data_5YKJ # _model_server_result.job_id uqQEdsUJAwhlRS2VOA0aLw _model_server_result.datetime_utc '2025-02-18 02:27:38' _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 5ykj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5YKJ # _exptl.entry_id 5YKJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 1 _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 90 _cell.entry_id 5YKJ _cell.length_a 84.03 _cell.length_b 84.03 _cell.length_c 62.784 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YKJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 C VAL 43 A VAL 90 1_555 A N CSO 44 A CSO 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.305 ? covale ? covale2 A C CSO 44 A CSO 91 1_555 A N THR 45 A THR 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.316 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 GOL sing 130 n n C1 C2 GOL sing 131 n n C1 H11 GOL sing 132 n n C1 H12 GOL sing 133 n n O1 HO1 GOL sing 134 n n C2 O2 GOL sing 135 n n C2 C3 GOL sing 136 n n C2 H2 GOL sing 137 n n O2 HO2 GOL sing 138 n n C3 O3 GOL sing 139 n n C3 H31 GOL sing 140 n n C3 H32 GOL sing 141 n n O3 HO3 GOL sing 142 n n # _atom_sites.entry_id 5YKJ _atom_sites.fract_transf_matrix[1][1] 0.011901 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011901 _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] 0.015928 _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 GOL A 1 301 1 GOL GOL . C 3 NA A 1 302 1 NA NA . D 4 HOH A 1 401 116 HOH HOH . D 4 HOH A 2 402 131 HOH HOH . D 4 HOH A 3 403 53 HOH HOH . D 4 HOH A 4 404 155 HOH HOH . D 4 HOH A 5 405 191 HOH HOH . D 4 HOH A 6 406 172 HOH HOH . D 4 HOH A 7 407 112 HOH HOH . D 4 HOH A 8 408 60 HOH HOH . D 4 HOH A 9 409 171 HOH HOH . D 4 HOH A 10 410 154 HOH HOH . D 4 HOH A 11 411 68 HOH HOH . D 4 HOH A 12 412 46 HOH HOH . D 4 HOH A 13 413 220 HOH HOH . D 4 HOH A 14 414 195 HOH HOH . D 4 HOH A 15 415 118 HOH HOH . D 4 HOH A 16 416 54 HOH HOH . D 4 HOH A 17 417 98 HOH HOH . D 4 HOH A 18 418 32 HOH HOH . D 4 HOH A 19 419 188 HOH HOH . D 4 HOH A 20 420 82 HOH HOH . D 4 HOH A 21 421 204 HOH HOH . D 4 HOH A 22 422 207 HOH HOH . D 4 HOH A 23 423 23 HOH HOH . D 4 HOH A 24 424 136 HOH HOH . D 4 HOH A 25 425 33 HOH HOH . D 4 HOH A 26 426 177 HOH HOH . D 4 HOH A 27 427 7 HOH HOH . D 4 HOH A 28 428 73 HOH HOH . D 4 HOH A 29 429 28 HOH HOH . D 4 HOH A 30 430 142 HOH HOH . D 4 HOH A 31 431 139 HOH HOH . D 4 HOH A 32 432 17 HOH HOH . D 4 HOH A 33 433 128 HOH HOH . D 4 HOH A 34 434 156 HOH HOH . D 4 HOH A 35 435 3 HOH HOH . D 4 HOH A 36 436 105 HOH HOH . D 4 HOH A 37 437 29 HOH HOH . D 4 HOH A 38 438 78 HOH HOH . D 4 HOH A 39 439 50 HOH HOH . D 4 HOH A 40 440 185 HOH HOH . D 4 HOH A 41 441 194 HOH HOH . D 4 HOH A 42 442 119 HOH HOH . D 4 HOH A 43 443 85 HOH HOH . D 4 HOH A 44 444 34 HOH HOH . D 4 HOH A 45 445 25 HOH HOH . D 4 HOH A 46 446 84 HOH HOH . D 4 HOH A 47 447 144 HOH HOH . D 4 HOH A 48 448 79 HOH HOH . D 4 HOH A 49 449 30 HOH HOH . D 4 HOH A 50 450 19 HOH HOH . D 4 HOH A 51 451 127 HOH HOH . D 4 HOH A 52 452 99 HOH HOH . D 4 HOH A 53 453 26 HOH HOH . D 4 HOH A 54 454 153 HOH HOH . D 4 HOH A 55 455 134 HOH HOH . D 4 HOH A 56 456 180 HOH HOH . D 4 HOH A 57 457 4 HOH HOH . D 4 HOH A 58 458 137 HOH HOH . D 4 HOH A 59 459 36 HOH HOH . D 4 HOH A 60 460 45 HOH HOH . D 4 HOH A 61 461 16 HOH HOH . D 4 HOH A 62 462 143 HOH HOH . D 4 HOH A 63 463 219 HOH HOH . D 4 HOH A 64 464 141 HOH HOH . D 4 HOH A 65 465 9 HOH HOH . D 4 HOH A 66 466 217 HOH HOH . D 4 HOH A 67 467 24 HOH HOH . D 4 HOH A 68 468 6 HOH HOH . D 4 HOH A 69 469 62 HOH HOH . D 4 HOH A 70 470 149 HOH HOH . D 4 HOH A 71 471 95 HOH HOH . D 4 HOH A 72 472 63 HOH HOH . D 4 HOH A 73 473 22 HOH HOH . D 4 HOH A 74 474 86 HOH HOH . D 4 HOH A 75 475 130 HOH HOH . D 4 HOH A 76 476 14 HOH HOH . D 4 HOH A 77 477 94 HOH HOH . D 4 HOH A 78 478 176 HOH HOH . D 4 HOH A 79 479 77 HOH HOH . D 4 HOH A 80 480 51 HOH HOH . D 4 HOH A 81 481 101 HOH HOH . D 4 HOH A 82 482 49 HOH HOH . D 4 HOH A 83 483 31 HOH HOH . D 4 HOH A 84 484 218 HOH HOH . D 4 HOH A 85 485 83 HOH HOH . D 4 HOH A 86 486 114 HOH HOH . D 4 HOH A 87 487 132 HOH HOH . D 4 HOH A 88 488 1 HOH HOH . D 4 HOH A 89 489 76 HOH HOH . D 4 HOH A 90 490 165 HOH HOH . D 4 HOH A 91 491 74 HOH HOH . D 4 HOH A 92 492 15 HOH HOH . D 4 HOH A 93 493 10 HOH HOH . D 4 HOH A 94 494 27 HOH HOH . D 4 HOH A 95 495 37 HOH HOH . D 4 HOH A 96 496 72 HOH HOH . D 4 HOH A 97 497 47 HOH HOH . D 4 HOH A 98 498 18 HOH HOH . D 4 HOH A 99 499 184 HOH HOH . D 4 HOH A 100 500 106 HOH HOH . D 4 HOH A 101 501 150 HOH HOH . D 4 HOH A 102 502 196 HOH HOH . D 4 HOH A 103 503 40 HOH HOH . D 4 HOH A 104 504 20 HOH HOH . D 4 HOH A 105 505 111 HOH HOH . D 4 HOH A 106 506 5 HOH HOH . D 4 HOH A 107 507 164 HOH HOH . D 4 HOH A 108 508 57 HOH HOH . D 4 HOH A 109 509 113 HOH HOH . D 4 HOH A 110 510 93 HOH HOH . D 4 HOH A 111 511 58 HOH HOH . D 4 HOH A 112 512 152 HOH HOH . D 4 HOH A 113 513 189 HOH HOH . D 4 HOH A 114 514 39 HOH HOH . D 4 HOH A 115 515 35 HOH HOH . D 4 HOH A 116 516 122 HOH HOH . D 4 HOH A 117 517 124 HOH HOH . D 4 HOH A 118 518 13 HOH HOH . D 4 HOH A 119 519 90 HOH HOH . D 4 HOH A 120 520 52 HOH HOH . D 4 HOH A 121 521 11 HOH HOH . D 4 HOH A 122 522 21 HOH HOH . D 4 HOH A 123 523 133 HOH HOH . D 4 HOH A 124 524 108 HOH HOH . D 4 HOH A 125 525 97 HOH HOH . D 4 HOH A 126 526 48 HOH HOH . D 4 HOH A 127 527 211 HOH HOH . D 4 HOH A 128 528 91 HOH HOH . D 4 HOH A 129 529 59 HOH HOH . D 4 HOH A 130 530 102 HOH HOH . D 4 HOH A 131 531 92 HOH HOH . D 4 HOH A 132 532 71 HOH HOH . D 4 HOH A 133 533 43 HOH HOH . D 4 HOH A 134 534 55 HOH HOH . D 4 HOH A 135 535 222 HOH HOH . D 4 HOH A 136 536 2 HOH HOH . D 4 HOH A 137 537 66 HOH HOH . D 4 HOH A 138 538 38 HOH HOH . D 4 HOH A 139 539 168 HOH HOH . D 4 HOH A 140 540 182 HOH HOH . D 4 HOH A 141 541 44 HOH HOH . D 4 HOH A 142 542 89 HOH HOH . D 4 HOH A 143 543 41 HOH HOH . D 4 HOH A 144 544 161 HOH HOH . D 4 HOH A 145 545 75 HOH HOH . D 4 HOH A 146 546 87 HOH HOH . D 4 HOH A 147 547 125 HOH HOH . D 4 HOH A 148 548 80 HOH HOH . D 4 HOH A 149 549 145 HOH HOH . D 4 HOH A 150 550 64 HOH HOH . D 4 HOH A 151 551 104 HOH HOH . D 4 HOH A 152 552 103 HOH HOH . D 4 HOH A 153 553 110 HOH HOH . D 4 HOH A 154 554 183 HOH HOH . D 4 HOH A 155 555 187 HOH HOH . D 4 HOH A 156 556 140 HOH HOH . D 4 HOH A 157 557 158 HOH HOH . D 4 HOH A 158 558 88 HOH HOH . D 4 HOH A 159 559 42 HOH HOH . D 4 HOH A 160 560 209 HOH HOH . D 4 HOH A 161 561 232 HOH HOH . D 4 HOH A 162 562 65 HOH HOH . D 4 HOH A 163 563 230 HOH HOH . D 4 HOH A 164 564 226 HOH HOH . D 4 HOH A 165 565 228 HOH HOH . D 4 HOH A 166 566 173 HOH HOH . D 4 HOH A 167 567 224 HOH HOH . D 4 HOH A 168 568 160 HOH HOH . D 4 HOH A 169 569 210 HOH HOH . D 4 HOH A 170 570 69 HOH HOH . D 4 HOH A 171 571 56 HOH HOH . D 4 HOH A 172 572 67 HOH HOH . D 4 HOH A 173 573 147 HOH HOH . D 4 HOH A 174 574 186 HOH HOH . D 4 HOH A 175 575 129 HOH HOH . D 4 HOH A 176 576 193 HOH HOH . D 4 HOH A 177 577 70 HOH HOH . D 4 HOH A 178 578 123 HOH HOH . D 4 HOH A 179 579 199 HOH HOH . D 4 HOH A 180 580 201 HOH HOH . D 4 HOH A 181 581 229 HOH HOH . D 4 HOH A 182 582 198 HOH HOH . D 4 HOH A 183 583 221 HOH HOH . D 4 HOH A 184 584 175 HOH HOH . D 4 HOH A 185 585 100 HOH HOH . D 4 HOH A 186 586 202 HOH HOH . D 4 HOH A 187 587 61 HOH HOH . D 4 HOH A 188 588 192 HOH HOH . D 4 HOH A 189 589 203 HOH HOH . D 4 HOH A 190 590 174 HOH HOH . D 4 HOH A 191 591 159 HOH HOH . D 4 HOH A 192 592 178 HOH HOH . D 4 HOH A 193 593 117 HOH HOH . D 4 HOH A 194 594 212 HOH HOH . D 4 HOH A 195 595 121 HOH HOH . D 4 HOH A 196 596 179 HOH HOH . D 4 HOH A 197 597 107 HOH HOH . D 4 HOH A 198 598 225 HOH HOH . D 4 HOH A 199 599 227 HOH HOH . D 4 HOH A 200 600 215 HOH HOH . D 4 HOH A 201 601 234 HOH HOH . D 4 HOH A 202 602 169 HOH HOH . D 4 HOH A 203 603 231 HOH HOH . D 4 HOH A 204 604 138 HOH HOH . D 4 HOH A 205 605 170 HOH HOH . D 4 HOH A 206 606 120 HOH HOH . D 4 HOH A 207 607 135 HOH HOH . D 4 HOH A 208 608 126 HOH HOH . D 4 HOH A 209 609 181 HOH HOH . D 4 HOH A 210 610 216 HOH HOH . D 4 HOH A 211 611 146 HOH HOH . D 4 HOH A 212 612 206 HOH HOH . D 4 HOH A 213 613 115 HOH HOH . D 4 HOH A 214 614 205 HOH HOH . D 4 HOH A 215 615 197 HOH HOH . D 4 HOH A 216 616 213 HOH HOH . D 4 HOH A 217 617 200 HOH HOH . D 4 HOH A 218 618 96 HOH HOH . D 4 HOH A 219 619 166 HOH HOH . D 4 HOH A 220 620 81 HOH HOH . D 4 HOH A 221 621 148 HOH HOH . D 4 HOH A 222 622 167 HOH HOH . D 4 HOH A 223 623 208 HOH HOH . D 4 HOH A 224 624 163 HOH HOH . D 4 HOH A 225 625 223 HOH HOH . D 4 HOH A 226 626 233 HOH HOH . D 4 HOH A 227 627 151 HOH HOH . D 4 HOH A 228 628 190 HOH HOH . D 4 HOH A 229 629 235 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 GOL . . . B 2 10.974 20.572 17.651 1 44.24 ? C1 GOL 301 A 1 HETATM 2 O O1 GOL . . . B 2 11.362 21.139 16.464 1 43.88 ? O1 GOL 301 A 1 HETATM 3 C C2 GOL . . . B 2 11.927 19.414 17.654 1 37.54 ? C2 GOL 301 A 1 HETATM 4 O O2 GOL . . . B 2 12.459 19.321 18.93 1 32.11 ? O2 GOL 301 A 1 HETATM 5 C C3 GOL . . . B 2 11.231 18.132 17.181 1 18.91 ? C3 GOL 301 A 1 HETATM 6 O O3 GOL . . . B 2 11.989 17.081 17.589 1 15.4 ? O3 GOL 301 A 1 HETATM 7 H H11 GOL . . . B 2 9.933 20.25 17.626 1 53.08 ? H11 GOL 301 A 1 HETATM 8 H H12 GOL . . . B 2 11.148 21.241 18.494 1 53.08 ? H12 GOL 301 A 1 HETATM 9 H HO1 GOL . . . B 2 10.781 21.902 16.261 1 52.65 ? HO1 GOL 301 A 1 HETATM 10 H H2 GOL . . . B 2 12.729 19.638 16.951 1 45.05 ? H2 GOL 301 A 1 HETATM 11 H HO2 GOL . . . B 2 11.744 19.113 19.568 1 38.53 ? HO2 GOL 301 A 1 HETATM 12 H H31 GOL . . . B 2 11.118 18.133 16.103 1 22.7 ? H31 GOL 301 A 1 HETATM 13 H H32 GOL . . . B 2 10.24 18.061 17.629 1 22.7 ? H32 GOL 301 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 13 #