data_5ZDM
#
_model_server_result.job_id            QsyZrvhL6TCwb4DBf3W45A 
_model_server_result.datetime_utc      '2025-07-16 14:27:04' 
_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          5zdm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":305}' 
#
_entry.id    5ZDM 
#
_exptl.entry_id    5ZDM 
_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    3 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          110.27 
_cell.angle_gamma         90 
_cell.entry_id            5ZDM 
_cell.length_a            40.474 
_cell.length_b            46.215 
_cell.length_c            52.504 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5ZDM 
_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        ? 
_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,E,F,G 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 E N N 
? 3 F 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
metalc ? metalc1 A OD1 ASN 113 A ASN 109 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? 
metalc ? metalc2 A OD1 ASP 129 A ASP 125 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? 
metalc ? metalc3 A O GLU 131 A GLU 127 1_555 C CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? 
metalc ? metalc4 A OE1 GLU 131 A GLU 127 1_555 C CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? 
metalc ? metalc5 A OD1 ASP 133 A ASP 129 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? 
metalc ? metalc6 A OD1 ASP 133 A ASP 129 1_555 C CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.852 ? 
metalc ? metalc7 A OD2 ASP 133 A ASP 129 1_555 C CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? 
metalc ? metalc8 A OD2 ASP 147 A ASP 143 1_555 C CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? 
metalc ? metalc9 A OE1 GLU 209 A GLU 205 1_555 B CA CA . A CA 301 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? 
metalc ? metalc10 A OE2 GLU 209 A GLU 205 1_555 B CA CA . A CA 301 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? 
metalc ? metalc11 B CA CA . A CA 301 1_555 G O HOH . A HOH 442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? 
metalc ? metalc12 B CA CA . A CA 301 1_555 G O HOH . A HOH 459 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? 
metalc ? metalc13 C CA CA . A CA 302 1_555 G O HOH . A HOH 433 2_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? 
metalc ? metalc14 C CA CA . A CA 302 1_555 G O HOH . A HOH 442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? 
#
_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 116 n n 
C1 C2 GOL sing 117 n n 
C1 H11 GOL sing 118 n n 
C1 H12 GOL sing 119 n n 
O1 HO1 GOL sing 120 n n 
C2 O2 GOL sing 121 n n 
C2 C3 GOL sing 122 n n 
C2 H2 GOL sing 123 n n 
O2 HO2 GOL sing 124 n n 
C3 O3 GOL sing 125 n n 
C3 H31 GOL sing 126 n n 
C3 H32 GOL sing 127 n n 
O3 HO3 GOL sing 128 n n 
#
_atom_sites.entry_id                     5ZDM 
_atom_sites.fract_transf_matrix[1][1]    0.024707 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.009126 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.021638 
_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]    0.020304 
_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 CA A 1 301 301 CA CA . 
C 2 CA A 1 302 302 CA CA . 
D 3 GOL A 1 303 303 GOL GOL . 
E 3 GOL A 1 304 304 GOL GOL . 
F 3 GOL A 1 305 305 GOL GOL . 
G 4 HOH A 1 401 203 HOH HOH . 
G 4 HOH A 2 402 187 HOH HOH . 
G 4 HOH A 3 403 193 HOH HOH . 
G 4 HOH A 4 404 55 HOH HOH . 
G 4 HOH A 5 405 50 HOH HOH . 
G 4 HOH A 6 406 134 HOH HOH . 
G 4 HOH A 7 407 201 HOH HOH . 
G 4 HOH A 8 408 92 HOH HOH . 
G 4 HOH A 9 409 184 HOH HOH . 
G 4 HOH A 10 410 44 HOH HOH . 
G 4 HOH A 11 411 204 HOH HOH . 
G 4 HOH A 12 412 90 HOH HOH . 
G 4 HOH A 13 413 119 HOH HOH . 
G 4 HOH A 14 414 112 HOH HOH . 
G 4 HOH A 15 415 107 HOH HOH . 
G 4 HOH A 16 416 79 HOH HOH . 
G 4 HOH A 17 417 209 HOH HOH . 
G 4 HOH A 18 418 139 HOH HOH . 
G 4 HOH A 19 419 93 HOH HOH . 
G 4 HOH A 20 420 121 HOH HOH . 
G 4 HOH A 21 421 12 HOH HOH . 
G 4 HOH A 22 422 65 HOH HOH . 
G 4 HOH A 23 423 124 HOH HOH . 
G 4 HOH A 24 424 29 HOH HOH . 
G 4 HOH A 25 425 63 HOH HOH . 
G 4 HOH A 26 426 43 HOH HOH . 
G 4 HOH A 27 427 192 HOH HOH . 
G 4 HOH A 28 428 171 HOH HOH . 
G 4 HOH A 29 429 126 HOH HOH . 
G 4 HOH A 30 430 113 HOH HOH . 
G 4 HOH A 31 431 173 HOH HOH . 
G 4 HOH A 32 432 51 HOH HOH . 
G 4 HOH A 33 433 170 HOH HOH . 
G 4 HOH A 34 434 40 HOH HOH . 
G 4 HOH A 35 435 89 HOH HOH . 
G 4 HOH A 36 436 16 HOH HOH . 
G 4 HOH A 37 437 141 HOH HOH . 
G 4 HOH A 38 438 105 HOH HOH . 
G 4 HOH A 39 439 82 HOH HOH . 
G 4 HOH A 40 440 56 HOH HOH . 
G 4 HOH A 41 441 108 HOH HOH . 
G 4 HOH A 42 442 169 HOH HOH . 
G 4 HOH A 43 443 183 HOH HOH . 
G 4 HOH A 44 444 84 HOH HOH . 
G 4 HOH A 45 445 27 HOH HOH . 
G 4 HOH A 46 446 73 HOH HOH . 
G 4 HOH A 47 447 7 HOH HOH . 
G 4 HOH A 48 448 3 HOH HOH . 
G 4 HOH A 49 449 17 HOH HOH . 
G 4 HOH A 50 450 39 HOH HOH . 
G 4 HOH A 51 451 20 HOH HOH . 
G 4 HOH A 52 452 117 HOH HOH . 
G 4 HOH A 53 453 147 HOH HOH . 
G 4 HOH A 54 454 28 HOH HOH . 
G 4 HOH A 55 455 130 HOH HOH . 
G 4 HOH A 56 456 131 HOH HOH . 
G 4 HOH A 57 457 8 HOH HOH . 
G 4 HOH A 58 458 99 HOH HOH . 
G 4 HOH A 59 459 168 HOH HOH . 
G 4 HOH A 60 460 57 HOH HOH . 
G 4 HOH A 61 461 97 HOH HOH . 
G 4 HOH A 62 462 172 HOH HOH . 
G 4 HOH A 63 463 85 HOH HOH . 
G 4 HOH A 64 464 174 HOH HOH . 
G 4 HOH A 65 465 146 HOH HOH . 
G 4 HOH A 66 466 144 HOH HOH . 
G 4 HOH A 67 467 18 HOH HOH . 
G 4 HOH A 68 468 120 HOH HOH . 
G 4 HOH A 69 469 5 HOH HOH . 
G 4 HOH A 70 470 88 HOH HOH . 
G 4 HOH A 71 471 86 HOH HOH . 
G 4 HOH A 72 472 198 HOH HOH . 
G 4 HOH A 73 473 179 HOH HOH . 
G 4 HOH A 74 474 186 HOH HOH . 
G 4 HOH A 75 475 162 HOH HOH . 
G 4 HOH A 76 476 145 HOH HOH . 
G 4 HOH A 77 477 22 HOH HOH . 
G 4 HOH A 78 478 74 HOH HOH . 
G 4 HOH A 79 479 78 HOH HOH . 
G 4 HOH A 80 480 81 HOH HOH . 
G 4 HOH A 81 481 94 HOH HOH . 
G 4 HOH A 82 482 61 HOH HOH . 
G 4 HOH A 83 483 54 HOH HOH . 
G 4 HOH A 84 484 110 HOH HOH . 
G 4 HOH A 85 485 2 HOH HOH . 
G 4 HOH A 86 486 96 HOH HOH . 
G 4 HOH A 87 487 95 HOH HOH . 
G 4 HOH A 88 488 46 HOH HOH . 
G 4 HOH A 89 489 206 HOH HOH . 
G 4 HOH A 90 490 104 HOH HOH . 
G 4 HOH A 91 491 72 HOH HOH . 
G 4 HOH A 92 492 42 HOH HOH . 
G 4 HOH A 93 493 67 HOH HOH . 
G 4 HOH A 94 494 32 HOH HOH . 
G 4 HOH A 95 495 41 HOH HOH . 
G 4 HOH A 96 496 21 HOH HOH . 
G 4 HOH A 97 497 1 HOH HOH . 
G 4 HOH A 98 498 62 HOH HOH . 
G 4 HOH A 99 499 98 HOH HOH . 
G 4 HOH A 100 500 37 HOH HOH . 
G 4 HOH A 101 501 75 HOH HOH . 
G 4 HOH A 102 502 23 HOH HOH . 
G 4 HOH A 103 503 185 HOH HOH . 
G 4 HOH A 104 504 149 HOH HOH . 
G 4 HOH A 105 505 83 HOH HOH . 
G 4 HOH A 106 506 6 HOH HOH . 
G 4 HOH A 107 507 59 HOH HOH . 
G 4 HOH A 108 508 64 HOH HOH . 
G 4 HOH A 109 509 123 HOH HOH . 
G 4 HOH A 110 510 77 HOH HOH . 
G 4 HOH A 111 511 15 HOH HOH . 
G 4 HOH A 112 512 38 HOH HOH . 
G 4 HOH A 113 513 76 HOH HOH . 
G 4 HOH A 114 514 140 HOH HOH . 
G 4 HOH A 115 515 129 HOH HOH . 
G 4 HOH A 116 516 31 HOH HOH . 
G 4 HOH A 117 517 100 HOH HOH . 
G 4 HOH A 118 518 24 HOH HOH . 
G 4 HOH A 119 519 178 HOH HOH . 
G 4 HOH A 120 520 80 HOH HOH . 
G 4 HOH A 121 521 49 HOH HOH . 
G 4 HOH A 122 522 13 HOH HOH . 
G 4 HOH A 123 523 19 HOH HOH . 
G 4 HOH A 124 524 161 HOH HOH . 
G 4 HOH A 125 525 114 HOH HOH . 
G 4 HOH A 126 526 10 HOH HOH . 
G 4 HOH A 127 527 14 HOH HOH . 
G 4 HOH A 128 528 71 HOH HOH . 
G 4 HOH A 129 529 111 HOH HOH . 
G 4 HOH A 130 530 70 HOH HOH . 
G 4 HOH A 131 531 30 HOH HOH . 
G 4 HOH A 132 532 210 HOH HOH . 
G 4 HOH A 133 533 103 HOH HOH . 
G 4 HOH A 134 534 68 HOH HOH . 
G 4 HOH A 135 535 35 HOH HOH . 
G 4 HOH A 136 536 26 HOH HOH . 
G 4 HOH A 137 537 52 HOH HOH . 
G 4 HOH A 138 538 91 HOH HOH . 
G 4 HOH A 139 539 102 HOH HOH . 
G 4 HOH A 140 540 148 HOH HOH . 
G 4 HOH A 141 541 188 HOH HOH . 
G 4 HOH A 142 542 66 HOH HOH . 
G 4 HOH A 143 543 45 HOH HOH . 
G 4 HOH A 144 544 36 HOH HOH . 
G 4 HOH A 145 545 196 HOH HOH . 
G 4 HOH A 146 546 60 HOH HOH . 
G 4 HOH A 147 547 109 HOH HOH . 
G 4 HOH A 148 548 135 HOH HOH . 
G 4 HOH A 149 549 9 HOH HOH . 
G 4 HOH A 150 550 47 HOH HOH . 
G 4 HOH A 151 551 25 HOH HOH . 
G 4 HOH A 152 552 191 HOH HOH . 
G 4 HOH A 153 553 106 HOH HOH . 
G 4 HOH A 154 554 101 HOH HOH . 
G 4 HOH A 155 555 11 HOH HOH . 
G 4 HOH A 156 556 69 HOH HOH . 
G 4 HOH A 157 557 143 HOH HOH . 
G 4 HOH A 158 558 87 HOH HOH . 
G 4 HOH A 159 559 189 HOH HOH . 
G 4 HOH A 160 560 202 HOH HOH . 
G 4 HOH A 161 561 151 HOH HOH . 
G 4 HOH A 162 562 34 HOH HOH . 
G 4 HOH A 163 563 118 HOH HOH . 
G 4 HOH A 164 564 4 HOH HOH . 
G 4 HOH A 165 565 128 HOH HOH . 
G 4 HOH A 166 566 142 HOH HOH . 
G 4 HOH A 167 567 137 HOH HOH . 
G 4 HOH A 168 568 136 HOH HOH . 
G 4 HOH A 169 569 175 HOH HOH . 
G 4 HOH A 170 570 48 HOH HOH . 
G 4 HOH A 171 571 199 HOH HOH . 
G 4 HOH A 172 572 158 HOH HOH . 
G 4 HOH A 173 573 200 HOH HOH . 
G 4 HOH A 174 574 122 HOH HOH . 
G 4 HOH A 175 575 164 HOH HOH . 
G 4 HOH A 176 576 205 HOH HOH . 
G 4 HOH A 177 577 180 HOH HOH . 
G 4 HOH A 178 578 53 HOH HOH . 
G 4 HOH A 179 579 127 HOH HOH . 
G 4 HOH A 180 580 152 HOH HOH . 
G 4 HOH A 181 581 163 HOH HOH . 
G 4 HOH A 182 582 197 HOH HOH . 
G 4 HOH A 183 583 195 HOH HOH . 
G 4 HOH A 184 584 116 HOH HOH . 
G 4 HOH A 185 585 33 HOH HOH . 
G 4 HOH A 186 586 132 HOH HOH . 
G 4 HOH A 187 587 167 HOH HOH . 
G 4 HOH A 188 588 58 HOH HOH . 
G 4 HOH A 189 589 133 HOH HOH . 
G 4 HOH A 190 590 207 HOH HOH . 
G 4 HOH A 191 591 154 HOH HOH . 
G 4 HOH A 192 592 125 HOH HOH . 
G 4 HOH A 193 593 160 HOH HOH . 
G 4 HOH A 194 594 166 HOH HOH . 
G 4 HOH A 195 595 208 HOH HOH . 
G 4 HOH A 196 596 159 HOH HOH . 
G 4 HOH A 197 597 194 HOH HOH . 
G 4 HOH A 198 598 155 HOH HOH . 
G 4 HOH A 199 599 165 HOH HOH . 
G 4 HOH A 200 600 156 HOH HOH . 
G 4 HOH A 201 601 157 HOH HOH . 
G 4 HOH A 202 602 153 HOH HOH . 
G 4 HOH A 203 603 190 HOH HOH . 
G 4 HOH A 204 604 150 HOH HOH . 
G 4 HOH A 205 605 115 HOH HOH . 
G 4 HOH A 206 606 138 HOH HOH . 
G 4 HOH A 207 607 181 HOH HOH . 
G 4 HOH A 208 608 177 HOH HOH . 
G 4 HOH A 209 609 176 HOH HOH . 
G 4 HOH A 210 610 182 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 . . . F 3 3.902 -10.132 9.215 1 35.05 ? C1 GOL 305 A 1 
HETATM 2 O O1 GOL . . . F 3 2.572 -9.751 9.192 1 34.72 ? O1 GOL 305 A 1 
HETATM 3 C C2 GOL . . . F 3 3.847 -11.554 9.759 1 40.87 ? C2 GOL 305 A 1 
HETATM 4 O O2 GOL . . . F 3 4.185 -12.636 8.894 1 39.43 ? O2 GOL 305 A 1 
HETATM 5 C C3 GOL . . . F 3 4.873 -11.631 10.842 1 34.34 ? C3 GOL 305 A 1 
HETATM 6 O O3 GOL . . . F 3 5.88 -12.598 10.588 1 35.85 ? O3 GOL 305 A 1 
#
_model_server_stats.io_time_ms              60 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           311 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           6 
#