data_4AYT # _model_server_result.job_id DCYaUtBtigW29G_pB0nxiQ _model_server_result.datetime_utc '2025-02-28 14:02:52' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 4ayt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1727}' # _entry.id 4AYT # _exptl.entry_id 4AYT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 1464.043 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description CARDIOLIPIN _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 4AYT _cell.length_a 175.11 _cell.length_b 175.11 _cell.length_c 49.55 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4AYT _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 6_555 -x,-x+y,-z+1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 16.516667 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 F N N ? 6 I N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A OG SER 384 A SER 534 1_555 C MG MG . A MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc2 A OE1 GLN 425 A GLN 575 1_555 C MG MG . A MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc3 C MG MG . A MG 801 1_555 D O3G ACP . A ACP 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc4 C MG MG . A MG 801 1_555 D O2B ACP . A ACP 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? # _chem_comp.formula 'C81 H156 O17 P2 -2' _chem_comp.formula_weight 1464.043 _chem_comp.id CDL _chem_comp.mon_nstd_flag . _chem_comp.name CARDIOLIPIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "DIPHOSPHATIDYL GLYCEROL;BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL" # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C1 O1 CDL sing 121 n n C1 CA2 CDL sing 122 n n C1 CB2 CDL sing 123 n n C1 H1 CDL sing 124 n n O1 H1O1 CDL sing 125 n n CA2 OA2 CDL sing 126 n n CA2 HA22 CDL sing 127 n n CA2 HA21 CDL sing 128 n n OA2 PA1 CDL sing 129 n n PA1 OA3 CDL doub 130 n n PA1 OA4 CDL sing 131 n n PA1 OA5 CDL sing 132 n n OA5 CA3 CDL sing 133 n n CA3 CA4 CDL sing 134 n n CA3 HA32 CDL sing 135 n n CA3 HA31 CDL sing 136 n n CA4 OA6 CDL sing 137 n n CA4 CA6 CDL sing 138 n n CA4 HA4 CDL sing 139 n n OA6 CA5 CDL sing 140 n n CA5 OA7 CDL doub 141 n n CA5 C11 CDL sing 142 n n C11 C12 CDL sing 143 n n C11 H112 CDL sing 144 n n C11 H111 CDL sing 145 n n C12 C13 CDL sing 146 n n C12 H122 CDL sing 147 n n C12 H121 CDL sing 148 n n C13 C14 CDL sing 149 n n C13 H132 CDL sing 150 n n C13 H131 CDL sing 151 n n C14 C15 CDL sing 152 n n C14 H142 CDL sing 153 n n C14 H141 CDL sing 154 n n C15 C16 CDL sing 155 n n C15 H152 CDL sing 156 n n C15 H151 CDL sing 157 n n C16 C17 CDL sing 158 n n C16 H162 CDL sing 159 n n C16 H161 CDL sing 160 n n C17 C18 CDL sing 161 n n C17 H172 CDL sing 162 n n C17 H171 CDL sing 163 n n C18 C19 CDL sing 164 n n C18 H182 CDL sing 165 n n C18 H181 CDL sing 166 n n C19 C20 CDL sing 167 n n C19 H192 CDL sing 168 n n C19 H191 CDL sing 169 n n C20 C21 CDL sing 170 n n C20 H202 CDL sing 171 n n C20 H201 CDL sing 172 n n C21 C22 CDL sing 173 n n C21 H212 CDL sing 174 n n C21 H211 CDL sing 175 n n C22 C23 CDL sing 176 n n C22 H222 CDL sing 177 n n C22 H221 CDL sing 178 n n C23 C24 CDL sing 179 n n C23 H232 CDL sing 180 n n C23 H231 CDL sing 181 n n C24 C25 CDL sing 182 n n C24 H242 CDL sing 183 n n C24 H241 CDL sing 184 n n C25 C26 CDL sing 185 n n C25 H252 CDL sing 186 n n C25 H251 CDL sing 187 n n C26 C27 CDL sing 188 n n C26 H262 CDL sing 189 n n C26 H261 CDL sing 190 n n C27 H273 CDL sing 191 n n C27 H272 CDL sing 192 n n C27 H271 CDL sing 193 n n CA6 OA8 CDL sing 194 n n CA6 HA62 CDL sing 195 n n CA6 HA61 CDL sing 196 n n OA8 CA7 CDL sing 197 n n CA7 OA9 CDL doub 198 n n CA7 C31 CDL sing 199 n n C31 C32 CDL sing 200 n n C31 H312 CDL sing 201 n n C31 H311 CDL sing 202 n n C32 C33 CDL sing 203 n n C32 H322 CDL sing 204 n n C32 H321 CDL sing 205 n n C33 C34 CDL sing 206 n n C33 H332 CDL sing 207 n n C33 H331 CDL sing 208 n n C34 C35 CDL sing 209 n n C34 H342 CDL sing 210 n n C34 H341 CDL sing 211 n n C35 C36 CDL sing 212 n n C35 H352 CDL sing 213 n n C35 H351 CDL sing 214 n n C36 C37 CDL sing 215 n n C36 H362 CDL sing 216 n n C36 H361 CDL sing 217 n n C37 C38 CDL sing 218 n n C37 H372 CDL sing 219 n n C37 H371 CDL sing 220 n n C38 C39 CDL sing 221 n n C38 H382 CDL sing 222 n n C38 H381 CDL sing 223 n n C39 C40 CDL sing 224 n n C39 H392 CDL sing 225 n n C39 H391 CDL sing 226 n n C40 C41 CDL sing 227 n n C40 H402 CDL sing 228 n n C40 H401 CDL sing 229 n n C41 C42 CDL sing 230 n n C41 H412 CDL sing 231 n n C41 H411 CDL sing 232 n n C42 C43 CDL sing 233 n n C42 H422 CDL sing 234 n n C42 H421 CDL sing 235 n n C43 C44 CDL sing 236 n n C43 H432 CDL sing 237 n n C43 H431 CDL sing 238 n n C44 C45 CDL sing 239 n n C44 H442 CDL sing 240 n n C44 H441 CDL sing 241 n n C45 C46 CDL sing 242 n n C45 H452 CDL sing 243 n n C45 H451 CDL sing 244 n n C46 C47 CDL sing 245 n n C46 H462 CDL sing 246 n n C46 H461 CDL sing 247 n n C47 H473 CDL sing 248 n n C47 H472 CDL sing 249 n n C47 H471 CDL sing 250 n n CB2 OB2 CDL sing 251 n n CB2 HB22 CDL sing 252 n n CB2 HB21 CDL sing 253 n n OB2 PB2 CDL sing 254 n n PB2 OB3 CDL doub 255 n n PB2 OB4 CDL sing 256 n n PB2 OB5 CDL sing 257 n n OB5 CB3 CDL sing 258 n n CB3 CB4 CDL sing 259 n n CB3 HB32 CDL sing 260 n n CB3 HB31 CDL sing 261 n n CB4 OB6 CDL sing 262 n n CB4 CB6 CDL sing 263 n n CB4 HB4 CDL sing 264 n n OB6 CB5 CDL sing 265 n n CB5 OB7 CDL doub 266 n n CB5 C51 CDL sing 267 n n C51 C52 CDL sing 268 n n C51 H512 CDL sing 269 n n C51 H511 CDL sing 270 n n C52 C53 CDL sing 271 n n C52 H522 CDL sing 272 n n C52 H521 CDL sing 273 n n C53 C54 CDL sing 274 n n C53 H532 CDL sing 275 n n C53 H531 CDL sing 276 n n C54 C55 CDL sing 277 n n C54 H542 CDL sing 278 n n C54 H541 CDL sing 279 n n C55 C56 CDL sing 280 n n C55 H552 CDL sing 281 n n C55 H551 CDL sing 282 n n C56 C57 CDL sing 283 n n C56 H562 CDL sing 284 n n C56 H561 CDL sing 285 n n C57 C58 CDL sing 286 n n C57 H572 CDL sing 287 n n C57 H571 CDL sing 288 n n C58 C59 CDL sing 289 n n C58 H582 CDL sing 290 n n C58 H581 CDL sing 291 n n C59 C60 CDL sing 292 n n C59 H592 CDL sing 293 n n C59 H591 CDL sing 294 n n C60 C61 CDL sing 295 n n C60 H602 CDL sing 296 n n C60 H601 CDL sing 297 n n C61 C62 CDL sing 298 n n C61 H612 CDL sing 299 n n C61 H611 CDL sing 300 n n C62 C63 CDL sing 301 n n C62 H622 CDL sing 302 n n C62 H621 CDL sing 303 n n C63 C64 CDL sing 304 n n C63 H632 CDL sing 305 n n C63 H631 CDL sing 306 n n C64 C65 CDL sing 307 n n C64 H642 CDL sing 308 n n C64 H641 CDL sing 309 n n C65 C66 CDL sing 310 n n C65 H652 CDL sing 311 n n C65 H651 CDL sing 312 n n C66 C67 CDL sing 313 n n C66 H662 CDL sing 314 n n C66 H661 CDL sing 315 n n C67 H673 CDL sing 316 n n C67 H672 CDL sing 317 n n C67 H671 CDL sing 318 n n CB6 OB8 CDL sing 319 n n CB6 HB62 CDL sing 320 n n CB6 HB61 CDL sing 321 n n OB8 CB7 CDL sing 322 n n CB7 OB9 CDL doub 323 n n CB7 C71 CDL sing 324 n n C71 C72 CDL sing 325 n n C71 H712 CDL sing 326 n n C71 H711 CDL sing 327 n n C72 C73 CDL sing 328 n n C72 H722 CDL sing 329 n n C72 H721 CDL sing 330 n n C73 C74 CDL sing 331 n n C73 H732 CDL sing 332 n n C73 H731 CDL sing 333 n n C74 C75 CDL sing 334 n n C74 H742 CDL sing 335 n n C74 H741 CDL sing 336 n n C75 C76 CDL sing 337 n n C75 H752 CDL sing 338 n n C75 H751 CDL sing 339 n n C76 C77 CDL sing 340 n n C76 H762 CDL sing 341 n n C76 H761 CDL sing 342 n n C77 C78 CDL sing 343 n n C77 H772 CDL sing 344 n n C77 H771 CDL sing 345 n n C78 C79 CDL sing 346 n n C78 H782 CDL sing 347 n n C78 H781 CDL sing 348 n n C79 C80 CDL sing 349 n n C79 H792 CDL sing 350 n n C79 H791 CDL sing 351 n n C80 C81 CDL sing 352 n n C80 H802 CDL sing 353 n n C80 H801 CDL sing 354 n n C81 C82 CDL sing 355 n n C81 H812 CDL sing 356 n n C81 H811 CDL sing 357 n n C82 C83 CDL sing 358 n n C82 H822 CDL sing 359 n n C82 H821 CDL sing 360 n n C83 C84 CDL sing 361 n n C83 H832 CDL sing 362 n n C83 H831 CDL sing 363 n n C84 C85 CDL sing 364 n n C84 H842 CDL sing 365 n n C84 H841 CDL sing 366 n n C85 C86 CDL sing 367 n n C85 H852 CDL sing 368 n n C85 H851 CDL sing 369 n n C86 C87 CDL sing 370 n n C86 H862 CDL sing 371 n n C86 H861 CDL sing 372 n n C87 H873 CDL sing 373 n n C87 H872 CDL sing 374 n n C87 H871 CDL sing 375 n n # _atom_sites.entry_id 4AYT _atom_sites.fract_transf_matrix[1][1] 0.005711 _atom_sites.fract_transf_matrix[1][2] 0.003297 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006594 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.020182 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 GLY A 1 1717 1717 GLY GLY . C 3 MG A 1 801 801 MG MG . D 4 ACP A 1 900 900 ACP ACP . E 5 LMT A 1 1720 1720 LMT LMT . F 6 CDL A 1 1721 1721 CDL CDL . G 5 LMT A 1 1723 1723 LMT LMT . H 5 LMT A 1 1724 1724 LMT LMT . I 6 CDL A 1 1727 1727 CDL CDL . J 7 HOH A 1 2001 2001 HOH HOH . J 7 HOH A 2 2002 2002 HOH HOH . J 7 HOH A 3 2003 2003 HOH HOH . J 7 HOH A 4 2004 2004 HOH HOH . J 7 HOH A 5 2005 2005 HOH HOH . J 7 HOH A 6 2006 2006 HOH HOH . J 7 HOH A 7 2007 2007 HOH HOH . J 7 HOH A 8 2008 2008 HOH HOH . J 7 HOH A 9 2009 2009 HOH HOH . J 7 HOH A 10 2010 2010 HOH HOH . J 7 HOH A 11 2011 2011 HOH HOH . J 7 HOH A 12 2012 2012 HOH HOH . J 7 HOH A 13 2013 2013 HOH HOH . J 7 HOH A 14 2014 2014 HOH HOH . J 7 HOH A 15 2015 2015 HOH HOH . J 7 HOH A 16 2016 2016 HOH HOH . J 7 HOH A 17 2017 2017 HOH HOH . J 7 HOH A 18 2018 2018 HOH HOH . J 7 HOH A 19 2019 2019 HOH HOH . J 7 HOH A 20 2020 2020 HOH HOH . J 7 HOH A 21 2021 2021 HOH HOH . J 7 HOH A 22 2022 2022 HOH HOH . J 7 HOH A 23 2023 2023 HOH HOH . J 7 HOH A 24 2024 2024 HOH HOH . J 7 HOH A 25 2025 2025 HOH HOH . J 7 HOH A 26 2026 2026 HOH HOH . J 7 HOH A 27 2027 2027 HOH HOH . J 7 HOH A 28 2028 2028 HOH HOH . J 7 HOH A 29 2029 2029 HOH HOH . J 7 HOH A 30 2030 2030 HOH HOH . J 7 HOH A 31 2031 2031 HOH HOH . J 7 HOH A 32 2032 2032 HOH HOH . J 7 HOH A 33 2033 2033 HOH HOH . J 7 HOH A 34 2034 2034 HOH HOH . J 7 HOH A 35 2035 2035 HOH HOH . J 7 HOH A 36 2036 2036 HOH HOH . J 7 HOH A 37 2037 2037 HOH HOH . J 7 HOH A 38 2038 2038 HOH HOH . J 7 HOH A 39 2039 2039 HOH HOH . J 7 HOH A 40 2040 2040 HOH HOH . J 7 HOH A 41 2041 2041 HOH HOH . J 7 HOH A 42 2042 2042 HOH HOH . J 7 HOH A 43 2043 2043 HOH HOH . J 7 HOH A 44 2044 2044 HOH HOH . J 7 HOH A 45 2045 2045 HOH HOH . J 7 HOH A 46 2046 2046 HOH HOH . J 7 HOH A 47 2047 2047 HOH HOH . J 7 HOH A 48 2048 2048 HOH HOH . J 7 HOH A 49 2049 2049 HOH HOH . J 7 HOH A 50 2050 2050 HOH HOH . J 7 HOH A 51 2051 2051 HOH HOH . J 7 HOH A 52 2052 2052 HOH HOH . J 7 HOH A 53 2053 2053 HOH HOH . J 7 HOH A 54 2054 2054 HOH HOH . J 7 HOH A 55 2055 2055 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C CA5 CDL . . . I 6 -69.436 88.743 10.113 1 57.69 ? CA5 CDL 1727 A 1 HETATM 2 C C11 CDL . . . I 6 -69.724 87.268 10.125 1 58.66 ? C11 CDL 1727 A 1 HETATM 3 C C12 CDL . . . I 6 -68.674 86.425 10.853 1 60.21 ? C12 CDL 1727 A 1 HETATM 4 C C13 CDL . . . I 6 -67.348 86.241 10.092 1 61.64 ? C13 CDL 1727 A 1 HETATM 5 C C14 CDL . . . I 6 -66.104 86.84 10.77 1 62.59 ? C14 CDL 1727 A 1 HETATM 6 C C15 CDL . . . I 6 -64.783 86.146 10.39 1 63.87 ? C15 CDL 1727 A 1 HETATM 7 C C16 CDL . . . I 6 -63.534 86.767 11.012 1 65.23 ? C16 CDL 1727 A 1 HETATM 8 C C17 CDL . . . I 6 -62.528 85.754 11.59 1 67 ? C17 CDL 1727 A 1 HETATM 9 C C18 CDL . . . I 6 -61.248 86.401 12.183 1 67.48 ? C18 CDL 1727 A 1 HETATM 10 C C19 CDL . . . I 6 -60.319 85.862 12.98 1 66.67 ? C19 CDL 1727 A 1 HETATM 11 C C20 CDL . . . I 6 -60.264 84.442 13.549 1 66.91 ? C20 CDL 1727 A 1 HETATM 12 C C21 CDL . . . I 6 -59.099 84.169 14.529 1 66.48 ? C21 CDL 1727 A 1 HETATM 13 C C22 CDL . . . I 6 -57.747 83.825 13.873 1 64.58 ? C22 CDL 1727 A 1 HETATM 14 C C23 CDL . . . I 6 -57.558 82.356 13.474 1 62.59 ? C23 CDL 1727 A 1 HETATM 15 C C24 CDL . . . I 6 -56.774 81.509 14.475 1 61.69 ? C24 CDL 1727 A 1 HETATM 16 C C25 CDL . . . I 6 -55.25 81.624 14.38 1 59.6 ? C25 CDL 1727 A 1 HETATM 17 C C26 CDL . . . I 6 -54.493 80.697 15.322 1 57.11 ? C26 CDL 1727 A 1 HETATM 18 C C27 CDL . . . I 6 -52.995 80.72 15.133 1 54.83 ? C27 CDL 1727 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 18 #