data_8YTD # _model_server_result.job_id LSfLKApZnhtD7ILVQkm9kA _model_server_result.datetime_utc '2024-10-30 03:29:11' _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 8ytd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":101}' # _entry.id 8YTD # _exptl.entry_id 8YTD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 62.068 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-ETHANEDIOL _entity.pdbx_number_of_molecules 4 _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 8YTD _cell.length_a 50.374 _cell.length_b 50.374 _cell.length_c 143.959 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YTD _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 ? 4 D N N ? 4 E N N ? 4 F N N ? 4 G 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 disulf ? disulf1 A SG CYS 20 A CYS 300 1_555 A SG CYS 65 A CYS 345 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? covale ? covale1 B C CYS 14 B CYS 13 1_555 B N2 GM1 15 B GM1 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.278 ? covale ? covale2 C C GLY 8 C GLY 8 1_555 C N MEA 9 C MEA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.311 ? covale ? covale3 C C MEA 9 C MEA 9 1_555 C N GLY 10 C GLY 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.292 ? # _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 8YTD _atom_sites.fract_transf_matrix[1][1] 0.019852 _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] 0.019852 _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] 0.006946 _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 D 4 EDO A 1 401 1 EDO EDO . E 4 EDO A 1 402 3 EDO EDO . F 4 EDO A 1 403 4 EDO EDO . G 4 EDO B 1 101 2 EDO EDO . H 5 HOH A 1 501 33 HOH HOH . H 5 HOH A 2 502 5 HOH HOH . H 5 HOH A 3 503 44 HOH HOH . H 5 HOH A 4 504 32 HOH HOH . H 5 HOH A 5 505 14 HOH HOH . H 5 HOH A 6 506 13 HOH HOH . H 5 HOH A 7 507 29 HOH HOH . H 5 HOH A 8 508 11 HOH HOH . H 5 HOH A 9 509 22 HOH HOH . H 5 HOH A 10 510 48 HOH HOH . H 5 HOH A 11 511 35 HOH HOH . H 5 HOH A 12 512 17 HOH HOH . H 5 HOH A 13 513 31 HOH HOH . H 5 HOH A 14 514 20 HOH HOH . H 5 HOH A 15 515 3 HOH HOH . H 5 HOH A 16 516 39 HOH HOH . H 5 HOH A 17 517 12 HOH HOH . H 5 HOH A 18 518 30 HOH HOH . H 5 HOH A 19 519 18 HOH HOH . H 5 HOH A 20 520 23 HOH HOH . H 5 HOH A 21 521 24 HOH HOH . H 5 HOH A 22 522 41 HOH HOH . H 5 HOH A 23 523 34 HOH HOH . H 5 HOH A 24 524 38 HOH HOH . H 5 HOH A 25 525 8 HOH HOH . H 5 HOH A 26 526 10 HOH HOH . H 5 HOH A 27 527 6 HOH HOH . H 5 HOH A 28 528 1 HOH HOH . H 5 HOH A 29 529 2 HOH HOH . H 5 HOH A 30 530 45 HOH HOH . H 5 HOH A 31 531 27 HOH HOH . H 5 HOH A 32 532 7 HOH HOH . H 5 HOH A 33 533 21 HOH HOH . H 5 HOH A 34 534 15 HOH HOH . H 5 HOH A 35 535 28 HOH HOH . H 5 HOH A 36 536 26 HOH HOH . H 5 HOH A 37 537 49 HOH HOH . H 5 HOH A 38 538 50 HOH HOH . I 5 HOH B 1 201 37 HOH HOH . I 5 HOH B 2 202 36 HOH HOH . I 5 HOH B 3 203 9 HOH HOH . I 5 HOH B 4 204 19 HOH HOH . I 5 HOH B 5 205 25 HOH HOH . I 5 HOH B 6 206 42 HOH HOH . I 5 HOH B 7 207 4 HOH HOH . I 5 HOH B 8 208 47 HOH HOH . I 5 HOH B 9 209 16 HOH HOH . I 5 HOH B 10 210 46 HOH HOH . J 5 HOH C 1 101 43 HOH HOH . J 5 HOH C 2 102 40 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 4 9.58 16.729 21.844 1 47.04 ? C1 EDO 101 B 1 HETATM 2 O O1 EDO . . . G 4 10.859 16.863 22.452 1 46.36 ? O1 EDO 101 B 1 HETATM 3 C C2 EDO . . . G 4 9.63 15.783 20.639 1 47.59 ? C2 EDO 101 B 1 HETATM 4 O O2 EDO . . . G 4 9.531 14.407 21.048 1 47.44 ? O2 EDO 101 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 4 #