residue DGD h 102
source : AS6

117) chain d
residue 291
type
sequence L
description binding site for residue DGD h 102
source : AS6

118) chain d
residue 266
type
sequence W
description binding site for residue LHG l 101
source : AS8

119) chain d
residue 273
type
sequence F
description binding site for residue LHG l 101
source : AS8

120) chain d
residue 161-193
type TRANSMEM
sequence PLGQSSWFFAPSFGVAAIFRFLLFFQGFHNWTL
description Helical => ECO:0000269|PubMed:33846594, ECO:0007744|PDB:7NHQ
source Swiss-Prot : SWS_FT_FI2

121) chain d
residue 289-352
type TRANSMEM
sequence LALNLRSYDFISQEIRAAEDPEFETFYTKNLLLNEGIRAW
MAPQDQPHENFVFPEEVLPRGNAL
description Helical => ECO:0000269|PubMed:33846594, ECO:0007744|PDB:7NHQ
source Swiss-Prot : SWS_FT_FI2

122) chain d
residue 266-288
type TRANSMEM
sequence WLHFFMLFVPVTGLWMSAIGVVG
description Helical => ECO:0000255|HAMAP-Rule:MF_00717
source Swiss-Prot : SWS_FT_FI1

123) chain d
residue 32-53
type TRANSMEM
sequence WSGILLFPCAYLALGGWLTGTT
description Helical => ECO:0000255|HAMAP-Rule:MF_00717
source Swiss-Prot : SWS_FT_FI1

124) chain d
residue 109-131
type TRANSMEM
sequence GLWTFIALHGAFGLIGFMLRQFE
description Helical => ECO:0000255|HAMAP-Rule:MF_00717
source Swiss-Prot : SWS_FT_FI1

125) chain d
residue 141-160
type TRANSMEM
sequence YNAIAFSAPIAVFVSVFLIY
description Helical => ECO:0000255|HAMAP-Rule:MF_00717
source Swiss-Prot : SWS_FT_FI1

126) chain d
residue 194-217
type TRANSMEM
sequence NPFHMMGVAGVLGGALLCAIHGAT
description Helical => ECO:0000255|HAMAP-Rule:MF_00717
source Swiss-Prot : SWS_FT_FI1

127) 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

128) chain d
residue 132-140
type TOPO_DOM
sequence IARLVGVRP
description Cytoplasmic => ECO:0000269|PubMed:33846594, ECO:0007744|PDB:7NHQ
source Swiss-Prot : SWS_FT_FI3

129) chain d
residue 218-265
type TOPO_DOM
sequence VENTLFQDGEGASTFRAFNPTQAEETYSMVTANRFWSQIF
GIAFSNKR
description Cytoplasmic => ECO:0000269|PubMed:33846594, ECO:0007744|PDB:7NHQ
source Swiss-Prot : SWS_FT_FI3

130) 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

131) 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

132) 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

133) 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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