data_6YEM # _model_server_result.job_id AoNqqHy1-B4B4cTVT_Tovw _model_server_result.datetime_utc '2024-11-13 20:00:57' _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 6yem # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":205}' # _entry.id 6YEM # _exptl.entry_id 6YEM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 306.267 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3,5,6,8-tetrakis(oxidanyl)-2-pentanoyl-naphthalene-1,4-dione _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 6YEM _cell.length_a 73.34 _cell.length_b 73.34 _cell.length_c 128.75 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YEM _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64 2 2' # _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,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 5 _struct_asym.id F _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 50 A HIS 41 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc2 A OD2 ASP 98 A ASP 108 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? metalc ? metalc3 A OD1 ASP 98 A ASP 108 1_555 C MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc4 A O ILE 110 A ILE 120 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc5 B MN MN . A MN 201 1_555 F O OOH . A OOH 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? metalc ? metalc6 B MN MN . A MN 201 1_555 F O6 OOH . A OOH 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.862 ? metalc ? metalc7 C MN MN . A MN 202 1_555 F O1 OOH . A OOH 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? metalc ? metalc8 C MN MN . A MN 202 1_555 F O OOH . A OOH 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc9 C MN MN . A MN 202 1_555 G O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc10 C MN MN . A MN 202 1_555 G O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? # _chem_comp.formula 'C15 H14 O7' _chem_comp.formula_weight 306.267 _chem_comp.id OOH _chem_comp.mon_nstd_flag . _chem_comp.name 3,5,6,8-tetrakis(oxidanyl)-2-pentanoyl-naphthalene-1,4-dione _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 O4 C7 OOH sing 237 n n O1 C6 OOH doub 238 n n C11 C12 OOH sing 239 n n C11 C10 OOH sing 240 n n C13 C12 OOH sing 241 n n C13 C14 OOH sing 242 n n C7 C6 OOH sing 243 n n C7 C8 OOH doub 244 n n C6 C4 OOH sing 245 n n O C5 OOH sing 246 n n C10 C8 OOH sing 247 n n C10 O3 OOH doub 248 n n C8 C9 OOH sing 249 n n C4 C5 OOH doub 250 n y C4 C3 OOH sing 251 n y C5 C OOH sing 252 n y C9 C3 OOH sing 253 n n C9 O2 OOH doub 254 n n C3 C2 OOH doub 255 n y C O6 OOH sing 256 n n C C1 OOH doub 257 n y C2 C1 OOH sing 258 n y C2 O5 OOH sing 259 n n O6 H1 OOH sing 260 n n O H2 OOH sing 261 n n C1 H3 OOH sing 262 n n O5 H4 OOH sing 263 n n C14 H5 OOH sing 264 n n C14 H6 OOH sing 265 n n C14 H7 OOH sing 266 n n C13 H8 OOH sing 267 n n C13 H9 OOH sing 268 n n C11 H10 OOH sing 269 n n C11 H11 OOH sing 270 n n C12 H12 OOH sing 271 n n C12 H13 OOH sing 272 n n O4 H14 OOH sing 273 n n # _atom_sites.entry_id 6YEM _atom_sites.fract_transf_matrix[1][1] 0.013635 _atom_sites.fract_transf_matrix[1][2] 0.007872 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015744 _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] 0.007767 _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 MN A 1 201 1 MN MN . C 2 MN A 1 202 2 MN MN . D 3 MG A 1 203 1 MG MG . E 4 CL A 1 204 2 CL CL . F 5 OOH A 1 205 1 OOH QB7 . G 6 HOH A 1 301 2 HOH HOH . G 6 HOH A 2 302 1 HOH HOH . G 6 HOH A 3 303 8 HOH HOH . G 6 HOH A 4 304 3 HOH HOH . G 6 HOH A 5 305 4 HOH HOH . G 6 HOH A 6 306 10 HOH HOH . G 6 HOH A 7 307 15 HOH HOH . G 6 HOH A 8 308 13 HOH HOH . G 6 HOH A 9 309 14 HOH HOH . G 6 HOH A 10 310 5 HOH HOH . G 6 HOH A 11 311 19 HOH HOH . G 6 HOH A 12 312 6 HOH HOH . G 6 HOH A 13 313 7 HOH HOH . G 6 HOH A 14 314 17 HOH HOH . G 6 HOH A 15 315 9 HOH HOH . G 6 HOH A 16 316 20 HOH HOH . G 6 HOH A 17 317 18 HOH HOH . G 6 HOH A 18 318 16 HOH HOH . G 6 HOH A 19 319 12 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 O O6 OOH . . . F 5 23.213 16.801 6.025 0.8 75.92 ? O6 OOH 205 A 1 HETATM 2 C C OOH . . . F 5 24.558 16.896 5.889 0.8 75.34 ? C OOH 205 A 1 HETATM 3 O O OOH . . . F 5 24.555 15.116 4.312 0.8 67.49 ? O OOH 205 A 1 HETATM 4 C C1 OOH . . . F 5 25.217 17.86 6.626 0.8 74.45 ? C1 OOH 205 A 1 HETATM 5 C C2 OOH . . . F 5 26.582 18.002 6.5 0.8 73.37 ? C2 OOH 205 A 1 HETATM 6 C C3 OOH . . . F 5 27.279 17.152 5.639 0.8 72.38 ? C3 OOH 205 A 1 HETATM 7 O O1 OOH . . . F 5 26.786 14.357 3.267 0.8 58.54 ? O1 OOH 205 A 1 HETATM 8 C C4 OOH . . . F 5 26.616 16.16 4.885 0.8 67.76 ? C4 OOH 205 A 1 HETATM 9 O O5 OOH . . . F 5 27.212 18.968 7.238 0.8 77.05 ? O5 OOH 205 A 1 HETATM 10 C C14 OOH . . . F 5 32.216 20.579 4.866 0.8 77.34 ? C14 OOH 205 A 1 HETATM 11 C C13 OOH . . . F 5 32.437 19.812 3.576 0.8 77.47 ? C13 OOH 205 A 1 HETATM 12 C C6 OOH . . . F 5 27.356 15.24 3.958 0.8 67.64 ? C6 OOH 205 A 1 HETATM 13 C C5 OOH . . . F 5 25.244 16.043 5.028 0.8 70.61 ? C5 OOH 205 A 1 HETATM 14 C C8 OOH . . . F 5 29.518 16.452 4.645 0.8 70.32 ? C8 OOH 205 A 1 HETATM 15 C C7 OOH . . . F 5 28.828 15.399 3.85 0.8 71.3 ? C7 OOH 205 A 1 HETATM 16 C C9 OOH . . . F 5 28.751 17.329 5.545 0.8 73.24 ? C9 OOH 205 A 1 HETATM 17 O O2 OOH . . . F 5 29.349 18.21 6.209 0.8 71.91 ? O2 OOH 205 A 1 HETATM 18 C C10 OOH . . . F 5 30.986 16.681 4.597 0.8 72.99 ? C10 OOH 205 A 1 HETATM 19 C C11 OOH . . . F 5 31.599 17.388 3.402 0.8 74.86 ? C11 OOH 205 A 1 HETATM 20 C C12 OOH . . . F 5 32.753 18.326 3.792 0.8 76.11 ? C12 OOH 205 A 1 HETATM 21 O O3 OOH . . . F 5 31.647 16.301 5.552 0.8 73.42 ? O3 OOH 205 A 1 HETATM 22 O O4 OOH . . . F 5 29.535 14.596 3.019 0.8 71.15 ? O4 OOH 205 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 236 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 22 #