data_6YKA
#
_model_server_result.job_id            kIGcSMDkrUzgBUl5jowqMg 
_model_server_result.datetime_utc      '2024-11-24 06:52:18' 
_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          6yka 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":404}' 
#
_entry.id    6YKA 
#
_exptl.entry_id    6YKA 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              62.068 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1,2-ETHANEDIOL 
_entity.pdbx_number_of_molecules    6 
_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            6YKA 
_cell.length_a            79.481 
_cell.length_b            79.481 
_cell.length_c            179.337 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6YKA 
_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    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,H,I,J,K,L,M,N,O,P 
_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
? 2 C N N 
? 2 D N N 
? 2 E N N 
? 2 F N N 
? 2 H N N 
? 2 L 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 B SG CYS 175 B CYS 175 1_555 M FE FE9 . B FE9 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? 
metalc ? metalc2 M FE FE9 . B FE9 403 1_555 P O HOH . B HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? 
#
_chem_comp.formula           'C2 H6 O2' 
_chem_comp.formula_weight    62.068 
_chem_comp.id                EDO 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1,2-ETHANEDIOL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'ETHYLENE GLYCOL' 
#
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 EDO sing 83 n n 
C1 C2 EDO sing 84 n n 
C1 H11 EDO sing 85 n n 
C1 H12 EDO sing 86 n n 
O1 HO1 EDO sing 87 n n 
C2 O2 EDO sing 88 n n 
C2 H21 EDO sing 89 n n 
C2 H22 EDO sing 90 n n 
O2 HO2 EDO sing 91 n n 
#
_atom_sites.entry_id                     6YKA 
_atom_sites.fract_transf_matrix[1][1]    0.012582 
_atom_sites.fract_transf_matrix[1][2]    0.007264 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014528 
_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]    0.005576 
_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 EDO A 1 401 401 EDO EDO . 
D 2 EDO A 1 402 501 EDO EDO . 
E 2 EDO A 1 403 601 EDO EDO . 
F 2 EDO A 1 404 701 EDO EDO . 
G 3 PGE A 1 405 801 PGE PE4 . 
H 2 EDO A 1 406 901 EDO EDO . 
I 4 GOL A 1 407 2 GOL GOL . 
J 4 GOL A 1 408 3 GOL GOL . 
K 3 PGE B 1 401 401 PGE PE4 . 
L 2 EDO B 1 402 501 EDO EDO . 
M 5 FE9 B 1 403 401 FE9 FE9 . 
N 4 GOL B 1 404 4 GOL GOL . 
O 6 HOH A 1 501 208 HOH HOH . 
O 6 HOH A 2 502 197 HOH HOH . 
O 6 HOH A 3 503 181 HOH HOH . 
O 6 HOH A 4 504 151 HOH HOH . 
O 6 HOH A 5 505 172 HOH HOH . 
O 6 HOH A 6 506 183 HOH HOH . 
O 6 HOH A 7 507 203 HOH HOH . 
O 6 HOH A 8 508 147 HOH HOH . 
O 6 HOH A 9 509 258 HOH HOH . 
O 6 HOH A 10 510 171 HOH HOH . 
O 6 HOH A 11 511 252 HOH HOH . 
O 6 HOH A 12 512 176 HOH HOH . 
O 6 HOH A 13 513 253 HOH HOH . 
O 6 HOH A 14 514 247 HOH HOH . 
O 6 HOH A 15 515 18 HOH HOH . 
O 6 HOH A 16 516 8 HOH HOH . 
O 6 HOH A 17 517 3 HOH HOH . 
O 6 HOH A 18 518 6 HOH HOH . 
O 6 HOH A 19 519 78 HOH HOH . 
O 6 HOH A 20 520 215 HOH HOH . 
O 6 HOH A 21 521 65 HOH HOH . 
O 6 HOH A 22 522 248 HOH HOH . 
O 6 HOH A 23 523 122 HOH HOH . 
O 6 HOH A 24 524 188 HOH HOH . 
O 6 HOH A 25 525 111 HOH HOH . 
O 6 HOH A 26 526 192 HOH HOH . 
O 6 HOH A 27 527 77 HOH HOH . 
O 6 HOH A 28 528 202 HOH HOH . 
O 6 HOH A 29 529 220 HOH HOH . 
O 6 HOH A 30 530 245 HOH HOH . 
O 6 HOH A 31 531 240 HOH HOH . 
O 6 HOH A 32 532 216 HOH HOH . 
O 6 HOH A 33 533 246 HOH HOH . 
O 6 HOH A 34 534 177 HOH HOH . 
O 6 HOH A 35 535 28 HOH HOH . 
O 6 HOH A 36 536 5 HOH HOH . 
O 6 HOH A 37 537 35 HOH HOH . 
O 6 HOH A 38 538 125 HOH HOH . 
O 6 HOH A 39 539 14 HOH HOH . 
O 6 HOH A 40 540 257 HOH HOH . 
O 6 HOH A 41 541 39 HOH HOH . 
O 6 HOH A 42 542 85 HOH HOH . 
O 6 HOH A 43 543 264 HOH HOH . 
O 6 HOH A 44 544 90 HOH HOH . 
O 6 HOH A 45 545 178 HOH HOH . 
O 6 HOH A 46 546 173 HOH HOH . 
O 6 HOH A 47 547 145 HOH HOH . 
O 6 HOH A 48 548 210 HOH HOH . 
O 6 HOH A 49 549 235 HOH HOH . 
O 6 HOH A 50 550 266 HOH HOH . 
O 6 HOH A 51 551 115 HOH HOH . 
O 6 HOH A 52 552 27 HOH HOH . 
O 6 HOH A 53 553 142 HOH HOH . 
O 6 HOH A 54 554 84 HOH HOH . 
O 6 HOH A 55 555 163 HOH HOH . 
O 6 HOH A 56 556 233 HOH HOH . 
O 6 HOH A 57 557 81 HOH HOH . 
O 6 HOH A 58 558 200 HOH HOH . 
O 6 HOH A 59 559 267 HOH HOH . 
O 6 HOH A 60 560 279 HOH HOH . 
O 6 HOH A 61 561 102 HOH HOH . 
O 6 HOH A 62 562 217 HOH HOH . 
O 6 HOH A 63 563 11 HOH HOH . 
O 6 HOH A 64 564 276 HOH HOH . 
O 6 HOH A 65 565 241 HOH HOH . 
O 6 HOH A 66 566 37 HOH HOH . 
O 6 HOH A 67 567 227 HOH HOH . 
O 6 HOH A 68 568 89 HOH HOH . 
O 6 HOH A 69 569 34 HOH HOH . 
O 6 HOH A 70 570 261 HOH HOH . 
O 6 HOH A 71 571 19 HOH HOH . 
O 6 HOH A 72 572 232 HOH HOH . 
O 6 HOH A 73 573 165 HOH HOH . 
O 6 HOH A 74 574 130 HOH HOH . 
O 6 HOH A 75 575 166 HOH HOH . 
O 6 HOH A 76 576 255 HOH HOH . 
O 6 HOH A 77 577 218 HOH HOH . 
O 6 HOH A 78 578 272 HOH HOH . 
O 6 HOH A 79 579 13 HOH HOH . 
O 6 HOH A 80 580 106 HOH HOH . 
O 6 HOH A 81 581 128 HOH HOH . 
O 6 HOH A 82 582 71 HOH HOH . 
O 6 HOH A 83 583 209 HOH HOH . 
O 6 HOH A 84 584 136 HOH HOH . 
O 6 HOH A 85 585 212 HOH HOH . 
O 6 HOH A 86 586 30 HOH HOH . 
O 6 HOH A 87 587 224 HOH HOH . 
O 6 HOH A 88 588 239 HOH HOH . 
O 6 HOH A 89 589 127 HOH HOH . 
O 6 HOH A 90 590 204 HOH HOH . 
O 6 HOH A 91 591 263 HOH HOH . 
O 6 HOH A 92 592 265 HOH HOH . 
O 6 HOH A 93 593 69 HOH HOH . 
O 6 HOH A 94 594 146 HOH HOH . 
O 6 HOH A 95 595 104 HOH HOH . 
O 6 HOH A 96 596 50 HOH HOH . 
O 6 HOH A 97 597 198 HOH HOH . 
O 6 HOH A 98 598 76 HOH HOH . 
O 6 HOH A 99 599 155 HOH HOH . 
O 6 HOH A 100 600 223 HOH HOH . 
O 6 HOH A 101 601 274 HOH HOH . 
O 6 HOH A 102 602 109 HOH HOH . 
O 6 HOH A 103 603 271 HOH HOH . 
O 6 HOH A 104 604 262 HOH HOH . 
O 6 HOH A 105 605 254 HOH HOH . 
O 6 HOH A 106 606 196 HOH HOH . 
O 6 HOH A 107 607 278 HOH HOH . 
O 6 HOH A 108 608 259 HOH HOH . 
P 6 HOH B 1 501 205 HOH HOH . 
P 6 HOH B 2 502 199 HOH HOH . 
P 6 HOH B 3 503 7 HOH HOH . 
P 6 HOH B 4 504 168 HOH HOH . 
P 6 HOH B 5 505 189 HOH HOH . 
P 6 HOH B 6 506 134 HOH HOH . 
P 6 HOH B 7 507 221 HOH HOH . 
P 6 HOH B 8 508 229 HOH HOH . 
P 6 HOH B 9 509 211 HOH HOH . 
P 6 HOH B 10 510 214 HOH HOH . 
P 6 HOH B 11 511 169 HOH HOH . 
P 6 HOH B 12 512 251 HOH HOH . 
P 6 HOH B 13 513 16 HOH HOH . 
P 6 HOH B 14 514 219 HOH HOH . 
P 6 HOH B 15 515 22 HOH HOH . 
P 6 HOH B 16 516 49 HOH HOH . 
P 6 HOH B 17 517 270 HOH HOH . 
P 6 HOH B 18 518 184 HOH HOH . 
P 6 HOH B 19 519 180 HOH HOH . 
P 6 HOH B 20 520 249 HOH HOH . 
P 6 HOH B 21 521 79 HOH HOH . 
P 6 HOH B 22 522 191 HOH HOH . 
P 6 HOH B 23 523 187 HOH HOH . 
P 6 HOH B 24 524 88 HOH HOH . 
P 6 HOH B 25 525 73 HOH HOH . 
P 6 HOH B 26 526 201 HOH HOH . 
P 6 HOH B 27 527 66 HOH HOH . 
P 6 HOH B 28 528 80 HOH HOH . 
P 6 HOH B 29 529 9 HOH HOH . 
P 6 HOH B 30 530 193 HOH HOH . 
P 6 HOH B 31 531 275 HOH HOH . 
P 6 HOH B 32 532 175 HOH HOH . 
P 6 HOH B 33 533 33 HOH HOH . 
P 6 HOH B 34 534 59 HOH HOH . 
P 6 HOH B 35 535 206 HOH HOH . 
P 6 HOH B 36 536 195 HOH HOH . 
P 6 HOH B 37 537 126 HOH HOH . 
P 6 HOH B 38 538 222 HOH HOH . 
P 6 HOH B 39 539 112 HOH HOH . 
P 6 HOH B 40 540 10 HOH HOH . 
P 6 HOH B 41 541 96 HOH HOH . 
P 6 HOH B 42 542 82 HOH HOH . 
P 6 HOH B 43 543 154 HOH HOH . 
P 6 HOH B 44 544 29 HOH HOH . 
P 6 HOH B 45 545 170 HOH HOH . 
P 6 HOH B 46 546 20 HOH HOH . 
P 6 HOH B 47 547 129 HOH HOH . 
P 6 HOH B 48 548 213 HOH HOH . 
P 6 HOH B 49 549 225 HOH HOH . 
P 6 HOH B 50 550 250 HOH HOH . 
P 6 HOH B 51 551 70 HOH HOH . 
P 6 HOH B 52 552 32 HOH HOH . 
P 6 HOH B 53 553 57 HOH HOH . 
P 6 HOH B 54 554 119 HOH HOH . 
P 6 HOH B 55 555 139 HOH HOH . 
P 6 HOH B 56 556 207 HOH HOH . 
P 6 HOH B 57 557 107 HOH HOH . 
P 6 HOH B 58 558 138 HOH HOH . 
P 6 HOH B 59 559 110 HOH HOH . 
P 6 HOH B 60 560 56 HOH HOH . 
P 6 HOH B 61 561 256 HOH HOH . 
P 6 HOH B 62 562 186 HOH HOH . 
P 6 HOH B 63 563 118 HOH HOH . 
P 6 HOH B 64 564 108 HOH HOH . 
P 6 HOH B 65 565 43 HOH HOH . 
P 6 HOH B 66 566 87 HOH HOH . 
P 6 HOH B 67 567 4 HOH HOH . 
P 6 HOH B 68 568 132 HOH HOH . 
P 6 HOH B 69 569 45 HOH HOH . 
P 6 HOH B 70 570 63 HOH HOH . 
P 6 HOH B 71 571 41 HOH HOH . 
P 6 HOH B 72 572 231 HOH HOH . 
P 6 HOH B 73 573 40 HOH HOH . 
P 6 HOH B 74 574 143 HOH HOH . 
P 6 HOH B 75 575 117 HOH HOH . 
P 6 HOH B 76 576 234 HOH HOH . 
P 6 HOH B 77 577 31 HOH HOH . 
P 6 HOH B 78 578 236 HOH HOH . 
P 6 HOH B 79 579 149 HOH HOH . 
P 6 HOH B 80 580 113 HOH HOH . 
P 6 HOH B 81 581 86 HOH HOH . 
P 6 HOH B 82 582 99 HOH HOH . 
P 6 HOH B 83 583 269 HOH HOH . 
P 6 HOH B 84 584 124 HOH HOH . 
P 6 HOH B 85 585 167 HOH HOH . 
P 6 HOH B 86 586 243 HOH HOH . 
P 6 HOH B 87 587 156 HOH HOH . 
P 6 HOH B 88 588 83 HOH HOH . 
P 6 HOH B 89 589 51 HOH HOH . 
P 6 HOH B 90 590 100 HOH HOH . 
P 6 HOH B 91 591 244 HOH HOH . 
P 6 HOH B 92 592 277 HOH HOH . 
P 6 HOH B 93 593 153 HOH HOH . 
P 6 HOH B 94 594 190 HOH HOH . 
P 6 HOH B 95 595 52 HOH HOH . 
P 6 HOH B 96 596 273 HOH HOH . 
P 6 HOH B 97 597 55 HOH HOH . 
P 6 HOH B 98 598 60 HOH HOH . 
P 6 HOH B 99 599 64 HOH HOH . 
P 6 HOH B 100 600 94 HOH HOH . 
P 6 HOH B 101 601 179 HOH HOH . 
P 6 HOH B 102 602 121 HOH HOH . 
P 6 HOH B 103 603 185 HOH HOH . 
P 6 HOH B 104 604 238 HOH HOH . 
P 6 HOH B 105 605 141 HOH HOH . 
P 6 HOH B 106 606 174 HOH HOH . 
P 6 HOH B 107 607 140 HOH HOH . 
P 6 HOH B 108 608 260 HOH HOH . 
P 6 HOH B 109 609 42 HOH HOH . 
P 6 HOH B 110 610 159 HOH HOH . 
P 6 HOH B 111 611 97 HOH HOH . 
P 6 HOH B 112 612 123 HOH HOH . 
P 6 HOH B 113 613 72 HOH HOH . 
P 6 HOH B 114 614 54 HOH HOH . 
P 6 HOH B 115 615 228 HOH HOH . 
P 6 HOH B 116 616 268 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 EDO . . . F 2 -62.833 21.661 27.083 1 87.29 ? C1 EDO 404 A 1 
HETATM 2 O O1 EDO . . . F 2 -61.893 20.976 27.921 1 85.11 ? O1 EDO 404 A 1 
HETATM 3 C C2 EDO . . . F 2 -63.304 20.744 25.955 1 85.17 ? C2 EDO 404 A 1 
HETATM 4 O O2 EDO . . . F 2 -64.724 20.555 26.02 1 84.98 ? O2 EDO 404 A 1 
#
_model_server_stats.io_time_ms              25 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           337 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           4 
#