data_7XJC # _model_server_result.job_id IFHd81sdUKZvu42efENcMg _model_server_result.datetime_utc '2024-11-22 15:44:00' _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 7xjc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 7XJC # _exptl.entry_id 7XJC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 653.157 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2,3-DI-PHYTANYL-GLYCEROL _entity.pdbx_number_of_molecules 14 _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 7XJC _cell.length_a 60.57 _cell.length_b 60.57 _cell.length_c 110.89 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7XJC _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,K,L,M,N,O,P,Q,R,S,T,U _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 2_635 -y+1,x-y-2,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 121.14 -104.910317 0 3 'crystal symmetry operation' 3_865 -x+y+3,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 151.425 52.455159 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D N N ? 3 E N N ? 3 F N N ? 3 G N N ? 3 I N N ? 3 J N N ? 3 K N N ? 3 L N N ? 3 M N N ? 3 N N N ? 3 O N N ? 3 P N N ? 3 Q 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 covale ? covale1 A NZ LYS 212 A LYS 216 1_555 B C15 RET . A RET 301 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.352 ? covale ? covale2 A NZ LYS 212 A LYS 216 1_555 B C15 RET . A RET 301 1_555 ? C ? ? C ? ? ? ? ? ? ? 1.344 ? # _chem_comp.formula 'C43 H88 O3' _chem_comp.formula_weight 653.157 _chem_comp.id L2P _chem_comp.mon_nstd_flag . _chem_comp.name 2,3-DI-PHYTANYL-GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-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 L2P sing 139 n n C1 C2 L2P sing 140 n n C1 H12 L2P sing 141 n n C1 H11 L2P sing 142 n n O1 C11 L2P sing 143 n n C2 O2 L2P sing 144 n n C2 C3 L2P sing 145 n n C2 H2 L2P sing 146 n n O2 C41 L2P sing 147 n n C3 O3 L2P sing 148 n n C3 H32 L2P sing 149 n n C3 H31 L2P sing 150 n n O3 H3O L2P sing 151 n n C11 C12 L2P sing 152 n n C11 H112 L2P sing 153 n n C11 H111 L2P sing 154 n n C12 C13 L2P sing 155 n n C12 H122 L2P sing 156 n n C12 H121 L2P sing 157 n n C13 C14 L2P sing 158 n n C13 C15 L2P sing 159 n n C13 H13 L2P sing 160 n n C14 H143 L2P sing 161 n n C14 H142 L2P sing 162 n n C14 H141 L2P sing 163 n n C15 C16 L2P sing 164 n n C15 H152 L2P sing 165 n n C15 H151 L2P sing 166 n n C16 C17 L2P sing 167 n n C16 H162 L2P sing 168 n n C16 H161 L2P sing 169 n n C17 C18 L2P sing 170 n n C17 H172 L2P sing 171 n n C17 H171 L2P sing 172 n n C18 C19 L2P sing 173 n n C18 C20 L2P sing 174 n n C18 H18 L2P sing 175 n n C19 H193 L2P sing 176 n n C19 H192 L2P sing 177 n n C19 H191 L2P sing 178 n n C20 C21 L2P sing 179 n n C20 H202 L2P sing 180 n n C20 H201 L2P sing 181 n n C21 C22 L2P sing 182 n n C21 H212 L2P sing 183 n n C21 H211 L2P sing 184 n n C22 C23 L2P sing 185 n n C22 H222 L2P sing 186 n n C22 H221 L2P sing 187 n n C23 C24 L2P sing 188 n n C23 C25 L2P sing 189 n n C23 H23 L2P sing 190 n n C24 H243 L2P sing 191 n n C24 H242 L2P sing 192 n n C24 H241 L2P sing 193 n n C25 C26 L2P sing 194 n n C25 H252 L2P sing 195 n n C25 H251 L2P sing 196 n n C26 C27 L2P sing 197 n n C26 H262 L2P sing 198 n n C26 H261 L2P sing 199 n n C27 C28 L2P sing 200 n n C27 H272 L2P sing 201 n n C27 H271 L2P sing 202 n n C28 C29 L2P sing 203 n n C28 C30 L2P sing 204 n n C28 H28 L2P sing 205 n n C29 H293 L2P sing 206 n n C29 H292 L2P sing 207 n n C29 H291 L2P sing 208 n n C30 H303 L2P sing 209 n n C30 H302 L2P sing 210 n n C30 H301 L2P sing 211 n n C41 C42 L2P sing 212 n n C41 H412 L2P sing 213 n n C41 H411 L2P sing 214 n n C42 C43 L2P sing 215 n n C42 H422 L2P sing 216 n n C42 H421 L2P sing 217 n n C43 C44 L2P sing 218 n n C43 C45 L2P sing 219 n n C43 H43 L2P sing 220 n n C44 H443 L2P sing 221 n n C44 H442 L2P sing 222 n n C44 H441 L2P sing 223 n n C45 C46 L2P sing 224 n n C45 H452 L2P sing 225 n n C45 H451 L2P sing 226 n n C46 C47 L2P sing 227 n n C46 H462 L2P sing 228 n n C46 H461 L2P sing 229 n n C47 C48 L2P sing 230 n n C47 H472 L2P sing 231 n n C47 H471 L2P sing 232 n n C48 C49 L2P sing 233 n n C48 C50 L2P sing 234 n n C48 H48 L2P sing 235 n n C49 H493 L2P sing 236 n n C49 H492 L2P sing 237 n n C49 H491 L2P sing 238 n n C50 C51 L2P sing 239 n n C50 H502 L2P sing 240 n n C50 H501 L2P sing 241 n n C51 C52 L2P sing 242 n n C51 H512 L2P sing 243 n n C51 H511 L2P sing 244 n n C52 C53 L2P sing 245 n n C52 H522 L2P sing 246 n n C52 H521 L2P sing 247 n n C53 C54 L2P sing 248 n n C53 C55 L2P sing 249 n n C53 H53 L2P sing 250 n n C54 H543 L2P sing 251 n n C54 H542 L2P sing 252 n n C54 H541 L2P sing 253 n n C55 C56 L2P sing 254 n n C55 H552 L2P sing 255 n n C55 H551 L2P sing 256 n n C56 C57 L2P sing 257 n n C56 H562 L2P sing 258 n n C56 H561 L2P sing 259 n n C57 C58 L2P sing 260 n n C57 H572 L2P sing 261 n n C57 H571 L2P sing 262 n n C58 C59 L2P sing 263 n n C58 C60 L2P sing 264 n n C58 H58 L2P sing 265 n n C59 H593 L2P sing 266 n n C59 H592 L2P sing 267 n n C59 H591 L2P sing 268 n n C60 H603 L2P sing 269 n n C60 H602 L2P sing 270 n n C60 H601 L2P sing 271 n n # _atom_sites.entry_id 7XJC _atom_sites.fract_transf_matrix[1][1] 0.01651 _atom_sites.fract_transf_matrix[1][2] 0.009532 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019064 _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] 0.009018 _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 RET A 1 301 301 RET RET . C 3 L2P A 1 302 302 L2P L2P . D 3 L2P A 1 303 303 L2P L2P . E 3 L2P A 1 304 304 L2P L2P . F 3 L2P A 1 305 305 L2P L2P . G 3 L2P A 1 306 306 L2P L2P . H 4 SQU A 1 307 312 SQU SQU . I 3 L2P A 1 308 313 L2P L2P . J 3 L2P A 1 309 315 L2P L2P . K 3 L2P A 1 310 320 L2P L2P . L 3 L2P A 1 311 322 L2P L2P . M 3 L2P A 1 312 323 L2P L2P . N 3 L2P A 1 313 324 L2P L2P . O 3 L2P A 1 314 327 L2P L2P . P 3 L2P A 1 315 328 L2P L2P . Q 3 L2P A 1 316 333 L2P L2P . R 4 SQU A 1 317 341 SQU SQU . S 4 SQU A 1 318 342 SQU SQU . T 4 SQU A 1 319 343 SQU SQU . U 5 HOH A 1 401 457 HOH HOH . U 5 HOH A 2 402 455 HOH HOH . U 5 HOH A 3 403 554 HOH HOH . U 5 HOH A 4 404 532 HOH HOH . U 5 HOH A 5 405 541 HOH HOH . U 5 HOH A 6 406 540 HOH HOH . U 5 HOH A 7 407 402 HOH HOH . U 5 HOH A 8 408 416 HOH HOH . U 5 HOH A 9 409 401 HOH HOH . U 5 HOH A 10 410 548 HOH HOH . U 5 HOH A 11 411 538 HOH HOH . U 5 HOH A 12 412 406 HOH HOH . U 5 HOH A 13 413 513 HOH HOH . U 5 HOH A 14 414 456 HOH HOH . U 5 HOH A 15 415 537 HOH HOH . U 5 HOH A 16 416 451 HOH HOH . U 5 HOH A 17 417 534 HOH HOH . U 5 HOH A 18 418 405 HOH HOH . U 5 HOH A 19 419 454 HOH HOH . U 5 HOH A 20 420 536 HOH HOH . U 5 HOH A 21 421 556 HOH HOH . U 5 HOH A 22 422 551 HOH HOH . U 5 HOH A 23 423 458 HOH HOH . U 5 HOH A 24 424 549 HOH HOH . U 5 HOH A 25 425 403 HOH HOH . U 5 HOH A 26 426 407 HOH HOH . U 5 HOH A 27 427 411 HOH HOH . U 5 HOH A 28 428 512 HOH HOH . U 5 HOH A 29 429 450 HOH HOH . U 5 HOH A 30 430 419 HOH HOH . U 5 HOH A 31 431 546 HOH HOH . U 5 HOH A 32 432 511 HOH HOH . U 5 HOH A 33 433 415 HOH HOH . U 5 HOH A 34 434 542 HOH HOH . U 5 HOH A 35 435 460 HOH HOH . U 5 HOH A 36 436 502 HOH HOH . U 5 HOH A 37 437 420 HOH HOH . U 5 HOH A 38 438 514 HOH HOH . U 5 HOH A 39 439 404 HOH HOH . U 5 HOH A 40 440 501 HOH HOH . U 5 HOH A 41 441 539 HOH HOH . U 5 HOH A 42 442 531 HOH HOH . U 5 HOH A 43 443 545 HOH HOH . U 5 HOH A 44 444 535 HOH HOH . U 5 HOH A 45 445 530 HOH HOH . U 5 HOH A 46 446 547 HOH HOH . U 5 HOH A 47 447 550 HOH HOH . U 5 HOH A 48 448 552 HOH HOH . U 5 HOH A 49 449 553 HOH HOH . U 5 HOH A 50 450 544 HOH HOH . U 5 HOH A 51 451 533 HOH HOH . U 5 HOH A 52 452 453 HOH HOH . U 5 HOH A 53 453 557 HOH HOH . U 5 HOH A 54 454 412 HOH HOH . U 5 HOH A 55 455 555 HOH HOH . U 5 HOH A 56 456 543 HOH HOH . U 5 HOH A 57 457 459 HOH HOH . U 5 HOH A 58 458 558 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 C1 L2P . . . D 3 85.681 0.719 -39.462 1 62.29 ? C1 L2P 303 A 1 HETATM 2 O O1 L2P . . . D 3 84.792 0.907 -38.314 1 58.53 ? O1 L2P 303 A 1 HETATM 3 C C2 L2P . . . D 3 86.593 -0.538 -39.413 1 44.81 ? C2 L2P 303 A 1 HETATM 4 O O2 L2P . . . D 3 86.636 -1.233 -38.145 1 31.36 ? O2 L2P 303 A 1 HETATM 5 C C3 L2P . . . D 3 86.653 -1.272 -40.762 1 47.07 ? C3 L2P 303 A 1 HETATM 6 O O3 L2P . . . D 3 86.665 -0.269 -41.855 1 64.85 ? O3 L2P 303 A 1 HETATM 7 C C11 L2P . . . D 3 83.635 1.764 -38.21 1 44.41 ? C11 L2P 303 A 1 HETATM 8 C C12 L2P . . . D 3 82.655 1.994 -39.378 1 56.86 ? C12 L2P 303 A 1 HETATM 9 C C13 L2P . . . D 3 81.984 3.378 -39.247 1 60.18 ? C13 L2P 303 A 1 HETATM 10 C C15 L2P . . . D 3 82.485 4.109 -37.976 1 56.54 ? C15 L2P 303 A 1 HETATM 11 C C16 L2P . . . D 3 81.391 4.91 -37.271 1 54.6 ? C16 L2P 303 A 1 HETATM 12 C C17 L2P . . . D 3 80.867 4.274 -35.981 1 53.85 ? C17 L2P 303 A 1 HETATM 13 C C18 L2P . . . D 3 79.501 4.814 -35.553 1 58.26 ? C18 L2P 303 A 1 HETATM 14 C C19 L2P . . . D 3 78.872 5.836 -36.51 1 67.33 ? C19 L2P 303 A 1 HETATM 15 C C20 L2P . . . D 3 79.418 5.259 -34.082 1 64.64 ? C20 L2P 303 A 1 HETATM 16 C C21 L2P . . . D 3 77.967 5.251 -33.569 1 64.58 ? C21 L2P 303 A 1 HETATM 17 C C22 L2P . . . D 3 77.471 3.896 -33.069 1 57.64 ? C22 L2P 303 A 1 HETATM 18 C C23 L2P . . . D 3 77.726 3.648 -31.576 1 69.56 ? C23 L2P 303 A 1 HETATM 19 C C25 L2P . . . D 3 78.87 4.427 -30.94 1 84.54 ? C25 L2P 303 A 1 HETATM 20 C C26 L2P . . . D 3 79.692 3.83 -29.803 1 79.59 ? C26 L2P 303 A 1 HETATM 21 C C27 L2P . . . D 3 81.089 3.295 -30.096 1 70.11 ? C27 L2P 303 A 1 HETATM 22 C C28 L2P . . . D 3 82.291 4.204 -29.858 1 62.17 ? C28 L2P 303 A 1 HETATM 23 C C29 L2P . . . D 3 83.472 3.576 -29.114 1 56.33 ? C29 L2P 303 A 1 HETATM 24 C C30 L2P . . . D 3 82.65 5.103 -31.053 1 83.59 ? C30 L2P 303 A 1 HETATM 25 C C41 L2P . . . D 3 86.99 -0.463 -36.938 1 32.49 ? C41 L2P 303 A 1 HETATM 26 C C42 L2P . . . D 3 86.954 -1.391 -35.694 1 28.42 ? C42 L2P 303 A 1 HETATM 27 C C43 L2P . . . D 3 86.423 -0.692 -34.433 1 37.87 ? C43 L2P 303 A 1 HETATM 28 C C45 L2P . . . D 3 86.027 -1.626 -33.29 1 42.14 ? C45 L2P 303 A 1 HETATM 29 C C46 L2P . . . D 3 84.897 -1.019 -32.418 1 40.39 ? C46 L2P 303 A 1 HETATM 30 C C47 L2P . . . D 3 85.203 -1.06 -30.927 1 42.96 ? C47 L2P 303 A 1 HETATM 31 C C48 L2P . . . D 3 84.639 0.071 -30.063 1 43.87 ? C48 L2P 303 A 1 HETATM 32 C C50 L2P . . . D 3 83.782 -0.384 -28.888 1 53.93 ? C50 L2P 303 A 1 HETATM 33 C C51 L2P . . . D 3 83.529 0.527 -27.704 1 37.9 ? C51 L2P 303 A 1 HETATM 34 C C52 L2P . . . D 3 84.57 0.643 -26.597 1 36.84 ? C52 L2P 303 A 1 HETATM 35 C C53 L2P . . . D 3 85.96 1.112 -27.048 1 47.3 ? C53 L2P 303 A 1 HETATM 36 C C55 L2P . . . D 3 86.745 2.128 -26.299 1 42.04 ? C55 L2P 303 A 1 HETATM 37 C C56 L2P . . . D 3 86.796 3.606 -26.675 1 32.24 ? C56 L2P 303 A 1 HETATM 38 C C57 L2P . . . D 3 86.4 4.507 -25.512 1 44.77 ? C57 L2P 303 A 1 HETATM 39 C C58 L2P . . . D 3 86.812 5.972 -25.586 1 48.25 ? C58 L2P 303 A 1 HETATM 40 C C59 L2P . . . D 3 86.127 6.899 -24.569 1 52.46 ? C59 L2P 303 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 248 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 40 #