data_5YR1 # _model_server_result.job_id E5ItsxYI6b49-3Aizfbm1w _model_server_result.datetime_utc '2025-07-08 05:36:21' _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 5yr1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":306}' # _entry.id 5YR1 # _exptl.entry_id 5YR1 _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 90 _cell.entry_id 5YR1 _cell.length_a 103.59 _cell.length_b 103.59 _cell.length_c 103.59 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YR1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 197 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6,7,8,9,10,11,12 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 5 'crystal symmetry operation' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 6 'crystal symmetry operation' 6_555 z,-x,-y 0 0 1 -1 0 0 0 -1 0 0 0 0 7 'crystal symmetry operation' 7_555 -z,-x,y 0 0 -1 -1 0 0 0 1 0 0 0 0 8 'crystal symmetry operation' 8_555 -z,x,-y 0 0 -1 1 0 0 0 -1 0 0 0 0 9 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 10 'crystal symmetry operation' 10_555 -y,z,-x 0 -1 0 0 0 1 -1 0 0 0 0 0 11 'crystal symmetry operation' 11_555 y,-z,-x 0 1 0 0 0 -1 -1 0 0 0 0 0 12 'crystal symmetry operation' 12_555 -y,-z,x 0 -1 0 0 0 -1 1 0 0 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N N ? 2 D N N ? 2 E N N ? 2 F N N ? 2 G N N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 73 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 73 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 83 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 83 _struct_conn.ptnr2_symmetry 9_555 _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 B _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 2.152 _struct_conn.pdbx_value_order ? # _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 5YR1 _atom_sites.fract_transf_matrix[1][1] 0.009653 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009653 _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] 0.009653 _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 EDO A 1 301 3 EDO EDO . C 2 EDO A 1 302 7 EDO EDO . D 2 EDO A 1 303 9 EDO EDO . E 2 EDO A 1 304 12 EDO EDO . F 2 EDO A 1 305 13 EDO EDO . G 2 EDO A 1 306 15 EDO EDO . H 3 HOH A 1 401 85 HOH HOH . H 3 HOH A 2 402 86 HOH HOH . H 3 HOH A 3 403 48 HOH HOH . H 3 HOH A 4 404 93 HOH HOH . H 3 HOH A 5 405 78 HOH HOH . H 3 HOH A 6 406 82 HOH HOH . H 3 HOH A 7 407 89 HOH HOH . H 3 HOH A 8 408 59 HOH HOH . H 3 HOH A 9 409 67 HOH HOH . H 3 HOH A 10 410 30 HOH HOH . H 3 HOH A 11 411 11 HOH HOH . H 3 HOH A 12 412 39 HOH HOH . H 3 HOH A 13 413 81 HOH HOH . H 3 HOH A 14 414 55 HOH HOH . H 3 HOH A 15 415 103 HOH HOH . H 3 HOH A 16 416 13 HOH HOH . H 3 HOH A 17 417 20 HOH HOH . H 3 HOH A 18 418 71 HOH HOH . H 3 HOH A 19 419 102 HOH HOH . H 3 HOH A 20 420 54 HOH HOH . H 3 HOH A 21 421 87 HOH HOH . H 3 HOH A 22 422 21 HOH HOH . H 3 HOH A 23 423 22 HOH HOH . H 3 HOH A 24 424 42 HOH HOH . H 3 HOH A 25 425 37 HOH HOH . H 3 HOH A 26 426 52 HOH HOH . H 3 HOH A 27 427 51 HOH HOH . H 3 HOH A 28 428 60 HOH HOH . H 3 HOH A 29 429 57 HOH HOH . H 3 HOH A 30 430 125 HOH HOH . H 3 HOH A 31 431 64 HOH HOH . H 3 HOH A 32 432 90 HOH HOH . H 3 HOH A 33 433 110 HOH HOH . H 3 HOH A 34 434 9 HOH HOH . H 3 HOH A 35 435 43 HOH HOH . H 3 HOH A 36 436 27 HOH HOH . H 3 HOH A 37 437 46 HOH HOH . H 3 HOH A 38 438 99 HOH HOH . H 3 HOH A 39 439 17 HOH HOH . H 3 HOH A 40 440 31 HOH HOH . H 3 HOH A 41 441 75 HOH HOH . H 3 HOH A 42 442 106 HOH HOH . H 3 HOH A 43 443 65 HOH HOH . H 3 HOH A 44 444 8 HOH HOH . H 3 HOH A 45 445 83 HOH HOH . H 3 HOH A 46 446 44 HOH HOH . H 3 HOH A 47 447 68 HOH HOH . H 3 HOH A 48 448 84 HOH HOH . H 3 HOH A 49 449 15 HOH HOH . H 3 HOH A 50 450 156 HOH HOH . H 3 HOH A 51 451 70 HOH HOH . H 3 HOH A 52 452 10 HOH HOH . H 3 HOH A 53 453 53 HOH HOH . H 3 HOH A 54 454 1 HOH HOH . H 3 HOH A 55 455 47 HOH HOH . H 3 HOH A 56 456 66 HOH HOH . H 3 HOH A 57 457 155 HOH HOH . H 3 HOH A 58 458 16 HOH HOH . H 3 HOH A 59 459 49 HOH HOH . H 3 HOH A 60 460 98 HOH HOH . H 3 HOH A 61 461 114 HOH HOH . H 3 HOH A 62 462 113 HOH HOH . H 3 HOH A 63 463 32 HOH HOH . H 3 HOH A 64 464 28 HOH HOH . H 3 HOH A 65 465 45 HOH HOH . H 3 HOH A 66 466 63 HOH HOH . H 3 HOH A 67 467 6 HOH HOH . H 3 HOH A 68 468 5 HOH HOH . H 3 HOH A 69 469 3 HOH HOH . H 3 HOH A 70 470 56 HOH HOH . H 3 HOH A 71 471 38 HOH HOH . H 3 HOH A 72 472 41 HOH HOH . H 3 HOH A 73 473 25 HOH HOH . H 3 HOH A 74 474 23 HOH HOH . H 3 HOH A 75 475 101 HOH HOH . H 3 HOH A 76 476 62 HOH HOH . H 3 HOH A 77 477 61 HOH HOH . H 3 HOH A 78 478 58 HOH HOH . H 3 HOH A 79 479 34 HOH HOH . H 3 HOH A 80 480 12 HOH HOH . H 3 HOH A 81 481 76 HOH HOH . H 3 HOH A 82 482 29 HOH HOH . H 3 HOH A 83 483 112 HOH HOH . H 3 HOH A 84 484 40 HOH HOH . H 3 HOH A 85 485 18 HOH HOH . H 3 HOH A 86 486 35 HOH HOH . H 3 HOH A 87 487 14 HOH HOH . H 3 HOH A 88 488 33 HOH HOH . H 3 HOH A 89 489 91 HOH HOH . H 3 HOH A 90 490 24 HOH HOH . H 3 HOH A 91 491 36 HOH HOH . H 3 HOH A 92 492 4 HOH HOH . H 3 HOH A 93 493 19 HOH HOH . H 3 HOH A 94 494 108 HOH HOH . H 3 HOH A 95 495 50 HOH HOH . H 3 HOH A 96 496 26 HOH HOH . H 3 HOH A 97 497 80 HOH HOH . H 3 HOH A 98 498 7 HOH HOH . H 3 HOH A 99 499 2 HOH HOH . H 3 HOH A 100 500 74 HOH HOH . H 3 HOH A 101 501 117 HOH HOH . H 3 HOH A 102 502 95 HOH HOH . H 3 HOH A 103 503 118 HOH HOH . H 3 HOH A 104 504 79 HOH HOH . H 3 HOH A 105 505 88 HOH HOH . H 3 HOH A 106 506 73 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 . . . G 2 -6.887 -34.661 -40.165 1 25.83 ? C1 EDO 306 A 1 HETATM 2 O O1 EDO . . . G 2 -8.267 -34.659 -39.878 1 25.64 ? O1 EDO 306 A 1 HETATM 3 C C2 EDO . . . G 2 -6.111 -34.519 -38.848 1 25.96 ? C2 EDO 306 A 1 HETATM 4 O O2 EDO . . . G 2 -4.724 -34.53 -39.188 1 32.17 ? O2 EDO 306 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 4 #