data_1X0K # _model_server_result.job_id nVHnq97lz19TYmaAPE-vpg _model_server_result.datetime_utc '2024-11-02 19:29:51' _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 1x0k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":280}' # _entry.id 1X0K # _exptl.entry_id 1X0K _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 4 _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 1X0K _cell.length_a 102.45 _cell.length_b 102.45 _cell.length_c 112.81 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1X0K _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 PISA,PQS _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 _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 1 102.45 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 51.225 88.724303 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 ? 4 H N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 MAN GLC C1 O1 . O2 HO2 . sing 2 ? 2 3 2 GAL MAN C1 O1 . O6 HO6 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B GLC 1 A 1 GLC 2 400 GLC 2 n B MAN 2 A 2 MAN 2 410 MAN 2 n B GAL 3 A 3 GAL 2 420 GAL # 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 216 1 LYS 216 1_555 C C15 RET . 1 RET 250 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.358 ? covale ? covale2 E O3 L2P . 1 L2P 270 1_555 B C1 GLC . A GLC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale3 B O2 GLC . A GLC 1 1_555 B C1 MAN . A MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale4 B O6 MAN . A MAN 2 1_555 B C1 GAL . A GAL 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? # _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 320 n n C1 O1 L3P sing 321 n n C1 H12 L3P sing 322 n n C1 H11 L3P sing 323 n n C2 C3 L3P sing 324 n n C2 O2 L3P sing 325 n n C2 H2 L3P sing 326 n n C3 O3 L3P sing 327 n n C3 H32 L3P sing 328 n n C3 H31 L3P sing 329 n n C4 C5 L3P sing 330 n n C4 O4 L3P sing 331 n n C4 H42 L3P sing 332 n n C4 H41 L3P sing 333 n n C5 C6 L3P sing 334 n n C5 O5 L3P sing 335 n n C5 H5 L3P sing 336 n n C6 O6 L3P sing 337 n n C6 H62 L3P sing 338 n n C6 H61 L3P sing 339 n n O1 C11 L3P sing 340 n n O2 C41 L3P sing 341 n n O3 P1 L3P sing 342 n n O4 P1 L3P sing 343 n n O5 H5O L3P sing 344 n n O6 P2 L3P sing 345 n n O1P P1 L3P doub 346 n n O2P P1 L3P sing 347 n n O4P P2 L3P doub 348 n n O5P P2 L3P sing 349 n n O6P P2 L3P sing 350 n n O6P HOP6 L3P sing 351 n n C11 C12 L3P sing 352 n n C11 H112 L3P sing 353 n n C11 H111 L3P sing 354 n n C12 C13 L3P sing 355 n n C12 H122 L3P sing 356 n n C12 H121 L3P sing 357 n n C13 C14 L3P sing 358 n n C13 C15 L3P sing 359 n n C13 H13 L3P sing 360 n n C14 H143 L3P sing 361 n n C14 H142 L3P sing 362 n n C14 H141 L3P sing 363 n n C15 C16 L3P sing 364 n n C15 H152 L3P sing 365 n n C15 H151 L3P sing 366 n n C16 C17 L3P sing 367 n n C16 H162 L3P sing 368 n n C16 H161 L3P sing 369 n n C17 C18 L3P sing 370 n n C17 H172 L3P sing 371 n n C17 H171 L3P sing 372 n n C18 C19 L3P sing 373 n n C18 C20 L3P sing 374 n n C18 H18 L3P sing 375 n n C19 H193 L3P sing 376 n n C19 H192 L3P sing 377 n n C19 H191 L3P sing 378 n n C20 C21 L3P sing 379 n n C20 H202 L3P sing 380 n n C20 H201 L3P sing 381 n n C21 C22 L3P sing 382 n n C21 H212 L3P sing 383 n n C21 H211 L3P sing 384 n n C22 C23 L3P sing 385 n n C22 H222 L3P sing 386 n n C22 H221 L3P sing 387 n n C23 C24 L3P sing 388 n n C23 C25 L3P sing 389 n n C23 H23 L3P sing 390 n n C24 H243 L3P sing 391 n n C24 H242 L3P sing 392 n n C24 H241 L3P sing 393 n n C25 C26 L3P sing 394 n n C25 H252 L3P sing 395 n n C25 H251 L3P sing 396 n n C26 C27 L3P sing 397 n n C26 H262 L3P sing 398 n n C26 H261 L3P sing 399 n n C27 C28 L3P sing 400 n n C27 H272 L3P sing 401 n n C27 H271 L3P sing 402 n n C28 C29 L3P sing 403 n n C28 C30 L3P sing 404 n n C28 H28 L3P sing 405 n n C29 H293 L3P sing 406 n n C29 H292 L3P sing 407 n n C29 H291 L3P sing 408 n n C30 H303 L3P sing 409 n n C30 H302 L3P sing 410 n n C30 H301 L3P sing 411 n n C41 C42 L3P sing 412 n n C41 H412 L3P sing 413 n n C41 H411 L3P sing 414 n n C42 C43 L3P sing 415 n n C42 H422 L3P sing 416 n n C42 H421 L3P sing 417 n n C43 C44 L3P sing 418 n n C43 C45 L3P sing 419 n n C43 H43 L3P sing 420 n n C44 H443 L3P sing 421 n n C44 H442 L3P sing 422 n n C44 H441 L3P sing 423 n n C45 C46 L3P sing 424 n n C45 H452 L3P sing 425 n n C45 H451 L3P sing 426 n n C46 C47 L3P sing 427 n n C46 H462 L3P sing 428 n n C46 H461 L3P sing 429 n n C47 C48 L3P sing 430 n n C47 H472 L3P sing 431 n n C47 H471 L3P sing 432 n n C48 C49 L3P sing 433 n n C48 C50 L3P sing 434 n n C48 H48 L3P sing 435 n n C49 H493 L3P sing 436 n n C49 H492 L3P sing 437 n n C49 H491 L3P sing 438 n n C50 C51 L3P sing 439 n n C50 H502 L3P sing 440 n n C50 H501 L3P sing 441 n n C51 C52 L3P sing 442 n n C51 H512 L3P sing 443 n n C51 H511 L3P sing 444 n n C52 C53 L3P sing 445 n n C52 H522 L3P sing 446 n n C52 H521 L3P sing 447 n n C53 C54 L3P sing 448 n n C53 C55 L3P sing 449 n n C53 H53 L3P sing 450 n n C54 H543 L3P sing 451 n n C54 H542 L3P sing 452 n n C54 H541 L3P sing 453 n n C55 C56 L3P sing 454 n n C55 H552 L3P sing 455 n n C55 H551 L3P sing 456 n n C56 C57 L3P sing 457 n n C56 H562 L3P sing 458 n n C56 H561 L3P sing 459 n n C57 C58 L3P sing 460 n n C57 H572 L3P sing 461 n n C57 H571 L3P sing 462 n n C58 C59 L3P sing 463 n n C58 C60 L3P sing 464 n n C58 H58 L3P sing 465 n n C59 H593 L3P sing 466 n n C59 H592 L3P sing 467 n n C59 H591 L3P sing 468 n n C60 H603 L3P sing 469 n n C60 H602 L3P sing 470 n n C60 H601 L3P sing 471 n n # _atom_sites.entry_id 1X0K _atom_sites.fract_transf_matrix[1][1] 0.009761 _atom_sites.fract_transf_matrix[1][2] 0.005635 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011271 _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] 0.008864 _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 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 4 L3P 1 1 300 300 L3P L3P . I 6 HOH 1 1 600 600 HOH HOH . I 6 HOH 1 2 601 601 HOH HOH . I 6 HOH 1 3 602 602 HOH HOH . I 6 HOH 1 4 603 603 HOH HOH . I 6 HOH 1 5 604 604 HOH HOH . I 6 HOH 1 6 605 605 HOH HOH . I 6 HOH 1 7 606 606 HOH HOH . I 6 HOH 1 8 607 607 HOH HOH . I 6 HOH 1 9 608 608 HOH HOH . I 6 HOH 1 10 609 609 HOH HOH . I 6 HOH 1 11 610 610 HOH HOH . I 6 HOH 1 12 611 611 HOH HOH . I 6 HOH 1 13 612 612 HOH HOH . I 6 HOH 1 14 613 613 HOH HOH . I 6 HOH 1 15 614 614 HOH HOH . I 6 HOH 1 16 615 615 HOH HOH . I 6 HOH 1 17 616 616 HOH HOH . I 6 HOH 1 18 617 617 HOH HOH . I 6 HOH 1 19 618 618 HOH HOH . I 6 HOH 1 20 619 619 HOH HOH . I 6 HOH 1 21 620 620 HOH HOH . I 6 HOH 1 22 621 621 HOH HOH . I 6 HOH 1 23 622 622 HOH HOH . I 6 HOH 1 24 623 623 HOH HOH . I 6 HOH 1 25 624 624 HOH HOH . I 6 HOH 1 26 625 625 HOH HOH . I 6 HOH 1 27 626 626 HOH HOH . I 6 HOH 1 28 627 627 HOH HOH . I 6 HOH 1 29 628 628 HOH HOH . I 6 HOH 1 30 629 629 HOH HOH . I 6 HOH 1 31 630 630 HOH HOH . I 6 HOH 1 32 631 631 HOH HOH . I 6 HOH 1 33 632 632 HOH HOH . I 6 HOH 1 34 633 633 HOH HOH . I 6 HOH 1 35 634 634 HOH HOH . I 6 HOH 1 36 635 635 HOH HOH . I 6 HOH 1 37 636 636 HOH HOH . I 6 HOH 1 38 637 637 HOH HOH . I 6 HOH 1 39 638 638 HOH HOH . I 6 HOH 1 40 639 639 HOH HOH . I 6 HOH 1 41 640 640 HOH HOH . I 6 HOH 1 42 641 641 HOH HOH . I 6 HOH 1 43 642 642 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 L3P . . . F 4 26.216 37.729 10.605 1 130.59 ? C1 L3P 280 1 1 HETATM 2 C C2 L3P . . . F 4 27.817 37.846 10.748 1 129.75 ? C2 L3P 280 1 1 HETATM 3 C C3 L3P . . . F 4 28.616 37.206 9.49 1 129.83 ? C3 L3P 280 1 1 HETATM 4 O O1 L3P . . . F 4 25.476 38.318 11.754 1 130.79 ? O1 L3P 280 1 1 HETATM 5 O O2 L3P . . . F 4 28.149 39.379 10.903 1 129 ? O2 L3P 280 1 1 HETATM 6 O O3 L3P . . . F 4 28.399 35.756 9.237 1 130 ? O3 L3P 280 1 1 HETATM 7 O O4 L3P . . . F 4 26.608 35.841 7.334 1 130.5 ? O4 L3P 280 1 1 HETATM 8 O O1P L3P . . . F 4 27.792 33.751 7.681 1 129.91 ? O1P L3P 280 1 1 HETATM 9 O O2P L3P . . . F 4 29.126 35.755 6.583 1 130.24 ? O2P L3P 280 1 1 HETATM 10 P P1 L3P . . . F 4 27.943 35.242 7.697 1 130.78 ? P1 L3P 280 1 1 HETATM 11 C C11 L3P . . . F 4 24.045 38.236 11.666 1 129.73 ? C11 L3P 280 1 1 HETATM 12 C C12 L3P . . . F 4 23.487 37.366 12.86 1 129.34 ? C12 L3P 280 1 1 HETATM 13 C C13 L3P . . . F 4 22.829 38.03 14.195 1 128.77 ? C13 L3P 280 1 1 HETATM 14 C C14 L3P . . . F 4 21.805 39.193 13.948 1 129.18 ? C14 L3P 280 1 1 HETATM 15 C C15 L3P . . . F 4 23.985 38.562 15.145 1 127.37 ? C15 L3P 280 1 1 HETATM 16 C C16 L3P . . . F 4 23.985 37.912 16.574 1 125.82 ? C16 L3P 280 1 1 HETATM 17 C C17 L3P . . . F 4 25.168 38.526 17.395 1 124.8 ? C17 L3P 280 1 1 HETATM 18 C C18 L3P . . . F 4 26.126 37.53 18.078 1 123.78 ? C18 L3P 280 1 1 HETATM 19 C C19 L3P . . . F 4 25.948 37.572 19.606 1 123.18 ? C19 L3P 280 1 1 HETATM 20 C C20 L3P . . . F 4 27.56 37.863 17.805 1 123.92 ? C20 L3P 280 1 1 HETATM 21 C C41 L3P . . . F 4 29.186 39.71 11.936 1 127.11 ? C41 L3P 280 1 1 HETATM 22 C C42 L3P . . . F 4 28.62 39.875 13.413 1 125.82 ? C42 L3P 280 1 1 HETATM 23 C C43 L3P . . . F 4 28.325 41.289 14.098 1 124.81 ? C43 L3P 280 1 1 HETATM 24 C C44 L3P . . . F 4 28.627 42.532 13.211 1 124.92 ? C44 L3P 280 1 1 HETATM 25 C C45 L3P . . . F 4 29.156 41.457 15.391 1 123.7 ? C45 L3P 280 1 1 HETATM 26 C C46 L3P . . . F 4 28.322 41.501 16.702 1 123.35 ? C46 L3P 280 1 1 HETATM 27 C C47 L3P . . . F 4 29.266 41.68 17.951 1 122.6 ? C47 L3P 280 1 1 HETATM 28 C C48 L3P . . . F 4 28.66 41.754 19.385 1 121.96 ? C48 L3P 280 1 1 HETATM 29 C C49 L3P . . . F 4 27.625 42.897 19.418 1 122.86 ? C49 L3P 280 1 1 HETATM 30 C C50 L3P . . . F 4 29.946 41.931 20.336 1 121.08 ? C50 L3P 280 1 1 HETATM 31 C C51 L3P . . . F 4 29.983 42.4 21.704 1 121.01 ? C51 L3P 280 1 1 HETATM 32 C C52 L3P . . . F 4 31.367 43.026 22.165 1 120.93 ? C52 L3P 280 1 1 HETATM 33 C C53 L3P . . . F 4 31.506 44.463 22.97 1 120.91 ? C53 L3P 280 1 1 HETATM 34 C C54 L3P . . . F 4 32.905 45.045 23.002 1 120.83 ? C54 L3P 280 1 1 HETATM 35 C C55 L3P . . . F 4 30.998 44.291 24.494 1 121.07 ? C55 L3P 280 1 1 HETATM 36 C C56 L3P . . . F 4 30.091 45.417 25.231 1 121.96 ? C56 L3P 280 1 1 HETATM 37 C C57 L3P . . . F 4 29.767 44.932 26.729 1 121.52 ? C57 L3P 280 1 1 HETATM 38 C C58 L3P . . . F 4 28.649 45.764 27.393 1 120.7 ? C58 L3P 280 1 1 HETATM 39 C C59 L3P . . . F 4 27.601 44.817 27.94 1 120.51 ? C59 L3P 280 1 1 HETATM 40 C C60 L3P . . . F 4 29.234 46.601 28.521 1 120.1 ? C60 L3P 280 1 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 351 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 40 #