data_6ONM # _model_server_result.job_id dRlavgNqnRptqjkRwMf4vQ _model_server_result.datetime_utc '2025-03-06 07:23:31' _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 6onm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":704}' # _entry.id 6ONM # _exptl.entry_id 6ONM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 350.19 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(3R)-8-fluoro-7-(fluoromethyl)-3-methylocta-1,6-dien-3-yl trihydrogen diphosphate' _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 90 _cell.entry_id 6ONM _cell.length_a 85.81 _cell.length_b 85.81 _cell.length_c 217.62 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6ONM _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id E _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 OD2 ASP 343 A ASP 343 1_555 B MN MN . A MN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc2 A OD1 ASP 343 A ASP 343 1_555 C MN MN . A MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? metalc ? metalc3 A OD2 ASP 347 A ASP 347 1_555 B MN MN . A MN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? metalc ? metalc4 A OD2 ASP 347 A ASP 347 1_555 C MN MN . A MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc5 A OD2 ASP 488 A ASP 488 1_555 D MN MN . A MN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc6 B MN MN . A MN 701 1_555 E O2A MWG . A MWG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.62 ? metalc ? metalc7 B MN MN . A MN 701 1_555 E O2B MWG . A MWG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc8 C MN MN . A MN 702 1_555 E O2B MWG . A MWG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.626 ? metalc ? metalc9 D MN MN . A MN 703 1_555 E O3B MWG . A MWG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? metalc ? metalc10 D MN MN . A MN 703 1_555 E O1A MWG . A MWG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? # _chem_comp.formula 'C10 H18 F2 O7 P2' _chem_comp.formula_weight 350.19 _chem_comp.id MWG _chem_comp.mon_nstd_flag . _chem_comp.name '(3R)-8-fluoro-7-(fluoromethyl)-3-methylocta-1,6-dien-3-yl trihydrogen diphosphate' _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 O1A PA MWG doub 237 n n O3B PB MWG doub 238 n n O2B PB MWG sing 239 n n O2A PA MWG sing 240 n n PA O1 MWG sing 241 n n PA O3A MWG sing 242 n n PB O3A MWG sing 243 n n PB O1B MWG sing 244 n n C1 C2 MWG doub 245 n n O1 C3 MWG sing 246 n n C2 C3 MWG sing 247 n n C3 C10 MWG sing 248 n n C3 C4 MWG sing 249 n n C4 C5 MWG sing 250 n n C5 C6 MWG sing 251 n n C6 C7 MWG doub 252 n n C7 C9 MWG sing 253 n n C7 C8 MWG sing 254 n n C9 F9 MWG sing 255 n n C8 F8 MWG sing 256 n n C1 H1 MWG sing 257 n n C1 H2 MWG sing 258 n n C2 H3 MWG sing 259 n n C4 H4 MWG sing 260 n n C4 H5 MWG sing 261 n n C5 H6 MWG sing 262 n n C5 H7 MWG sing 263 n n C6 H8 MWG sing 264 n n C8 H9 MWG sing 265 n n C8 H10 MWG sing 266 n n C9 H11 MWG sing 267 n n C9 H12 MWG sing 268 n n C10 H13 MWG sing 269 n n C10 H14 MWG sing 270 n n C10 H15 MWG sing 271 n n O1B H16 MWG sing 272 n n O2A H17 MWG sing 273 n n O2B H18 MWG sing 274 n n # _atom_sites.entry_id 6ONM _atom_sites.fract_transf_matrix[1][1] 0.011654 _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] 0.011654 _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] 0.004595 _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 1 701 1 MN MN . C 2 MN A 1 702 2 MN MN . D 2 MN A 1 703 3 MN MN . E 3 MWG A 1 704 1 MWG DFL . F 4 HOH A 1 801 1 HOH HOH . F 4 HOH A 2 802 5 HOH HOH . F 4 HOH A 3 803 2 HOH HOH . F 4 HOH A 4 804 4 HOH HOH . F 4 HOH A 5 805 16 HOH HOH . F 4 HOH A 6 806 22 HOH HOH . F 4 HOH A 7 807 14 HOH HOH . F 4 HOH A 8 808 13 HOH HOH . F 4 HOH A 9 809 3 HOH HOH . F 4 HOH A 10 810 18 HOH HOH . F 4 HOH A 11 811 8 HOH HOH . F 4 HOH A 12 812 10 HOH HOH . F 4 HOH A 13 813 15 HOH HOH . F 4 HOH A 14 814 7 HOH HOH . F 4 HOH A 15 815 11 HOH HOH . F 4 HOH A 16 816 21 HOH HOH . F 4 HOH A 17 817 23 HOH HOH . F 4 HOH A 18 818 6 HOH HOH . F 4 HOH A 19 819 19 HOH HOH . F 4 HOH A 20 820 20 HOH HOH . F 4 HOH A 21 821 9 HOH HOH . F 4 HOH A 22 822 12 HOH HOH . F 4 HOH A 23 823 17 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 MWG . . . E 3 -5.538 12.819 -22.774 1 90.69 ? C1 MWG 704 A 1 HETATM 2 C C2 MWG . . . E 3 -5.941 13.024 -21.522 1 97.41 ? C2 MWG 704 A 1 HETATM 3 C C3 MWG . . . E 3 -7.432 12.956 -21.138 1 90.88 ? C3 MWG 704 A 1 HETATM 4 C C4 MWG . . . E 3 -7.774 14.179 -20.248 1 85.01 ? C4 MWG 704 A 1 HETATM 5 C C5 MWG . . . E 3 -6.623 14.436 -19.268 1 83.4 ? C5 MWG 704 A 1 HETATM 6 C C6 MWG . . . E 3 -7.094 15.383 -18.124 1 74.33 ? C6 MWG 704 A 1 HETATM 7 C C7 MWG . . . E 3 -7.627 14.874 -16.987 1 71.72 ? C7 MWG 704 A 1 HETATM 8 C C8 MWG . . . E 3 -8.101 15.841 -15.828 1 64.15 ? C8 MWG 704 A 1 HETATM 9 C C9 MWG . . . E 3 -7.778 13.323 -16.8 1 76.68 ? C9 MWG 704 A 1 HETATM 10 O O1 MWG . . . E 3 -8.231 13.048 -22.291 1 88.79 ? O1 MWG 704 A 1 HETATM 11 C C10 MWG . . . E 3 -7.652 11.698 -20.301 1 79.22 ? C10 MWG 704 A 1 HETATM 12 F F8 MWG . . . E 3 -8.718 15.128 -14.838 1 67.35 ? F8 MWG 704 A 1 HETATM 13 F F9 MWG . . . E 3 -8.048 13.063 -15.487 1 74.93 ? F9 MWG 704 A 1 HETATM 14 O O1A MWG . . . E 3 -9.42 11.962 -24.324 1 91.45 ? O1A MWG 704 A 1 HETATM 15 O O1B MWG . . . E 3 -12.15 9.526 -21.842 1 72.29 ? O1B MWG 704 A 1 HETATM 16 O O2A MWG . . . E 3 -7.669 10.635 -23.216 1 69.11 ? O2A MWG 704 A 1 HETATM 17 O O2B MWG . . . E 3 -10.399 8.802 -23.411 1 71.83 ? O2B MWG 704 A 1 HETATM 18 O O3A MWG . . . E 3 -9.991 10.942 -22.011 1 78.09 ? O3A MWG 704 A 1 HETATM 19 O O3B MWG . . . E 3 -11.767 10.781 -23.907 1 68.96 ? O3B MWG 704 A 1 HETATM 20 P PA MWG . . . E 3 -8.814 11.617 -22.975 1 76.15 ? PA MWG 704 A 1 HETATM 21 P PB MWG . . . E 3 -11.088 9.993 -22.825 1 79.3 ? PB MWG 704 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 21 #