data_1X0I # _model_server_result.job_id qEh-QfQzcWYYDrLVMSFyGg _model_server_result.datetime_utc '2024-11-23 23:20:24' _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 1x0i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":280}' # _entry.id 1X0I # _exptl.entry_id 1X0I _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 885.179 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 1X0I _cell.length_a 102.64 _cell.length_b 102.64 _cell.length_c 109.04 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1X0I _symmetry.cell_setting ? _symmetry.Int_Tables_number 177 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 6 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _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_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 102.64 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 51.32 88.888847 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 D N N ? 4 F N N ? 4 G N N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NZ _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 216 _struct_conn.ptnr1_auth_asym_id 1 _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 216 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id C15 _struct_conn.ptnr2_label_comp_id RET _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id 1 _struct_conn.ptnr2_auth_comp_id RET _struct_conn.ptnr2_auth_seq_id 250 _struct_conn.ptnr2_symmetry 1_555 _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 1.356 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C46 H94 O11 P2 -2' _chem_comp.formula_weight 885.179 _chem_comp.id L3P _chem_comp.mon_nstd_flag . _chem_comp.name "2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 C2 L3P sing 272 n n C1 O1 L3P sing 273 n n C1 H12 L3P sing 274 n n C1 H11 L3P sing 275 n n C2 C3 L3P sing 276 n n C2 O2 L3P sing 277 n n C2 H2 L3P sing 278 n n C3 O3 L3P sing 279 n n C3 H32 L3P sing 280 n n C3 H31 L3P sing 281 n n C4 C5 L3P sing 282 n n C4 O4 L3P sing 283 n n C4 H42 L3P sing 284 n n C4 H41 L3P sing 285 n n C5 C6 L3P sing 286 n n C5 O5 L3P sing 287 n n C5 H5 L3P sing 288 n n C6 O6 L3P sing 289 n n C6 H62 L3P sing 290 n n C6 H61 L3P sing 291 n n O1 C11 L3P sing 292 n n O2 C41 L3P sing 293 n n O3 P1 L3P sing 294 n n O4 P1 L3P sing 295 n n O5 H5O L3P sing 296 n n O6 P2 L3P sing 297 n n O1P P1 L3P doub 298 n n O2P P1 L3P sing 299 n n O4P P2 L3P doub 300 n n O5P P2 L3P sing 301 n n O6P P2 L3P sing 302 n n O6P HOP6 L3P sing 303 n n C11 C12 L3P sing 304 n n C11 H112 L3P sing 305 n n C11 H111 L3P sing 306 n n C12 C13 L3P sing 307 n n C12 H122 L3P sing 308 n n C12 H121 L3P sing 309 n n C13 C14 L3P sing 310 n n C13 C15 L3P sing 311 n n C13 H13 L3P sing 312 n n C14 H143 L3P sing 313 n n C14 H142 L3P sing 314 n n C14 H141 L3P sing 315 n n C15 C16 L3P sing 316 n n C15 H152 L3P sing 317 n n C15 H151 L3P sing 318 n n C16 C17 L3P sing 319 n n C16 H162 L3P sing 320 n n C16 H161 L3P sing 321 n n C17 C18 L3P sing 322 n n C17 H172 L3P sing 323 n n C17 H171 L3P sing 324 n n C18 C19 L3P sing 325 n n C18 C20 L3P sing 326 n n C18 H18 L3P sing 327 n n C19 H193 L3P sing 328 n n C19 H192 L3P sing 329 n n C19 H191 L3P sing 330 n n C20 C21 L3P sing 331 n n C20 H202 L3P sing 332 n n C20 H201 L3P sing 333 n n C21 C22 L3P sing 334 n n C21 H212 L3P sing 335 n n C21 H211 L3P sing 336 n n C22 C23 L3P sing 337 n n C22 H222 L3P sing 338 n n C22 H221 L3P sing 339 n n C23 C24 L3P sing 340 n n C23 C25 L3P sing 341 n n C23 H23 L3P sing 342 n n C24 H243 L3P sing 343 n n C24 H242 L3P sing 344 n n C24 H241 L3P sing 345 n n C25 C26 L3P sing 346 n n C25 H252 L3P sing 347 n n C25 H251 L3P sing 348 n n C26 C27 L3P sing 349 n n C26 H262 L3P sing 350 n n C26 H261 L3P sing 351 n n C27 C28 L3P sing 352 n n C27 H272 L3P sing 353 n n C27 H271 L3P sing 354 n n C28 C29 L3P sing 355 n n C28 C30 L3P sing 356 n n C28 H28 L3P sing 357 n n C29 H293 L3P sing 358 n n C29 H292 L3P sing 359 n n C29 H291 L3P sing 360 n n C30 H303 L3P sing 361 n n C30 H302 L3P sing 362 n n C30 H301 L3P sing 363 n n C41 C42 L3P sing 364 n n C41 H412 L3P sing 365 n n C41 H411 L3P sing 366 n n C42 C43 L3P sing 367 n n C42 H422 L3P sing 368 n n C42 H421 L3P sing 369 n n C43 C44 L3P sing 370 n n C43 C45 L3P sing 371 n n C43 H43 L3P sing 372 n n C44 H443 L3P sing 373 n n C44 H442 L3P sing 374 n n C44 H441 L3P sing 375 n n C45 C46 L3P sing 376 n n C45 H452 L3P sing 377 n n C45 H451 L3P sing 378 n n C46 C47 L3P sing 379 n n C46 H462 L3P sing 380 n n C46 H461 L3P sing 381 n n C47 C48 L3P sing 382 n n C47 H472 L3P sing 383 n n C47 H471 L3P sing 384 n n C48 C49 L3P sing 385 n n C48 C50 L3P sing 386 n n C48 H48 L3P sing 387 n n C49 H493 L3P sing 388 n n C49 H492 L3P sing 389 n n C49 H491 L3P sing 390 n n C50 C51 L3P sing 391 n n C50 H502 L3P sing 392 n n C50 H501 L3P sing 393 n n C51 C52 L3P sing 394 n n C51 H512 L3P sing 395 n n C51 H511 L3P sing 396 n n C52 C53 L3P sing 397 n n C52 H522 L3P sing 398 n n C52 H521 L3P sing 399 n n C53 C54 L3P sing 400 n n C53 C55 L3P sing 401 n n C53 H53 L3P sing 402 n n C54 H543 L3P sing 403 n n C54 H542 L3P sing 404 n n C54 H541 L3P sing 405 n n C55 C56 L3P sing 406 n n C55 H552 L3P sing 407 n n C55 H551 L3P sing 408 n n C56 C57 L3P sing 409 n n C56 H562 L3P sing 410 n n C56 H561 L3P sing 411 n n C57 C58 L3P sing 412 n n C57 H572 L3P sing 413 n n C57 H571 L3P sing 414 n n C58 C59 L3P sing 415 n n C58 C60 L3P sing 416 n n C58 H58 L3P sing 417 n n C59 H593 L3P sing 418 n n C59 H592 L3P sing 419 n n C59 H591 L3P sing 420 n n C60 H603 L3P sing 421 n n C60 H602 L3P sing 422 n n C60 H601 L3P sing 423 n n # _atom_sites.entry_id 1X0I _atom_sites.fract_transf_matrix[1][1] 0.009743 _atom_sites.fract_transf_matrix[1][2] 0.005625 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01125 _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] 0.009171 _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 SO4 1 1 700 700 SO4 SO4 . C 3 RET 1 1 250 250 RET RET . D 4 L3P 1 1 260 260 L3P L3P . E 5 L2P 1 1 270 270 L2P L2P . F 4 L3P 1 1 280 280 L3P L3P . G 4 L3P 1 1 290 290 L3P L3P . H 6 HOH 1 1 601 601 HOH HOH . H 6 HOH 1 2 602 602 HOH HOH . H 6 HOH 1 3 603 603 HOH HOH . H 6 HOH 1 4 605 605 HOH HOH . H 6 HOH 1 5 606 606 HOH HOH . H 6 HOH 1 6 607 607 HOH HOH . H 6 HOH 1 7 608 608 HOH HOH . H 6 HOH 1 8 609 609 HOH HOH . H 6 HOH 1 9 610 610 HOH HOH . H 6 HOH 1 10 611 611 HOH HOH . H 6 HOH 1 11 612 612 HOH HOH . H 6 HOH 1 12 613 613 HOH HOH . H 6 HOH 1 13 621 621 HOH HOH . H 6 HOH 1 14 622 622 HOH HOH . H 6 HOH 1 15 623 623 HOH HOH . H 6 HOH 1 16 624 624 HOH HOH . H 6 HOH 1 17 625 625 HOH HOH . H 6 HOH 1 18 626 626 HOH HOH . H 6 HOH 1 19 627 627 HOH HOH . H 6 HOH 1 20 628 628 HOH HOH . H 6 HOH 1 21 631 631 HOH HOH . H 6 HOH 1 22 632 632 HOH HOH . H 6 HOH 1 23 633 633 HOH HOH . H 6 HOH 1 24 634 634 HOH HOH . H 6 HOH 1 25 635 635 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 C11 L3P . . . F 4 54.635 4.214 10.847 1 83.35 ? C11 L3P 280 1 1 HETATM 2 C C12 L3P . . . F 4 53.954 3.488 12.101 1 84.25 ? C12 L3P 280 1 1 HETATM 3 C C13 L3P . . . F 4 54.818 3.688 13.454 1 85.04 ? C13 L3P 280 1 1 HETATM 4 C C14 L3P . . . F 4 56.269 3.09 13.278 1 85.17 ? C14 L3P 280 1 1 HETATM 5 C C15 L3P . . . F 4 54.08 2.954 14.635 1 85.19 ? C15 L3P 280 1 1 HETATM 6 C C16 L3P . . . F 4 53.62 3.975 15.717 1 84.92 ? C16 L3P 280 1 1 HETATM 7 C C17 L3P . . . F 4 52.089 3.897 15.883 1 86.85 ? C17 L3P 280 1 1 HETATM 8 C C18 L3P . . . F 4 51.66 3.044 17.234 1 87.69 ? C18 L3P 280 1 1 HETATM 9 C C19 L3P . . . F 4 51.281 1.563 16.888 1 88.09 ? C19 L3P 280 1 1 HETATM 10 C C20 L3P . . . F 4 50.411 3.826 17.929 1 87.91 ? C20 L3P 280 1 1 HETATM 11 C C21 L3P . . . F 4 50.744 4.402 19.347 1 87.16 ? C21 L3P 280 1 1 HETATM 12 C C22 L3P . . . F 4 49.445 5.112 19.879 1 87.14 ? C22 L3P 280 1 1 HETATM 13 C C23 L3P . . . F 4 48.733 4.255 21 1 87.15 ? C23 L3P 280 1 1 HETATM 14 C C24 L3P . . . F 4 47.46 3.68 20.358 1 88.18 ? C24 L3P 280 1 1 HETATM 15 C C25 L3P . . . F 4 48.371 5.181 22.278 1 86.28 ? C25 L3P 280 1 1 HETATM 16 C C26 L3P . . . F 4 47.664 4.352 23.426 1 85.88 ? C26 L3P 280 1 1 HETATM 17 C C27 L3P . . . F 4 48.755 3.846 24.496 1 86.64 ? C27 L3P 280 1 1 HETATM 18 C C28 L3P . . . F 4 48.068 2.979 25.657 1 85.75 ? C28 L3P 280 1 1 HETATM 19 C C29 L3P . . . F 4 48.793 1.705 25.817 1 84.84 ? C29 L3P 280 1 1 HETATM 20 C C30 L3P . . . F 4 48.097 3.744 26.997 1 85.94 ? C30 L3P 280 1 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 582 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 20 #