data_6J7X # _model_server_result.job_id LhcR9aE6-iUA1gogwtYAsg _model_server_result.datetime_utc '2024-11-19 18:23:21' _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 6j7x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 6J7X # _exptl.entry_id 6J7X _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 450.443 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'GERANYLGERANYL 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 6J7X _cell.length_a 119.169 _cell.length_b 119.169 _cell.length_c 211.006 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6J7X _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 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 _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C20 H36 O7 P2' _chem_comp.formula_weight 450.443 _chem_comp.id GRG _chem_comp.mon_nstd_flag . _chem_comp.name 'GERANYLGERANYL 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 C20 C18 GRG sing 133 n n C20 H201 GRG sing 134 n n C20 H202 GRG sing 135 n n C20 H203 GRG sing 136 n n C19 C18 GRG sing 137 n n C19 H191 GRG sing 138 n n C19 H192 GRG sing 139 n n C19 H193 GRG sing 140 n n C18 C17 GRG doub 141 n n C17 C16 GRG sing 142 n n C17 H17 GRG sing 143 n n C16 C15 GRG sing 144 n n C16 H161 GRG sing 145 n n C16 H162 GRG sing 146 n n C14 C13 GRG sing 147 n n C14 H141 GRG sing 148 n n C14 H142 GRG sing 149 n n C14 H143 GRG sing 150 n n C13 C15 GRG sing 151 n n C13 C12 GRG doub 152 e n C15 H151 GRG sing 153 n n C15 H152 GRG sing 154 n n C12 C11 GRG sing 155 n n C12 H12 GRG sing 156 n n C11 C9 GRG sing 157 n n C11 H111 GRG sing 158 n n C11 H112 GRG sing 159 n n C9 C8 GRG sing 160 n n C9 HC91 GRG sing 161 n n C9 HC92 GRG sing 162 n n C8 C10 GRG sing 163 n n C8 C7 GRG doub 164 e n C10 H101 GRG sing 165 n n C10 H102 GRG sing 166 n n C10 H103 GRG sing 167 n n C7 C6 GRG sing 168 n n C7 HC7 GRG sing 169 n n C6 C5 GRG sing 170 n n C6 HC61 GRG sing 171 n n C6 HC62 GRG sing 172 n n C5 C3 GRG sing 173 n n C5 HC51 GRG sing 174 n n C5 HC52 GRG sing 175 n n C3 C4 GRG sing 176 n n C3 C2 GRG doub 177 e n C4 HC41 GRG sing 178 n n C4 HC42 GRG sing 179 n n C4 HC43 GRG sing 180 n n C2 C1 GRG sing 181 n n C2 HC2 GRG sing 182 n n C1 O1 GRG sing 183 n n C1 HC11 GRG sing 184 n n C1 HC12 GRG sing 185 n n O1 PA GRG sing 186 n n PA O1A GRG sing 187 n n PA O3A GRG sing 188 n n PA O2A GRG doub 189 n n O1A H1AO GRG sing 190 n n O3A PB GRG sing 191 n n PB O1B GRG sing 192 n n PB O2B GRG sing 193 n n PB O3B GRG doub 194 n n O1B H1BO GRG sing 195 n n O2B H2BO GRG sing 196 n n # _atom_sites.entry_id 6J7X _atom_sites.fract_transf_matrix[1][1] 0.008391 _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] 0.008391 _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] 0.004739 _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 GRG B 1 401 401 GRG GRG . E 5 FMT B 1 402 402 FMT FMT . # 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 C20 GRG . . . D 4 -39.735 8.917 25.554 1 76.45 ? C20 GRG 401 B 1 HETATM 2 C C19 GRG . . . D 4 -40.775 10.002 23.409 1 46.6 ? C19 GRG 401 B 1 HETATM 3 C C18 GRG . . . D 4 -40.757 8.893 24.434 1 70.43 ? C18 GRG 401 B 1 HETATM 4 C C17 GRG . . . D 4 -41.666 7.862 24.357 1 73.94 ? C17 GRG 401 B 1 HETATM 5 C C16 GRG . . . D 4 -42.705 7.827 23.229 1 58.96 ? C16 GRG 401 B 1 HETATM 6 C C14 GRG . . . D 4 -43.878 4.783 23.466 1 59.45 ? C14 GRG 401 B 1 HETATM 7 C C13 GRG . . . D 4 -43.981 5.987 24.377 1 72.88 ? C13 GRG 401 B 1 HETATM 8 C C15 GRG . . . D 4 -44.076 7.391 23.774 1 55.39 ? C15 GRG 401 B 1 HETATM 9 C C12 GRG . . . D 4 -43.997 5.82 25.745 1 75.9 ? C12 GRG 401 B 1 HETATM 10 C C11 GRG . . . D 4 -43.902 4.406 26.351 1 79.85 ? C11 GRG 401 B 1 HETATM 11 C C9 GRG . . . D 4 -43.853 4.508 27.902 1 66.22 ? C9 GRG 401 B 1 HETATM 12 C C8 GRG . . . D 4 -44.9 3.568 28.513 1 66.37 ? C8 GRG 401 B 1 HETATM 13 C C10 GRG . . . D 4 -46.359 3.885 28.373 1 62.25 ? C10 GRG 401 B 1 HETATM 14 C C7 GRG . . . D 4 -44.504 2.432 29.196 1 73.78 ? C7 GRG 401 B 1 HETATM 15 C C6 GRG . . . D 4 -45.552 1.505 29.8 1 68 ? C6 GRG 401 B 1 HETATM 16 C C5 GRG . . . D 4 -45.702 0.255 28.91 1 70.64 ? C5 GRG 401 B 1 HETATM 17 C C3 GRG . . . D 4 -45.959 -0.974 29.79 1 70.19 ? C3 GRG 401 B 1 HETATM 18 C C4 GRG . . . D 4 -47.363 -1.29 30.237 1 57.77 ? C4 GRG 401 B 1 HETATM 19 C C2 GRG . . . D 4 -44.913 -1.78 30.162 1 79.62 ? C2 GRG 401 B 1 HETATM 20 C C1 GRG . . . D 4 -45.148 -3.002 31.035 1 92.44 ? C1 GRG 401 B 1 HETATM 21 O O1 GRG . . . D 4 -45.288 -2.601 32.395 1 93.67 ? O1 GRG 401 B 1 HETATM 22 P PA GRG . . . D 4 -44.569 -3.459 33.518 1 97.75 ? PA GRG 401 B 1 HETATM 23 O O1A GRG . . . D 4 -45.301 -4.765 33.69 1 82.54 ? O1A GRG 401 B 1 HETATM 24 O O3A GRG . . . D 4 -43.066 -3.757 33.067 1 122.65 ? O3A GRG 401 B 1 HETATM 25 O O2A GRG . . . D 4 -44.579 -2.694 34.824 1 91.38 ? O2A GRG 401 B 1 HETATM 26 P PB GRG . . . D 4 -41.785 -2.987 33.595 1 124.47 ? PB GRG 401 B 1 HETATM 27 O O1B GRG . . . D 4 -40.541 -3.672 33.083 1 126.32 ? O1B GRG 401 B 1 HETATM 28 O O2B GRG . . . D 4 -41.771 -2.994 35.102 1 124.61 ? O2B GRG 401 B 1 HETATM 29 O O3B GRG . . . D 4 -41.812 -1.565 33.09 1 107.37 ? O3B GRG 401 B 1 # _model_server_stats.io_time_ms 72 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 29 #