data_9EBK
#
_model_server_result.job_id            DCRpgjMP2-ug1mNNe2C3lg 
_model_server_result.datetime_utc      '2025-07-08 09:45:16' 
_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          9ebk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":502}' 
#
_entry.id    9EBK 
#
_exptl.entry_id    9EBK 
_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            9EBK 
_cell.length_a            66.51 
_cell.length_b            66.51 
_cell.length_c            478.694 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9EBK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    'P 61 2 (x,y,z+5/12)' 
_symmetry.space_group_name_H-M     'P 61 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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 
#
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 NE2 HIS 66 B HIS 66 1_555 C FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? 
metalc ? metalc2 A NE2 HIS 223 B HIS 223 1_555 E FE HEM . A HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? 
metalc ? metalc3 C FE HEM . B HEM 501 1_555 B NE2 HIS 223 A HIS 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? 
metalc ? metalc4 B NE2 HIS 66 A HIS 66 1_555 E FE HEM . A HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? 
#
_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 129 n n 
C1 C2 GOL sing 130 n n 
C1 H11 GOL sing 131 n n 
C1 H12 GOL sing 132 n n 
O1 HO1 GOL sing 133 n n 
C2 O2 GOL sing 134 n n 
C2 C3 GOL sing 135 n n 
C2 H2 GOL sing 136 n n 
O2 HO2 GOL sing 137 n n 
C3 O3 GOL sing 138 n n 
C3 H31 GOL sing 139 n n 
C3 H32 GOL sing 140 n n 
O3 HO3 GOL sing 141 n n 
#
_atom_sites.entry_id                     9EBK 
_atom_sites.fract_transf_matrix[1][1]    0.015035 
_atom_sites.fract_transf_matrix[1][2]    0.008681 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.017361 
_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]    0.002089 
_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 2 HEM B 1 501 501 HEM HEM . 
D 3 GOL B 1 502 1 GOL GOL . 
E 2 HEM A 1 301 502 HEM HEM . 
F 4 HOH B 1 601 27 HOH HOH . 
F 4 HOH B 2 602 93 HOH HOH . 
F 4 HOH B 3 603 82 HOH HOH . 
F 4 HOH B 4 604 108 HOH HOH . 
F 4 HOH B 5 605 185 HOH HOH . 
F 4 HOH B 6 606 23 HOH HOH . 
F 4 HOH B 7 607 158 HOH HOH . 
F 4 HOH B 8 608 147 HOH HOH . 
F 4 HOH B 9 609 69 HOH HOH . 
F 4 HOH B 10 610 36 HOH HOH . 
F 4 HOH B 11 611 22 HOH HOH . 
F 4 HOH B 12 612 4 HOH HOH . 
F 4 HOH B 13 613 202 HOH HOH . 
F 4 HOH B 14 614 1 HOH HOH . 
F 4 HOH B 15 615 182 HOH HOH . 
F 4 HOH B 16 616 14 HOH HOH . 
F 4 HOH B 17 617 123 HOH HOH . 
F 4 HOH B 18 618 75 HOH HOH . 
F 4 HOH B 19 619 42 HOH HOH . 
F 4 HOH B 20 620 164 HOH HOH . 
F 4 HOH B 21 621 34 HOH HOH . 
F 4 HOH B 22 622 171 HOH HOH . 
F 4 HOH B 23 623 30 HOH HOH . 
F 4 HOH B 24 624 218 HOH HOH . 
F 4 HOH B 25 625 76 HOH HOH . 
F 4 HOH B 26 626 226 HOH HOH . 
F 4 HOH B 27 627 18 HOH HOH . 
F 4 HOH B 28 628 78 HOH HOH . 
F 4 HOH B 29 629 121 HOH HOH . 
F 4 HOH B 30 630 28 HOH HOH . 
F 4 HOH B 31 631 19 HOH HOH . 
F 4 HOH B 32 632 12 HOH HOH . 
F 4 HOH B 33 633 40 HOH HOH . 
F 4 HOH B 34 634 56 HOH HOH . 
F 4 HOH B 35 635 52 HOH HOH . 
F 4 HOH B 36 636 103 HOH HOH . 
F 4 HOH B 37 637 183 HOH HOH . 
F 4 HOH B 38 638 221 HOH HOH . 
F 4 HOH B 39 639 48 HOH HOH . 
F 4 HOH B 40 640 53 HOH HOH . 
F 4 HOH B 41 641 45 HOH HOH . 
F 4 HOH B 42 642 181 HOH HOH . 
F 4 HOH B 43 643 13 HOH HOH . 
F 4 HOH B 44 644 49 HOH HOH . 
F 4 HOH B 45 645 80 HOH HOH . 
F 4 HOH B 46 646 233 HOH HOH . 
F 4 HOH B 47 647 200 HOH HOH . 
F 4 HOH B 48 648 3 HOH HOH . 
F 4 HOH B 49 649 7 HOH HOH . 
F 4 HOH B 50 650 115 HOH HOH . 
F 4 HOH B 51 651 178 HOH HOH . 
F 4 HOH B 52 652 169 HOH HOH . 
F 4 HOH B 53 653 44 HOH HOH . 
F 4 HOH B 54 654 86 HOH HOH . 
F 4 HOH B 55 655 197 HOH HOH . 
F 4 HOH B 56 656 140 HOH HOH . 
F 4 HOH B 57 657 225 HOH HOH . 
F 4 HOH B 58 658 216 HOH HOH . 
F 4 HOH B 59 659 155 HOH HOH . 
F 4 HOH B 60 660 177 HOH HOH . 
F 4 HOH B 61 661 142 HOH HOH . 
F 4 HOH B 62 662 220 HOH HOH . 
F 4 HOH B 63 663 176 HOH HOH . 
F 4 HOH B 64 664 73 HOH HOH . 
F 4 HOH B 65 665 79 HOH HOH . 
F 4 HOH B 66 666 198 HOH HOH . 
F 4 HOH B 67 667 184 HOH HOH . 
F 4 HOH B 68 668 134 HOH HOH . 
F 4 HOH B 69 669 31 HOH HOH . 
F 4 HOH B 70 670 173 HOH HOH . 
F 4 HOH B 71 671 186 HOH HOH . 
F 4 HOH B 72 672 43 HOH HOH . 
F 4 HOH B 73 673 227 HOH HOH . 
F 4 HOH B 74 674 180 HOH HOH . 
F 4 HOH B 75 675 232 HOH HOH . 
F 4 HOH B 76 676 163 HOH HOH . 
F 4 HOH B 77 677 206 HOH HOH . 
G 4 HOH A 1 401 50 HOH HOH . 
G 4 HOH A 2 402 17 HOH HOH . 
G 4 HOH A 3 403 149 HOH HOH . 
G 4 HOH A 4 404 161 HOH HOH . 
G 4 HOH A 5 405 6 HOH HOH . 
G 4 HOH A 6 406 210 HOH HOH . 
G 4 HOH A 7 407 55 HOH HOH . 
G 4 HOH A 8 408 219 HOH HOH . 
G 4 HOH A 9 409 70 HOH HOH . 
G 4 HOH A 10 410 46 HOH HOH . 
G 4 HOH A 11 411 10 HOH HOH . 
G 4 HOH A 12 412 97 HOH HOH . 
G 4 HOH A 13 413 204 HOH HOH . 
G 4 HOH A 14 414 16 HOH HOH . 
G 4 HOH A 15 415 166 HOH HOH . 
G 4 HOH A 16 416 172 HOH HOH . 
G 4 HOH A 17 417 72 HOH HOH . 
G 4 HOH A 18 418 9 HOH HOH . 
G 4 HOH A 19 419 37 HOH HOH . 
G 4 HOH A 20 420 68 HOH HOH . 
G 4 HOH A 21 421 107 HOH HOH . 
G 4 HOH A 22 422 213 HOH HOH . 
G 4 HOH A 23 423 203 HOH HOH . 
G 4 HOH A 24 424 29 HOH HOH . 
G 4 HOH A 25 425 61 HOH HOH . 
G 4 HOH A 26 426 112 HOH HOH . 
G 4 HOH A 27 427 65 HOH HOH . 
G 4 HOH A 28 428 175 HOH HOH . 
G 4 HOH A 29 429 39 HOH HOH . 
G 4 HOH A 30 430 113 HOH HOH . 
G 4 HOH A 31 431 24 HOH HOH . 
G 4 HOH A 32 432 33 HOH HOH . 
G 4 HOH A 33 433 90 HOH HOH . 
G 4 HOH A 34 434 32 HOH HOH . 
G 4 HOH A 35 435 222 HOH HOH . 
G 4 HOH A 36 436 59 HOH HOH . 
G 4 HOH A 37 437 156 HOH HOH . 
G 4 HOH A 38 438 160 HOH HOH . 
G 4 HOH A 39 439 47 HOH HOH . 
G 4 HOH A 40 440 60 HOH HOH . 
G 4 HOH A 41 441 58 HOH HOH . 
G 4 HOH A 42 442 2 HOH HOH . 
G 4 HOH A 43 443 57 HOH HOH . 
G 4 HOH A 44 444 54 HOH HOH . 
G 4 HOH A 45 445 223 HOH HOH . 
G 4 HOH A 46 446 77 HOH HOH . 
G 4 HOH A 47 447 152 HOH HOH . 
G 4 HOH A 48 448 67 HOH HOH . 
G 4 HOH A 49 449 153 HOH HOH . 
G 4 HOH A 50 450 191 HOH HOH . 
G 4 HOH A 51 451 195 HOH HOH . 
G 4 HOH A 52 452 217 HOH HOH . 
G 4 HOH A 53 453 196 HOH HOH . 
G 4 HOH A 54 454 38 HOH HOH . 
G 4 HOH A 55 455 20 HOH HOH . 
G 4 HOH A 56 456 83 HOH HOH . 
G 4 HOH A 57 457 189 HOH HOH . 
G 4 HOH A 58 458 179 HOH HOH . 
G 4 HOH A 59 459 207 HOH HOH . 
G 4 HOH A 60 460 188 HOH HOH . 
G 4 HOH A 61 461 229 HOH HOH . 
G 4 HOH A 62 462 135 HOH HOH . 
G 4 HOH A 63 463 214 HOH HOH . 
G 4 HOH A 64 464 150 HOH HOH . 
G 4 HOH A 65 465 84 HOH HOH . 
G 4 HOH A 66 466 228 HOH HOH . 
G 4 HOH A 67 467 62 HOH HOH . 
G 4 HOH A 68 468 85 HOH HOH . 
G 4 HOH A 69 469 194 HOH HOH . 
G 4 HOH A 70 470 208 HOH HOH . 
G 4 HOH A 71 471 162 HOH HOH . 
G 4 HOH A 72 472 89 HOH HOH . 
G 4 HOH A 73 473 212 HOH HOH . 
G 4 HOH A 74 474 96 HOH HOH . 
G 4 HOH A 75 475 154 HOH HOH . 
G 4 HOH A 76 476 174 HOH HOH . 
G 4 HOH A 77 477 146 HOH HOH . 
G 4 HOH A 78 478 192 HOH HOH . 
G 4 HOH A 79 479 145 HOH HOH . 
G 4 HOH A 80 480 230 HOH HOH . 
G 4 HOH A 81 481 231 HOH HOH . 
G 4 HOH A 82 482 11 HOH HOH . 
G 4 HOH A 83 483 63 HOH HOH . 
G 4 HOH A 84 484 148 HOH HOH . 
G 4 HOH A 85 485 199 HOH HOH . 
G 4 HOH A 86 486 170 HOH HOH . 
G 4 HOH A 87 487 190 HOH HOH . 
G 4 HOH A 88 488 224 HOH HOH . 
G 4 HOH A 89 489 143 HOH HOH . 
G 4 HOH A 90 490 215 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 -6.314 1.943 -4.524 1 70.77 ? C1 GOL 502 B 1 
HETATM 2 O O1 GOL . . . D 3 -7.305 0.948 -4.37 1 64.87 ? O1 GOL 502 B 1 
HETATM 3 C C2 GOL . . . D 3 -5.487 2.06 -3.242 1 78.98 ? C2 GOL 502 B 1 
HETATM 4 O O2 GOL . . . D 3 -4.657 0.93 -3.073 1 82.27 ? O2 GOL 502 B 1 
HETATM 5 C C3 GOL . . . D 3 -4.63 3.322 -3.28 1 77.29 ? C3 GOL 502 B 1 
HETATM 6 O O3 GOL . . . D 3 -3.871 3.372 -2.095 1 78.98 ? O3 GOL 502 B 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           227 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           6 
#