eF-site ID 5kaf-d PDB Code 5kaf Chain d click to enlarge 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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