data_5DN1
#
_model_server_result.job_id            APMiD7D2ctqSwcQGYBKmLA 
_model_server_result.datetime_utc      '2024-12-25 04:13:37' 
_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          5dn1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":303}' 
#
_entry.id    5DN1 
#
_exptl.entry_id    5DN1 
_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          90 
_cell.angle_gamma         120 
_cell.entry_id            5DN1 
_cell.length_a            65.208 
_cell.length_b            65.208 
_cell.length_c            104.538 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5DN1 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 31 2 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                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_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 167 n n 
C1 C2 GOL sing 168 n n 
C1 H11 GOL sing 169 n n 
C1 H12 GOL sing 170 n n 
O1 HO1 GOL sing 171 n n 
C2 O2 GOL sing 172 n n 
C2 C3 GOL sing 173 n n 
C2 H2 GOL sing 174 n n 
O2 HO2 GOL sing 175 n n 
C3 O3 GOL sing 176 n n 
C3 H31 GOL sing 177 n n 
C3 H32 GOL sing 178 n n 
O3 HO3 GOL sing 179 n n 
#
_atom_sites.entry_id                     5DN1 
_atom_sites.fract_transf_matrix[1][1]    0.015336 
_atom_sites.fract_transf_matrix[1][2]    0.008854 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.017708 
_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]    0.009566 
_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 A 1 301 2 SO4 SO4 . 
C 2 SO4 A 1 302 3 SO4 SO4 . 
D 3 GOL A 1 303 1 GOL GOL . 
E 4 AMZ A 1 304 1 AMZ AMZ . 
F 5 HOH A 1 401 256 HOH HOH . 
F 5 HOH A 2 402 152 HOH HOH . 
F 5 HOH A 3 403 239 HOH HOH . 
F 5 HOH A 4 404 233 HOH HOH . 
F 5 HOH A 5 405 178 HOH HOH . 
F 5 HOH A 6 406 192 HOH HOH . 
F 5 HOH A 7 407 190 HOH HOH . 
F 5 HOH A 8 408 104 HOH HOH . 
F 5 HOH A 9 409 247 HOH HOH . 
F 5 HOH A 10 410 27 HOH HOH . 
F 5 HOH A 11 411 125 HOH HOH . 
F 5 HOH A 12 412 157 HOH HOH . 
F 5 HOH A 13 413 205 HOH HOH . 
F 5 HOH A 14 414 228 HOH HOH . 
F 5 HOH A 15 415 187 HOH HOH . 
F 5 HOH A 16 416 37 HOH HOH . 
F 5 HOH A 17 417 196 HOH HOH . 
F 5 HOH A 18 418 171 HOH HOH . 
F 5 HOH A 19 419 51 HOH HOH . 
F 5 HOH A 20 420 225 HOH HOH . 
F 5 HOH A 21 421 188 HOH HOH . 
F 5 HOH A 22 422 61 HOH HOH . 
F 5 HOH A 23 423 102 HOH HOH . 
F 5 HOH A 24 424 59 HOH HOH . 
F 5 HOH A 25 425 183 HOH HOH . 
F 5 HOH A 26 426 130 HOH HOH . 
F 5 HOH A 27 427 149 HOH HOH . 
F 5 HOH A 28 428 82 HOH HOH . 
F 5 HOH A 29 429 176 HOH HOH . 
F 5 HOH A 30 430 17 HOH HOH . 
F 5 HOH A 31 431 85 HOH HOH . 
F 5 HOH A 32 432 18 HOH HOH . 
F 5 HOH A 33 433 115 HOH HOH . 
F 5 HOH A 34 434 123 HOH HOH . 
F 5 HOH A 35 435 234 HOH HOH . 
F 5 HOH A 36 436 21 HOH HOH . 
F 5 HOH A 37 437 79 HOH HOH . 
F 5 HOH A 38 438 53 HOH HOH . 
F 5 HOH A 39 439 142 HOH HOH . 
F 5 HOH A 40 440 131 HOH HOH . 
F 5 HOH A 41 441 25 HOH HOH . 
F 5 HOH A 42 442 168 HOH HOH . 
F 5 HOH A 43 443 68 HOH HOH . 
F 5 HOH A 44 444 129 HOH HOH . 
F 5 HOH A 45 445 29 HOH HOH . 
F 5 HOH A 46 446 16 HOH HOH . 
F 5 HOH A 47 447 204 HOH HOH . 
F 5 HOH A 48 448 105 HOH HOH . 
F 5 HOH A 49 449 93 HOH HOH . 
F 5 HOH A 50 450 57 HOH HOH . 
F 5 HOH A 51 451 35 HOH HOH . 
F 5 HOH A 52 452 189 HOH HOH . 
F 5 HOH A 53 453 10 HOH HOH . 
F 5 HOH A 54 454 139 HOH HOH . 
F 5 HOH A 55 455 41 HOH HOH . 
F 5 HOH A 56 456 52 HOH HOH . 
F 5 HOH A 57 457 208 HOH HOH . 
F 5 HOH A 58 458 36 HOH HOH . 
F 5 HOH A 59 459 145 HOH HOH . 
F 5 HOH A 60 460 110 HOH HOH . 
F 5 HOH A 61 461 197 HOH HOH . 
F 5 HOH A 62 462 150 HOH HOH . 
F 5 HOH A 63 463 117 HOH HOH . 
F 5 HOH A 64 464 73 HOH HOH . 
F 5 HOH A 65 465 1 HOH HOH . 
F 5 HOH A 66 466 23 HOH HOH . 
F 5 HOH A 67 467 3 HOH HOH . 
F 5 HOH A 68 468 30 HOH HOH . 
F 5 HOH A 69 469 11 HOH HOH . 
F 5 HOH A 70 470 47 HOH HOH . 
F 5 HOH A 71 471 28 HOH HOH . 
F 5 HOH A 72 472 84 HOH HOH . 
F 5 HOH A 73 473 114 HOH HOH . 
F 5 HOH A 74 474 81 HOH HOH . 
F 5 HOH A 75 475 235 HOH HOH . 
F 5 HOH A 76 476 22 HOH HOH . 
F 5 HOH A 77 477 50 HOH HOH . 
F 5 HOH A 78 478 55 HOH HOH . 
F 5 HOH A 79 479 232 HOH HOH . 
F 5 HOH A 80 480 120 HOH HOH . 
F 5 HOH A 81 481 8 HOH HOH . 
F 5 HOH A 82 482 230 HOH HOH . 
F 5 HOH A 83 483 19 HOH HOH . 
F 5 HOH A 84 484 163 HOH HOH . 
F 5 HOH A 85 485 48 HOH HOH . 
F 5 HOH A 86 486 46 HOH HOH . 
F 5 HOH A 87 487 90 HOH HOH . 
F 5 HOH A 88 488 34 HOH HOH . 
F 5 HOH A 89 489 126 HOH HOH . 
F 5 HOH A 90 490 147 HOH HOH . 
F 5 HOH A 91 491 186 HOH HOH . 
F 5 HOH A 92 492 158 HOH HOH . 
F 5 HOH A 93 493 148 HOH HOH . 
F 5 HOH A 94 494 7 HOH HOH . 
F 5 HOH A 95 495 26 HOH HOH . 
F 5 HOH A 96 496 43 HOH HOH . 
F 5 HOH A 97 497 75 HOH HOH . 
F 5 HOH A 98 498 109 HOH HOH . 
F 5 HOH A 99 499 113 HOH HOH . 
F 5 HOH A 100 500 20 HOH HOH . 
F 5 HOH A 101 501 14 HOH HOH . 
F 5 HOH A 102 502 100 HOH HOH . 
F 5 HOH A 103 503 136 HOH HOH . 
F 5 HOH A 104 504 161 HOH HOH . 
F 5 HOH A 105 505 6 HOH HOH . 
F 5 HOH A 106 506 219 HOH HOH . 
F 5 HOH A 107 507 119 HOH HOH . 
F 5 HOH A 108 508 86 HOH HOH . 
F 5 HOH A 109 509 236 HOH HOH . 
F 5 HOH A 110 510 67 HOH HOH . 
F 5 HOH A 111 511 96 HOH HOH . 
F 5 HOH A 112 512 24 HOH HOH . 
F 5 HOH A 113 513 78 HOH HOH . 
F 5 HOH A 114 514 4 HOH HOH . 
F 5 HOH A 115 515 56 HOH HOH . 
F 5 HOH A 116 516 12 HOH HOH . 
F 5 HOH A 117 517 164 HOH HOH . 
F 5 HOH A 118 518 127 HOH HOH . 
F 5 HOH A 119 519 5 HOH HOH . 
F 5 HOH A 120 520 42 HOH HOH . 
F 5 HOH A 121 521 166 HOH HOH . 
F 5 HOH A 122 522 238 HOH HOH . 
F 5 HOH A 123 523 101 HOH HOH . 
F 5 HOH A 124 524 91 HOH HOH . 
F 5 HOH A 125 525 195 HOH HOH . 
F 5 HOH A 126 526 31 HOH HOH . 
F 5 HOH A 127 527 191 HOH HOH . 
F 5 HOH A 128 528 69 HOH HOH . 
F 5 HOH A 129 529 45 HOH HOH . 
F 5 HOH A 130 530 38 HOH HOH . 
F 5 HOH A 131 531 95 HOH HOH . 
F 5 HOH A 132 532 40 HOH HOH . 
F 5 HOH A 133 533 252 HOH HOH . 
F 5 HOH A 134 534 62 HOH HOH . 
F 5 HOH A 135 535 184 HOH HOH . 
F 5 HOH A 136 536 65 HOH HOH . 
F 5 HOH A 137 537 244 HOH HOH . 
F 5 HOH A 138 538 143 HOH HOH . 
F 5 HOH A 139 539 209 HOH HOH . 
F 5 HOH A 140 540 177 HOH HOH . 
F 5 HOH A 141 541 154 HOH HOH . 
F 5 HOH A 142 542 138 HOH HOH . 
F 5 HOH A 143 543 76 HOH HOH . 
F 5 HOH A 144 544 141 HOH HOH . 
F 5 HOH A 145 545 159 HOH HOH . 
F 5 HOH A 146 546 245 HOH HOH . 
F 5 HOH A 147 547 251 HOH HOH . 
F 5 HOH A 148 548 99 HOH HOH . 
F 5 HOH A 149 549 58 HOH HOH . 
F 5 HOH A 150 550 9 HOH HOH . 
F 5 HOH A 151 551 32 HOH HOH . 
F 5 HOH A 152 552 97 HOH HOH . 
F 5 HOH A 153 553 137 HOH HOH . 
F 5 HOH A 154 554 106 HOH HOH . 
F 5 HOH A 155 555 74 HOH HOH . 
F 5 HOH A 156 556 193 HOH HOH . 
F 5 HOH A 157 557 144 HOH HOH . 
F 5 HOH A 158 558 221 HOH HOH . 
F 5 HOH A 159 559 70 HOH HOH . 
F 5 HOH A 160 560 156 HOH HOH . 
F 5 HOH A 161 561 175 HOH HOH . 
F 5 HOH A 162 562 15 HOH HOH . 
F 5 HOH A 163 563 71 HOH HOH . 
F 5 HOH A 164 564 227 HOH HOH . 
F 5 HOH A 165 565 162 HOH HOH . 
F 5 HOH A 166 566 83 HOH HOH . 
F 5 HOH A 167 567 172 HOH HOH . 
F 5 HOH A 168 568 181 HOH HOH . 
F 5 HOH A 169 569 77 HOH HOH . 
F 5 HOH A 170 570 155 HOH HOH . 
F 5 HOH A 171 571 218 HOH HOH . 
F 5 HOH A 172 572 254 HOH HOH . 
F 5 HOH A 173 573 170 HOH HOH . 
F 5 HOH A 174 574 250 HOH HOH . 
F 5 HOH A 175 575 212 HOH HOH . 
F 5 HOH A 176 576 13 HOH HOH . 
F 5 HOH A 177 577 253 HOH HOH . 
F 5 HOH A 178 578 98 HOH HOH . 
F 5 HOH A 179 579 223 HOH HOH . 
F 5 HOH A 180 580 122 HOH HOH . 
F 5 HOH A 181 581 44 HOH HOH . 
F 5 HOH A 182 582 116 HOH HOH . 
F 5 HOH A 183 583 80 HOH HOH . 
F 5 HOH A 184 584 180 HOH HOH . 
F 5 HOH A 185 585 89 HOH HOH . 
F 5 HOH A 186 586 72 HOH HOH . 
F 5 HOH A 187 587 198 HOH HOH . 
F 5 HOH A 188 588 207 HOH HOH . 
F 5 HOH A 189 589 255 HOH HOH . 
F 5 HOH A 190 590 200 HOH HOH . 
F 5 HOH A 191 591 241 HOH HOH . 
F 5 HOH A 192 592 179 HOH HOH . 
F 5 HOH A 193 593 49 HOH HOH . 
F 5 HOH A 194 594 226 HOH HOH . 
F 5 HOH A 195 595 92 HOH HOH . 
F 5 HOH A 196 596 185 HOH HOH . 
F 5 HOH A 197 597 39 HOH HOH . 
F 5 HOH A 198 598 146 HOH HOH . 
F 5 HOH A 199 599 2 HOH HOH . 
F 5 HOH A 200 600 134 HOH HOH . 
F 5 HOH A 201 601 33 HOH HOH . 
F 5 HOH A 202 602 243 HOH HOH . 
F 5 HOH A 203 603 103 HOH HOH . 
F 5 HOH A 204 604 160 HOH HOH . 
F 5 HOH A 205 605 210 HOH HOH . 
F 5 HOH A 206 606 112 HOH HOH . 
F 5 HOH A 207 607 108 HOH HOH . 
F 5 HOH A 208 608 174 HOH HOH . 
F 5 HOH A 209 609 220 HOH HOH . 
F 5 HOH A 210 610 135 HOH HOH . 
F 5 HOH A 211 611 124 HOH HOH . 
F 5 HOH A 212 612 246 HOH HOH . 
F 5 HOH A 213 613 63 HOH HOH . 
F 5 HOH A 214 614 133 HOH HOH . 
F 5 HOH A 215 615 199 HOH HOH . 
F 5 HOH A 216 616 94 HOH HOH . 
F 5 HOH A 217 617 215 HOH HOH . 
F 5 HOH A 218 618 173 HOH HOH . 
F 5 HOH A 219 619 153 HOH HOH . 
F 5 HOH A 220 620 201 HOH HOH . 
F 5 HOH A 221 621 140 HOH HOH . 
F 5 HOH A 222 622 229 HOH HOH . 
F 5 HOH A 223 623 213 HOH HOH . 
F 5 HOH A 224 624 64 HOH HOH . 
F 5 HOH A 225 625 202 HOH HOH . 
F 5 HOH A 226 626 132 HOH HOH . 
F 5 HOH A 227 627 217 HOH HOH . 
F 5 HOH A 228 628 60 HOH HOH . 
F 5 HOH A 229 629 194 HOH HOH . 
F 5 HOH A 230 630 231 HOH HOH . 
F 5 HOH A 231 631 128 HOH HOH . 
F 5 HOH A 232 632 248 HOH HOH . 
F 5 HOH A 233 633 214 HOH HOH . 
F 5 HOH A 234 634 107 HOH HOH . 
F 5 HOH A 235 635 88 HOH HOH . 
F 5 HOH A 236 636 242 HOH HOH . 
F 5 HOH A 237 637 121 HOH HOH . 
F 5 HOH A 238 638 224 HOH HOH . 
F 5 HOH A 239 639 203 HOH HOH . 
F 5 HOH A 240 640 182 HOH HOH . 
F 5 HOH A 241 641 111 HOH HOH . 
F 5 HOH A 242 642 222 HOH HOH . 
F 5 HOH A 243 643 118 HOH HOH . 
F 5 HOH A 244 644 66 HOH HOH . 
F 5 HOH A 245 645 237 HOH HOH . 
F 5 HOH A 246 646 206 HOH HOH . 
F 5 HOH A 247 647 216 HOH HOH . 
F 5 HOH A 248 648 54 HOH HOH . 
F 5 HOH A 249 649 249 HOH HOH . 
F 5 HOH A 250 650 240 HOH HOH . 
F 5 HOH A 251 651 87 HOH HOH . 
F 5 HOH A 252 652 211 HOH HOH . 
F 5 HOH A 253 653 165 HOH HOH . 
F 5 HOH A 254 654 167 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 . . . D 3 5.324 51.265 -3.552 1 35.07 ? C1 GOL 303 A 1 
HETATM 2 O O1 GOL . . . D 3 6.115 51.386 -4.717 1 38.12 ? O1 GOL 303 A 1 
HETATM 3 C C2 GOL . . . D 3 4.577 52.574 -3.347 1 29.19 ? C2 GOL 303 A 1 
HETATM 4 O O2 GOL . . . D 3 3.867 52.923 -4.517 1 29.43 ? O2 GOL 303 A 1 
HETATM 5 C C3 GOL . . . D 3 5.571 53.683 -2.998 1 18.68 ? C3 GOL 303 A 1 
HETATM 6 O O3 GOL . . . D 3 6.021 53.479 -1.674 1 26.6 ? O3 GOL 303 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           309 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           6 
#