data_5EKH # _model_server_result.job_id WbpsfzuCox7X4uT2gE6LaA _model_server_result.datetime_utc '2024-10-19 23:38:31' _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 5ekh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 5EKH # _exptl.entry_id 5EKH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 3 _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 104.04 _cell.angle_gamma 90 _cell.entry_id 5EKH _cell.length_a 42.38 _cell.length_b 41.39 _cell.length_c 72.11 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EKH _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 3 _struct_asym.id C _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 metalc ? metalc1 A OG SER 73 A SER 73 1_555 E NA NA . A NA 304 1_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc2 A NE2 HIS 94 A HIS 94 1_555 B ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc3 A NE2 HIS 96 A HIS 96 1_555 B ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc4 A ND1 HIS 119 A HIS 119 1_555 B ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc5 A OG SER 219 A SER 220 1_555 E NA NA . A NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc6 B ZN ZN . A ZN 301 1_555 D N10 5RD . A 5RD 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.921 ? metalc ? metalc7 E NA NA . A NA 304 1_555 F O HOH . A HOH 465 2_547 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc8 E NA NA . A NA 304 1_555 F O HOH . A HOH 477 1_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc9 E NA NA . A NA 304 1_555 F O HOH . A HOH 478 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? metalc ? metalc10 E NA NA . A NA 304 1_555 F O HOH . A HOH 493 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? # _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 163 n n C1 C2 GOL sing 164 n n C1 H11 GOL sing 165 n n C1 H12 GOL sing 166 n n O1 HO1 GOL sing 167 n n C2 O2 GOL sing 168 n n C2 C3 GOL sing 169 n n C2 H2 GOL sing 170 n n O2 HO2 GOL sing 171 n n C3 O3 GOL sing 172 n n C3 H31 GOL sing 173 n n C3 H32 GOL sing 174 n n O3 HO3 GOL sing 175 n n # _atom_sites.entry_id 5EKH _atom_sites.fract_transf_matrix[1][1] 0.023596 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005901 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.02416 _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] 0.014295 _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 ZN A 1 301 1 ZN ZN . C 3 GOL A 1 302 1 GOL GOL . D 4 5RD A 1 303 1 5RD TG1 . E 5 NA A 1 304 1 NA NA . F 6 HOH A 1 401 243 HOH HOH . F 6 HOH A 2 402 137 HOH HOH . F 6 HOH A 3 403 245 HOH HOH . F 6 HOH A 4 404 131 HOH HOH . F 6 HOH A 5 405 247 HOH HOH . F 6 HOH A 6 406 206 HOH HOH . F 6 HOH A 7 407 45 HOH HOH . F 6 HOH A 8 408 166 HOH HOH . F 6 HOH A 9 409 59 HOH HOH . F 6 HOH A 10 410 148 HOH HOH . F 6 HOH A 11 411 189 HOH HOH . F 6 HOH A 12 412 151 HOH HOH . F 6 HOH A 13 413 266 HOH HOH . F 6 HOH A 14 414 203 HOH HOH . F 6 HOH A 15 415 218 HOH HOH . F 6 HOH A 16 416 23 HOH HOH . F 6 HOH A 17 417 238 HOH HOH . F 6 HOH A 18 418 183 HOH HOH . F 6 HOH A 19 419 96 HOH HOH . F 6 HOH A 20 420 43 HOH HOH . F 6 HOH A 21 421 38 HOH HOH . F 6 HOH A 22 422 6 HOH HOH . F 6 HOH A 23 423 139 HOH HOH . F 6 HOH A 24 424 235 HOH HOH . F 6 HOH A 25 425 44 HOH HOH . F 6 HOH A 26 426 106 HOH HOH . F 6 HOH A 27 427 258 HOH HOH . F 6 HOH A 28 428 4 HOH HOH . F 6 HOH A 29 429 60 HOH HOH . F 6 HOH A 30 430 265 HOH HOH . F 6 HOH A 31 431 83 HOH HOH . F 6 HOH A 32 432 20 HOH HOH . F 6 HOH A 33 433 244 HOH HOH . F 6 HOH A 34 434 95 HOH HOH . F 6 HOH A 35 435 273 HOH HOH . F 6 HOH A 36 436 180 HOH HOH . F 6 HOH A 37 437 267 HOH HOH . F 6 HOH A 38 438 27 HOH HOH . F 6 HOH A 39 439 54 HOH HOH . F 6 HOH A 40 440 232 HOH HOH . F 6 HOH A 41 441 51 HOH HOH . F 6 HOH A 42 442 121 HOH HOH . F 6 HOH A 43 443 10 HOH HOH . F 6 HOH A 44 444 191 HOH HOH . F 6 HOH A 45 445 231 HOH HOH . F 6 HOH A 46 446 159 HOH HOH . F 6 HOH A 47 447 240 HOH HOH . F 6 HOH A 48 448 18 HOH HOH . F 6 HOH A 49 449 9 HOH HOH . F 6 HOH A 50 450 227 HOH HOH . F 6 HOH A 51 451 77 HOH HOH . F 6 HOH A 52 452 99 HOH HOH . F 6 HOH A 53 453 12 HOH HOH . F 6 HOH A 54 454 213 HOH HOH . F 6 HOH A 55 455 248 HOH HOH . F 6 HOH A 56 456 49 HOH HOH . F 6 HOH A 57 457 22 HOH HOH . F 6 HOH A 58 458 194 HOH HOH . F 6 HOH A 59 459 123 HOH HOH . F 6 HOH A 60 460 65 HOH HOH . F 6 HOH A 61 461 57 HOH HOH . F 6 HOH A 62 462 110 HOH HOH . F 6 HOH A 63 463 250 HOH HOH . F 6 HOH A 64 464 11 HOH HOH . F 6 HOH A 65 465 48 HOH HOH . F 6 HOH A 66 466 185 HOH HOH . F 6 HOH A 67 467 88 HOH HOH . F 6 HOH A 68 468 19 HOH HOH . F 6 HOH A 69 469 205 HOH HOH . F 6 HOH A 70 470 144 HOH HOH . F 6 HOH A 71 471 53 HOH HOH . F 6 HOH A 72 472 35 HOH HOH . F 6 HOH A 73 473 193 HOH HOH . F 6 HOH A 74 474 21 HOH HOH . F 6 HOH A 75 475 253 HOH HOH . F 6 HOH A 76 476 24 HOH HOH . F 6 HOH A 77 477 225 HOH HOH . F 6 HOH A 78 478 25 HOH HOH . F 6 HOH A 79 479 172 HOH HOH . F 6 HOH A 80 480 50 HOH HOH . F 6 HOH A 81 481 29 HOH HOH . F 6 HOH A 82 482 74 HOH HOH . F 6 HOH A 83 483 75 HOH HOH . F 6 HOH A 84 484 181 HOH HOH . F 6 HOH A 85 485 16 HOH HOH . F 6 HOH A 86 486 114 HOH HOH . F 6 HOH A 87 487 171 HOH HOH . F 6 HOH A 88 488 229 HOH HOH . F 6 HOH A 89 489 15 HOH HOH . F 6 HOH A 90 490 41 HOH HOH . F 6 HOH A 91 491 1 HOH HOH . F 6 HOH A 92 492 147 HOH HOH . F 6 HOH A 93 493 14 HOH HOH . F 6 HOH A 94 494 36 HOH HOH . F 6 HOH A 95 495 33 HOH HOH . F 6 HOH A 96 496 261 HOH HOH . F 6 HOH A 97 497 195 HOH HOH . F 6 HOH A 98 498 47 HOH HOH . F 6 HOH A 99 499 26 HOH HOH . F 6 HOH A 100 500 104 HOH HOH . F 6 HOH A 101 501 32 HOH HOH . F 6 HOH A 102 502 269 HOH HOH . F 6 HOH A 103 503 2 HOH HOH . F 6 HOH A 104 504 149 HOH HOH . F 6 HOH A 105 505 270 HOH HOH . F 6 HOH A 106 506 262 HOH HOH . F 6 HOH A 107 507 28 HOH HOH . F 6 HOH A 108 508 184 HOH HOH . F 6 HOH A 109 509 127 HOH HOH . F 6 HOH A 110 510 170 HOH HOH . F 6 HOH A 111 511 3 HOH HOH . F 6 HOH A 112 512 201 HOH HOH . F 6 HOH A 113 513 81 HOH HOH . F 6 HOH A 114 514 252 HOH HOH . F 6 HOH A 115 515 120 HOH HOH . F 6 HOH A 116 516 85 HOH HOH . F 6 HOH A 117 517 46 HOH HOH . F 6 HOH A 118 518 55 HOH HOH . F 6 HOH A 119 519 56 HOH HOH . F 6 HOH A 120 520 146 HOH HOH . F 6 HOH A 121 521 8 HOH HOH . F 6 HOH A 122 522 64 HOH HOH . F 6 HOH A 123 523 17 HOH HOH . F 6 HOH A 124 524 7 HOH HOH . F 6 HOH A 125 525 78 HOH HOH . F 6 HOH A 126 526 199 HOH HOH . F 6 HOH A 127 527 152 HOH HOH . F 6 HOH A 128 528 177 HOH HOH . F 6 HOH A 129 529 186 HOH HOH . F 6 HOH A 130 530 42 HOH HOH . F 6 HOH A 131 531 233 HOH HOH . F 6 HOH A 132 532 113 HOH HOH . F 6 HOH A 133 533 138 HOH HOH . F 6 HOH A 134 534 86 HOH HOH . F 6 HOH A 135 535 61 HOH HOH . F 6 HOH A 136 536 202 HOH HOH . F 6 HOH A 137 537 58 HOH HOH . F 6 HOH A 138 538 136 HOH HOH . F 6 HOH A 139 539 84 HOH HOH . F 6 HOH A 140 540 82 HOH HOH . F 6 HOH A 141 541 242 HOH HOH . F 6 HOH A 142 542 13 HOH HOH . F 6 HOH A 143 543 226 HOH HOH . F 6 HOH A 144 544 198 HOH HOH . F 6 HOH A 145 545 263 HOH HOH . F 6 HOH A 146 546 182 HOH HOH . F 6 HOH A 147 547 124 HOH HOH . F 6 HOH A 148 548 91 HOH HOH . F 6 HOH A 149 549 254 HOH HOH . F 6 HOH A 150 550 67 HOH HOH . F 6 HOH A 151 551 93 HOH HOH . F 6 HOH A 152 552 150 HOH HOH . F 6 HOH A 153 553 236 HOH HOH . F 6 HOH A 154 554 30 HOH HOH . F 6 HOH A 155 555 94 HOH HOH . F 6 HOH A 156 556 37 HOH HOH . F 6 HOH A 157 557 100 HOH HOH . F 6 HOH A 158 558 204 HOH HOH . F 6 HOH A 159 559 98 HOH HOH . F 6 HOH A 160 560 249 HOH HOH . F 6 HOH A 161 561 132 HOH HOH . F 6 HOH A 162 562 178 HOH HOH . F 6 HOH A 163 563 196 HOH HOH . F 6 HOH A 164 564 34 HOH HOH . F 6 HOH A 165 565 130 HOH HOH . F 6 HOH A 166 566 157 HOH HOH . F 6 HOH A 167 567 5 HOH HOH . F 6 HOH A 168 568 239 HOH HOH . F 6 HOH A 169 569 68 HOH HOH . F 6 HOH A 170 570 111 HOH HOH . F 6 HOH A 171 571 52 HOH HOH . F 6 HOH A 172 572 173 HOH HOH . F 6 HOH A 173 573 125 HOH HOH . F 6 HOH A 174 574 102 HOH HOH . F 6 HOH A 175 575 142 HOH HOH . F 6 HOH A 176 576 256 HOH HOH . F 6 HOH A 177 577 70 HOH HOH . F 6 HOH A 178 578 223 HOH HOH . F 6 HOH A 179 579 210 HOH HOH . F 6 HOH A 180 580 241 HOH HOH . F 6 HOH A 181 581 73 HOH HOH . F 6 HOH A 182 582 40 HOH HOH . F 6 HOH A 183 583 141 HOH HOH . F 6 HOH A 184 584 179 HOH HOH . F 6 HOH A 185 585 107 HOH HOH . F 6 HOH A 186 586 190 HOH HOH . F 6 HOH A 187 587 97 HOH HOH . F 6 HOH A 188 588 246 HOH HOH . F 6 HOH A 189 589 31 HOH HOH . F 6 HOH A 190 590 163 HOH HOH . F 6 HOH A 191 591 140 HOH HOH . F 6 HOH A 192 592 168 HOH HOH . F 6 HOH A 193 593 271 HOH HOH . F 6 HOH A 194 594 79 HOH HOH . F 6 HOH A 195 595 66 HOH HOH . F 6 HOH A 196 596 162 HOH HOH . F 6 HOH A 197 597 72 HOH HOH . F 6 HOH A 198 598 230 HOH HOH . F 6 HOH A 199 599 153 HOH HOH . F 6 HOH A 200 600 76 HOH HOH . F 6 HOH A 201 601 143 HOH HOH . F 6 HOH A 202 602 160 HOH HOH . F 6 HOH A 203 603 118 HOH HOH . F 6 HOH A 204 604 222 HOH HOH . F 6 HOH A 205 605 112 HOH HOH . F 6 HOH A 206 606 63 HOH HOH . F 6 HOH A 207 607 264 HOH HOH . F 6 HOH A 208 608 211 HOH HOH . F 6 HOH A 209 609 39 HOH HOH . F 6 HOH A 210 610 145 HOH HOH . F 6 HOH A 211 611 272 HOH HOH . F 6 HOH A 212 612 237 HOH HOH . F 6 HOH A 213 613 105 HOH HOH . F 6 HOH A 214 614 90 HOH HOH . F 6 HOH A 215 615 116 HOH HOH . F 6 HOH A 216 616 251 HOH HOH . F 6 HOH A 217 617 208 HOH HOH . F 6 HOH A 218 618 126 HOH HOH . F 6 HOH A 219 619 119 HOH HOH . F 6 HOH A 220 620 135 HOH HOH . F 6 HOH A 221 621 259 HOH HOH . F 6 HOH A 222 622 175 HOH HOH . F 6 HOH A 223 623 197 HOH HOH . F 6 HOH A 224 624 87 HOH HOH . F 6 HOH A 225 625 165 HOH HOH . F 6 HOH A 226 626 187 HOH HOH . F 6 HOH A 227 627 158 HOH HOH . F 6 HOH A 228 628 71 HOH HOH . F 6 HOH A 229 629 92 HOH HOH . F 6 HOH A 230 630 212 HOH HOH . F 6 HOH A 231 631 219 HOH HOH . F 6 HOH A 232 632 161 HOH HOH . F 6 HOH A 233 633 128 HOH HOH . F 6 HOH A 234 634 255 HOH HOH . F 6 HOH A 235 635 188 HOH HOH . F 6 HOH A 236 636 62 HOH HOH . F 6 HOH A 237 637 200 HOH HOH . F 6 HOH A 238 638 129 HOH HOH . F 6 HOH A 239 639 164 HOH HOH . F 6 HOH A 240 640 268 HOH HOH . F 6 HOH A 241 641 69 HOH HOH . F 6 HOH A 242 642 209 HOH HOH . F 6 HOH A 243 643 101 HOH HOH . F 6 HOH A 244 644 228 HOH HOH . F 6 HOH A 245 645 103 HOH HOH . F 6 HOH A 246 646 260 HOH HOH . F 6 HOH A 247 647 154 HOH HOH . F 6 HOH A 248 648 89 HOH HOH . F 6 HOH A 249 649 108 HOH HOH . F 6 HOH A 250 650 220 HOH HOH . F 6 HOH A 251 651 174 HOH HOH . F 6 HOH A 252 652 207 HOH HOH . F 6 HOH A 253 653 80 HOH HOH . F 6 HOH A 254 654 214 HOH HOH . F 6 HOH A 255 655 109 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 . . . C 3 -0.558 -0.537 81.719 1 12 ? C1 GOL 302 A 1 HETATM 2 O O1 GOL . . . C 3 0.74 -0.677 81.178 1 12.25 ? O1 GOL 302 A 1 HETATM 3 C C2 GOL . . . C 3 -1.295 0.626 81.082 1 10.92 ? C2 GOL 302 A 1 HETATM 4 O O2 GOL . . . C 3 -1.445 0.379 79.7 1 10.35 ? O2 GOL 302 A 1 HETATM 5 C C3 GOL . . . C 3 -0.565 1.94 81.296 1 12.4 ? C3 GOL 302 A 1 HETATM 6 O O3 GOL . . . C 3 -1.387 3.019 80.887 1 13.03 ? O3 GOL 302 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 414 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 6 #