eF-site ID 5kai-a
PDB Code 5kai
Chain a

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Title NH3-bound RT XFEL structure of Photosystem II 500 ms after the 2nd illumination (2F) at 2.8 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 28
type
sequence L
description binding site for residue LMG a 701
source : AK7

2) chain a
residue 45
type
sequence T
description binding site for residue LMG a 701
source : AK7

3) chain a
residue 170
type
sequence D
description binding site for residue OEX a 702
source : AK8

4) chain a
residue 189
type
sequence E
description binding site for residue OEX a 702
source : AK8

5) chain a
residue 332
type
sequence H
description binding site for residue OEX a 702
source : AK8

6) chain a
residue 333
type
sequence E
description binding site for residue OEX a 702
source : AK8

7) chain a
residue 337
type
sequence H
description binding site for residue OEX a 702
source : AK8

8) chain a
residue 342
type
sequence D
description binding site for residue OEX a 702
source : AK8

9) chain a
residue 344
type
sequence A
description binding site for residue OEX a 702
source : AK8

10) chain a
residue 215
type
sequence H
description binding site for residue FE2 a 703
source : AK9

11) chain a
residue 272
type
sequence H
description binding site for residue FE2 a 703
source : AK9

12) chain a
residue 181
type
sequence N
description binding site for residue CL a 704
source : AL1

13) chain a
residue 332
type
sequence H
description binding site for residue CL a 704
source : AL1

14) chain a
residue 333
type
sequence E
description binding site for residue CL a 704
source : AL1

15) chain a
residue 337
type
sequence H
description binding site for residue CL a 705
source : AL2

16) chain a
residue 338
type
sequence N
description binding site for residue CL a 705
source : AL2

17) chain a
residue 339
type
sequence F
description binding site for residue CL a 705
source : AL2

18) chain a
residue 215
type
sequence H
description binding site for residue BCT a 706
source : AL3

19) chain a
residue 244
type
sequence E
description binding site for residue BCT a 706
source : AL3

20) chain a
residue 246
type
sequence Y
description binding site for residue BCT a 706
source : AL3

21) chain a
residue 272
type
sequence H
description binding site for residue BCT a 706
source : AL3

22) chain a
residue 147
type
sequence Y
description binding site for residue CLA a 707
source : AL4

23) chain a
residue 150
type
sequence P
description binding site for residue CLA a 707
source : AL4

24) chain a
residue 153
type
sequence S
description binding site for residue CLA a 707
source : AL4

25) chain a
residue 157
type
sequence V
description binding site for residue CLA a 707
source : AL4

26) chain a
residue 183
type
sequence M
description binding site for residue CLA a 707
source : AL4

27) chain a
residue 186
type
sequence F
description binding site for residue CLA a 707
source : AL4

28) chain a
residue 192
type
sequence I
description binding site for residue CLA a 707
source : AL4

29) chain a
residue 193
type
sequence L
description binding site for residue CLA a 707
source : AL4

30) chain a
residue 198
type
sequence H
description binding site for residue CLA a 707
source : AL4

31) chain a
residue 201
type
sequence G
description binding site for residue CLA a 707
source : AL4

32) chain a
residue 206
type
sequence F
description binding site for residue CLA a 707
source : AL4

33) chain a
residue 286
type
sequence T
description binding site for residue CLA a 707
source : AL4

34) chain a
residue 290
type
sequence I
description binding site for residue CLA a 707
source : AL4

35) chain a
residue 199
type
sequence Q
description binding site for residue CLA a 708
source : AL5

36) chain a
residue 202
type
sequence V
description binding site for residue CLA a 708
source : AL5

37) chain a
residue 203
type
sequence A
description binding site for residue CLA a 708
source : AL5

38) chain a
residue 207
type
sequence G
description binding site for residue CLA a 708
source : AL5

39) chain a
residue 210
type
sequence L
description binding site for residue CLA a 708
source : AL5

40) chain a
residue 278
type
sequence W
description binding site for residue CLA a 708
source : AL5

41) chain a
residue 41
type
sequence L
description binding site for residue PHO a 709
source : AL6

42) chain a
residue 44
type
sequence A
description binding site for residue PHO a 709
source : AL6

43) chain a
residue 45
type
sequence T
description binding site for residue PHO a 709
source : AL6

44) chain a
residue 119
type
sequence F
description binding site for residue PHO a 709
source : AL6

45) chain a
residue 126
type
sequence Y
description binding site for residue PHO a 709
source : AL6

46) chain a
residue 130
type
sequence Q
description binding site for residue PHO a 709
source : AL6

47) chain a
residue 147
type
sequence Y
description binding site for residue PHO a 709
source : AL6

48) chain a
residue 279
type
sequence P
description binding site for residue PHO a 709
source : AL6

49) chain a
residue 283
type
sequence V
description binding site for residue PHO a 709
source : AL6

50) chain a
residue 206
type
sequence F
description binding site for residue PHO a 710
source : AL7

51) chain a
residue 210
type
sequence L
description binding site for residue PHO a 710
source : AL7

52) chain a
residue 214
type
sequence M
description binding site for residue PHO a 710
source : AL7

53) chain a
residue 258
type
sequence L
description binding site for residue PHO a 710
source : AL7

54) chain a
residue 36
type
sequence I
description binding site for residue CLA a 711
source : AL8

55) chain a
residue 93
type
sequence F
description binding site for residue CLA a 711
source : AL8

56) chain a
residue 95
type
sequence P
description binding site for residue CLA a 711
source : AL8

57) chain a
residue 96
type
sequence I
description binding site for residue CLA a 711
source : AL8

58) chain a
residue 114
type
sequence L
description binding site for residue CLA a 711
source : AL8

59) chain a
residue 118
type
sequence H
description binding site for residue CLA a 711
source : AL8

60) chain a
residue 42
type
sequence L
description binding site for residue BCR a 712
source : AL9

61) chain a
residue 43
type
sequence A
description binding site for residue BCR a 712
source : AL9

62) chain a
residue 214
type
sequence M
description binding site for residue PL9 a 713
source : AM1

63) chain a
residue 215
type
sequence H
description binding site for residue PL9 a 713
source : AM1

64) chain a
residue 218
type
sequence L
description binding site for residue PL9 a 713
source : AM1

65) chain a
residue 255
type
sequence F
description binding site for residue PL9 a 713
source : AM1

66) chain a
residue 264
type
sequence S
description binding site for residue PL9 a 713
source : AM1

67) chain a
residue 265
type
sequence F
description binding site for residue PL9 a 713
source : AM1

68) chain a
residue 271
type
sequence L
description binding site for residue PL9 a 713
source : AM1

69) chain a
residue 200
type
sequence L
description binding site for residue SQD a 714
source : AM2

70) chain a
residue 203
type
sequence A
description binding site for residue SQD a 714
source : AM2

71) chain a
residue 267
type
sequence N
description binding site for residue SQD a 714
source : AM2

72) chain a
residue 270
type
sequence S
description binding site for residue SQD a 714
source : AM2

73) chain a
residue 274
type
sequence F
description binding site for residue SQD a 714
source : AM2

74) chain a
residue 278
type
sequence W
description binding site for residue SQD a 714
source : AM2

75) chain a
residue 281
type
sequence V
description binding site for residue SQD a 714
source : AM2

76) chain a
residue 93
type
sequence F
description binding site for residue LMG a 715
source : AM3

77) chain a
residue 97
type
sequence W
description binding site for residue LMG a 715
source : AM3

78) chain a
residue 98
type
sequence E
description binding site for residue LMG a 715
source : AM3

79) chain a
residue 172
type
sequence M
description binding site for residue CLA a 719
source : AM4

80) chain a
residue 176
type
sequence I
description binding site for residue CLA a 719
source : AM4

81) chain a
residue 179
type
sequence T
description binding site for residue CLA a 719
source : AM4

82) chain a
residue 180
type
sequence F
description binding site for residue CLA a 719
source : AM4

83) chain a
residue 183
type
sequence M
description binding site for residue CLA a 719
source : AM4

84) chain a
residue 140
type
sequence R
description binding site for residue LHG a 720
source : AM5

85) chain a
residue 142
type
sequence W
description binding site for residue LHG a 720
source : AM5

86) chain a
residue 273
type
sequence F
description binding site for residue LHG a 720
source : AM5

87) chain a
residue 232
type
sequence S
description binding site for residue LHG b 629
source : AP3

88) chain a
residue 234
type
sequence N
description binding site for residue LHG b 629
source : AP3

89) chain a
residue 121
type
sequence L
description binding site for residue CLA c 505
source : AP8

90) chain a
residue 131
type
sequence W
description binding site for residue CLA c 505
source : AP8

91) chain a
residue 155
type
sequence F
description binding site for residue DGD c 516
source : AR1

92) chain a
residue 163
type
sequence I
description binding site for residue DGD c 516
source : AR1

93) chain a
residue 197
type
sequence F
description binding site for residue DGD c 517
source : AR2

94) chain a
residue 199
type
sequence Q
description binding site for residue DGD c 518
source : AR3

95) chain a
residue 200
type
sequence L
description binding site for residue DGD c 518
source : AR3

96) chain a
residue 278
type
sequence W
description binding site for residue DGD c 518
source : AR3

97) chain a
residue 300
type
sequence F
description binding site for residue DGD c 518
source : AR3

98) chain a
residue 301
type
sequence N
description binding site for residue DGD c 518
source : AR3

99) chain a
residue 305
type
sequence S
description binding site for residue DGD c 518
source : AR3

100) chain a
residue 183
type
sequence M
description binding site for residue CLA d 402
source : AR6

101) chain a
residue 52
type
sequence F
description binding site for residue PL9 d 405
source : AR9

102) chain a
residue 232
type
sequence S
description binding site for residue LHG d 406
source : AS1

103) chain a
residue 234
type
sequence N
description binding site for residue LHG d 406
source : AS1

104) chain a
residue 258
type
sequence L
description binding site for residue LHG e 101
source : AS4

105) chain a
residue 260
type
sequence F
description binding site for residue LHG e 101
source : AS4

106) chain a
residue 262
type
sequence Y
description binding site for residue LHG e 101
source : AS4

107) 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

108) 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

109) 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

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

111) chain a
residue 118
type MOD_RES
sequence H
description N-formylmethionine => ECO:0000269|PubMed:19219048, ECO:0000269|PubMed:20558739
source Swiss-Prot : SWS_FT_FI4

112) chain a
residue 198
type MOD_RES
sequence H
description N-formylmethionine => ECO:0000269|PubMed:19219048, ECO:0000269|PubMed:20558739
source Swiss-Prot : SWS_FT_FI4

113) chain a
residue 126
type MOD_RES
sequence Y
description N-formylmethionine => ECO:0000269|PubMed:19219048, ECO:0000269|PubMed:20558739
source Swiss-Prot : SWS_FT_FI5

114) chain a
residue 215
type MOD_RES
sequence H
description N-formylmethionine => ECO:0000269|PubMed:19219048, ECO:0000269|PubMed:20558739
source Swiss-Prot : SWS_FT_FI5

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

116) chain a
residue 170
type BINDING
sequence D
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

117) chain a
residue 189
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

118) 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

119) 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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