eF-site ID 5kaf-a PDB Code 5kaf Chain a 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 a:  ANLWERFCNWVTSTDNRLYVGWFGVIMIPTLLAATICFVI AFIAAPPVDIDGIREPVSGSLLYGNNIITGAVVPSSNAIG LHFYPIWEAASLDEWLYNGGPYQLIIFHFLLGASCYMGRQ WELSYRLGMRPWICVAYSAPLASAFAVFLIYPIGQGSFSD GMPLGISGTFNFMIVFQAEHNILMHPFHQLGVAGVFGGAL FCAMHGSLVTSSLIRETTETESANYGYKFGQEEETYNIVA AHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGVWFTALGI STMAFNLNGFNFNHSVIDAKGNVINTWADIINRANLGMEV MHERNAHNFPLDLA Description Functional site 1) chain a residue 41 type sequence L description binding site for residue LMG B 625 source : AG5 2) chain a residue 42 type sequence L description binding site for residue LMG B 625 source : AG5 3) chain a residue 45 type sequence T description binding site for residue LMG B 625 source : AG5 4) chain a residue 170 type sequence D description binding site for residue OEX a 601 source : AL1 5) chain a residue 189 type sequence E description binding site for residue OEX a 601 source : AL1 6) chain a residue 332 type sequence H description binding site for residue OEX a 601 source : AL1 7) chain a residue 333 type sequence E description binding site for residue OEX a 601 source : AL1 8) chain a residue 337 type sequence H description binding site for residue OEX a 601 source : AL1 9) chain a residue 342 type sequence D description binding site for residue OEX a 601 source : AL1 10) chain a residue 344 type sequence A description binding site for residue OEX a 601 source : AL1 11) chain a residue 215 type sequence H description binding site for residue FE2 a 602 source : AL2 12) chain a residue 272 type sequence H description binding site for residue FE2 a 602 source : AL2 13) chain a residue 332 type sequence H description binding site for residue CL a 603 source : AL3 14) chain a residue 333 type sequence E description binding site for residue CL a 603 source : AL3 15) chain a residue 338 type sequence N description binding site for residue CL a 604 source : AL4 16) chain a residue 339 type sequence F description binding site for residue CL a 604 source : AL4 17) chain a residue 215 type sequence H description binding site for residue BCT a 605 source : AL5 18) chain a residue 244 type sequence E description binding site for residue BCT a 605 source : AL5 19) chain a residue 246 type sequence Y description binding site for residue BCT a 605 source : AL5 20) chain a residue 272 type sequence H description binding site for residue BCT a 605 source : AL5 21) chain a residue 150 type sequence P description binding site for residue CLA a 606 source : AL6 22) chain a residue 153 type sequence S description binding site for residue CLA a 606 source : AL6 23) chain a residue 157 type sequence V description binding site for residue CLA a 606 source : AL6 24) chain a residue 183 type sequence M description binding site for residue CLA a 606 source : AL6 25) chain a residue 186 type sequence F description binding site for residue CLA a 606 source : AL6 26) chain a residue 192 type sequence I description binding site for residue CLA a 606 source : AL6 27) chain a residue 193 type sequence L description binding site for residue CLA a 606 source : AL6 28) chain a residue 198 type sequence H description binding site for residue CLA a 606 source : AL6 29) chain a residue 201 type sequence G description binding site for residue CLA a 606 source : AL6 30) chain a residue 202 type sequence V description binding site for residue CLA a 606 source : AL6 31) chain a residue 286 type sequence T description binding site for residue CLA a 606 source : AL6 32) chain a residue 290 type sequence I description binding site for residue CLA a 606 source : AL6 33) chain a residue 199 type sequence Q description binding site for residue CLA a 607 source : AL7 34) chain a residue 202 type sequence V description binding site for residue CLA a 607 source : AL7 35) chain a residue 203 type sequence A description binding site for residue CLA a 607 source : AL7 36) chain a residue 206 type sequence F description binding site for residue CLA a 607 source : AL7 37) chain a residue 207 type sequence G description binding site for residue CLA a 607 source : AL7 38) chain a residue 278 type sequence W description binding site for residue CLA a 607 source : AL7 39) chain a residue 41 type sequence L description binding site for residue PHO a 608 source : AL8 40) chain a residue 44 type sequence A description binding site for residue PHO a 608 source : AL8 41) chain a residue 45 type sequence T description binding site for residue PHO a 608 source : AL8 42) chain a residue 48 type sequence F description binding site for residue PHO a 608 source : AL8 43) chain a residue 126 type sequence Y description binding site for residue PHO a 608 source : AL8 44) chain a residue 130 type sequence Q description binding site for residue PHO a 608 source : AL8 45) chain a residue 146 type sequence A description binding site for residue PHO a 608 source : AL8 46) chain a residue 147 type sequence Y description binding site for residue PHO a 608 source : AL8 47) chain a residue 279 type sequence P description binding site for residue PHO a 608 source : AL8 48) chain a residue 283 type sequence V description binding site for residue PHO a 608 source : AL8 49) chain a residue 39 type sequence P description binding site for residue CLA a 609 source : AL9 50) chain a residue 93 type sequence F description binding site for residue CLA a 609 source : AL9 51) chain a residue 94 type sequence Y description binding site for residue CLA a 609 source : AL9 52) chain a residue 95 type sequence P description binding site for residue CLA a 609 source : AL9 53) chain a residue 96 type sequence I description binding site for residue CLA a 609 source : AL9 54) chain a residue 97 type sequence W description binding site for residue CLA a 609 source : AL9 55) chain a residue 114 type sequence L description binding site for residue CLA a 609 source : AL9 56) chain a residue 117 type sequence F description binding site for residue CLA a 609 source : AL9 57) chain a residue 118 type sequence H description binding site for residue CLA a 609 source : AL9 58) chain a residue 43 type sequence A description binding site for residue BCR a 610 source : AM1 59) chain a residue 50 type sequence I description binding site for residue BCR a 610 source : AM1 60) chain a residue 215 type sequence H description binding site for residue PL9 a 611 source : AM2 61) chain a residue 218 type sequence L description binding site for residue PL9 a 611 source : AM2 62) chain a residue 263 type sequence A description binding site for residue PL9 a 611 source : AM2 63) chain a residue 264 type sequence S description binding site for residue PL9 a 611 source : AM2 64) chain a residue 265 type sequence F description binding site for residue PL9 a 611 source : AM2 65) chain a residue 271 type sequence L description binding site for residue PL9 a 611 source : AM2 66) chain a residue 275 type sequence L description binding site for residue PL9 a 611 source : AM2 67) chain a residue 157 type sequence V description binding site for residue CLA a 612 source : AM3 68) chain a residue 158 type sequence F description binding site for residue CLA a 612 source : AM3 69) chain a residue 172 type sequence M description binding site for residue CLA a 612 source : AM3 70) chain a residue 176 type sequence I description binding site for residue CLA a 612 source : AM3 71) chain a residue 179 type sequence T description binding site for residue CLA a 612 source : AM3 72) chain a residue 180 type sequence F description binding site for residue CLA a 612 source : AM3 73) chain a residue 183 type sequence M description binding site for residue CLA a 612 source : AM3 74) chain a residue 232 type sequence S description binding site for residue LHG a 613 source : AM4 75) chain a residue 234 type sequence N description binding site for residue LHG a 613 source : AM4 76) chain a residue 140 type sequence R description binding site for residue LHG a 614 source : AM5 77) chain a residue 142 type sequence W description binding site for residue LHG a 614 source : AM5 78) chain a residue 273 type sequence F description binding site for residue LHG a 614 source : AM5 79) chain a residue 258 type sequence L description binding site for residue LHG a 615 source : AM6 80) chain a residue 260 type sequence F description binding site for residue LHG a 615 source : AM6 81) chain a residue 262 type sequence Y description binding site for residue LHG a 615 source : AM6 82) chain a residue 263 type sequence A description binding site for residue LHG a 615 source : AM6 83) chain a residue 267 type sequence N description binding site for residue SQD c 501 source : AP3 84) chain a residue 270 type sequence S description binding site for residue SQD c 501 source : AP3 85) chain a residue 274 type sequence F description binding site for residue SQD c 501 source : AP3 86) chain a residue 278 type sequence W description binding site for residue SQD c 501 source : AP3 87) chain a residue 97 type sequence W description binding site for residue LMG c 502 source : AP4 88) chain a residue 98 type sequence E description binding site for residue LMG c 502 source : AP4 89) chain a residue 33 type sequence F description binding site for residue CLA c 507 source : AP9 90) chain a residue 131 type sequence W description binding site for residue CLA c 507 source : AP9 91) chain a residue 155 type sequence F description binding site for residue DGD c 518 source : AR2 92) chain a residue 297 type sequence L description binding site for residue DGD c 519 source : AR3 93) chain a residue 199 type sequence Q description binding site for residue DGD c 520 source : AR4 94) chain a residue 300 type sequence F description binding site for residue DGD c 520 source : AR4 95) chain a residue 301 type sequence N description binding site for residue DGD c 520 source : AR4 96) chain a residue 305 type sequence S description binding site for residue DGD c 520 source : AR4 97) chain a residue 209 type sequence A description binding site for residue PHO d 401 source : AR7 98) chain a residue 210 type sequence L description binding site for residue PHO d 401 source : AR7 99) chain a residue 214 type sequence M description binding site for residue PHO d 401 source : AR7 100) chain a residue 258 type sequence L description binding site for residue PHO d 401 source : AR7 101) chain a residue 206 type sequence F description binding site for residue CLA d 403 source : AR8 102) chain a residue 52 type sequence F description binding site for residue PL9 d 408 source : AS4 103) chain a residue 232 type sequence S description binding site for residue LHG l 101 source : AT2 104) chain a residue 234 type sequence N description binding site for residue LHG l 101 source : AT2 105) 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 106) 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 107) 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 108) 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 109) chain a residue 118 type MOD_RES sequence H description N-acetylmethionine => ECO:0000269|PubMed:19219048, ECO:0000269|PubMed:20558739 source Swiss-Prot : SWS_FT_FI4 110) chain a residue 198 type MOD_RES sequence H description N-acetylmethionine => ECO:0000269|PubMed:19219048, ECO:0000269|PubMed:20558739 source Swiss-Prot : SWS_FT_FI4 111) chain a residue 126 type MOD_RES sequence Y description N-acetylthreonine => ECO:0000269|PubMed:19219048, ECO:0000269|PubMed:20558739 source Swiss-Prot : SWS_FT_FI5 112) chain a residue 215 type MOD_RES sequence H description N-acetylthreonine => ECO:0000269|PubMed:19219048, ECO:0000269|PubMed:20558739 source Swiss-Prot : SWS_FT_FI5 113) chain a residue 272 type MOD_RES sequence H description N-acetylthreonine => ECO:0000269|PubMed:19219048, ECO:0000269|PubMed:20558739 source Swiss-Prot : SWS_FT_FI5 114) 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 115) chain a residue 344 type SITE sequence A description Cleavage; by CtpA => ECO:0000255|HAMAP-Rule:MF_01379 source Swiss-Prot : SWS_FT_FI14 116) 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 117) 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

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