data_7PDF # _model_server_result.job_id Xx7i9nA8VVHg4nb7q71Img _model_server_result.datetime_utc '2025-07-07 19:17:06' _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 7pdf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 7PDF # _exptl.entry_id 7PDF _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 539.246 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _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 7PDF _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7PDF _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 ? _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 3 _struct_asym.id C _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 B OG SER 54 B SER 54 1_555 D MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.596 ? metalc ? metalc2 B OG1 THR 205 B THR 204 1_555 D MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc3 C O3B GSP . B GSP 501 1_555 D MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.668 ? metalc ? metalc4 C O2G GSP . B GSP 501 1_555 D MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.885 ? metalc ? metalc5 C O3G GSP . B GSP 501 1_555 D MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? metalc ? metalc6 C O1B GSP . B GSP 501 1_555 D MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc7 C O2B GSP . B GSP 501 1_555 D MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.916 ? # _chem_comp.formula 'C10 H16 N5 O13 P3 S' _chem_comp.formula_weight 539.246 _chem_comp.id GSP _chem_comp.mon_nstd_flag . _chem_comp.name "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _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 PG O3B GSP sing 129 n n PG S1G GSP doub 130 n n PG O2G GSP sing 131 n n PG O3G GSP sing 132 n n O3B PB GSP sing 133 n n O2G HOG2 GSP sing 134 n n O3G HOG3 GSP sing 135 n n PB O1B GSP doub 136 n n PB O2B GSP sing 137 n n PB O3A GSP sing 138 n n O2B HOB2 GSP sing 139 n n PA O1A GSP doub 140 n n PA O2A GSP sing 141 n n PA O3A GSP sing 142 n n PA O5' GSP sing 143 n n O2A HOA2 GSP sing 144 n n O5' C5' GSP sing 145 n n C5' C4' GSP sing 146 n n C5' "H5'1" GSP sing 147 n n C5' "H5'2" GSP sing 148 n n C4' O4' GSP sing 149 n n C4' C3' GSP sing 150 n n C4' H4' GSP sing 151 n n O4' C1' GSP sing 152 n n C3' O3' GSP sing 153 n n C3' C2' GSP sing 154 n n C3' H3' GSP sing 155 n n O3' HO3' GSP sing 156 n n C2' O2' GSP sing 157 n n C2' C1' GSP sing 158 n n C2' H2' GSP sing 159 n n O2' HO2' GSP sing 160 n n C1' N9 GSP sing 161 n n C1' H1' GSP sing 162 n n N9 C8 GSP sing 163 n y N9 C4 GSP sing 164 n y C8 N7 GSP doub 165 n y C8 H8 GSP sing 166 n n N7 C5 GSP sing 167 n y C5 C6 GSP sing 168 n n C5 C4 GSP doub 169 n y C6 O6 GSP doub 170 n n C6 N1 GSP sing 171 n n N1 C2 GSP sing 172 n n N1 HN1 GSP sing 173 n n C2 N2 GSP sing 174 n n C2 N3 GSP doub 175 n n N2 HN21 GSP sing 176 n n N2 HN22 GSP sing 177 n n N3 C4 GSP sing 178 n n # _atom_sites.entry_id 7PDF _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 C 3 GSP B 1 501 395 GSP GSP . D 4 MG B 1 502 396 MG MG . # 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 P PG GSP . . . C 3 48.302 157.09 117.516 1 72.9 ? PG GSP 501 B 1 HETATM 2 O O3B GSP . . . C 3 48.112 157.754 118.956 1 72.9 ? O3B GSP 501 B 1 HETATM 3 S S1G GSP . . . C 3 46.827 156.474 116.963 1 72.9 ? S1G GSP 501 B 1 HETATM 4 O O2G GSP . . . C 3 48.79 158.182 116.563 1 72.9 ? O2G GSP 501 B 1 HETATM 5 O O3G GSP . . . C 3 49.342 155.972 117.593 1 72.9 ? O3G GSP 501 B 1 HETATM 6 P PB GSP . . . C 3 49.177 158.859 119.41 1 72.9 ? PB GSP 501 B 1 HETATM 7 O O1B GSP . . . C 3 50.449 158.207 119.761 1 72.9 ? O1B GSP 501 B 1 HETATM 8 O O2B GSP . . . C 3 49.384 159.815 118.312 1 72.9 ? O2B GSP 501 B 1 HETATM 9 P PA GSP . . . C 3 47.688 160.911 120.435 1 72.9 ? PA GSP 501 B 1 HETATM 10 O O1A GSP . . . C 3 48.604 162.052 120.3 1 72.9 ? O1A GSP 501 B 1 HETATM 11 O O2A GSP . . . C 3 46.856 160.77 119.235 1 72.9 ? O2A GSP 501 B 1 HETATM 12 O O3A GSP . . . C 3 48.511 159.565 120.687 1 72.9 ? O3A GSP 501 B 1 HETATM 13 O O5' GSP . . . C 3 46.773 161.09 121.732 1 72.9 ? O5' GSP 501 B 1 HETATM 14 C C5' GSP . . . C 3 45.455 160.599 121.695 1 72.9 ? C5' GSP 501 B 1 HETATM 15 C C4' GSP . . . C 3 44.504 161.484 122.494 1 72.9 ? C4' GSP 501 B 1 HETATM 16 O O4' GSP . . . C 3 44.747 161.339 123.875 1 72.9 ? O4' GSP 501 B 1 HETATM 17 C C3' GSP . . . C 3 44.683 162.948 122.175 1 72.9 ? C3' GSP 501 B 1 HETATM 18 O O3' GSP . . . C 3 43.407 163.525 122.089 1 72.9 ? O3' GSP 501 B 1 HETATM 19 C C2' GSP . . . C 3 45.368 163.536 123.375 1 72.9 ? C2' GSP 501 B 1 HETATM 20 O O2' GSP . . . C 3 44.813 164.795 123.637 1 72.9 ? O2' GSP 501 B 1 HETATM 21 C C1' GSP . . . C 3 44.962 162.594 124.475 1 72.9 ? C1' GSP 501 B 1 HETATM 22 N N9 GSP . . . C 3 46.001 162.497 125.504 1 72.9 ? N9 GSP 501 B 1 HETATM 23 C C8 GSP . . . C 3 47.27 162.016 125.364 1 72.9 ? C8 GSP 501 B 1 HETATM 24 N N7 GSP . . . C 3 47.887 162.102 126.562 1 72.9 ? N7 GSP 501 B 1 HETATM 25 C C5 GSP . . . C 3 47.026 162.632 127.454 1 72.9 ? C5 GSP 501 B 1 HETATM 26 C C6 GSP . . . C 3 47.133 162.936 128.796 1 72.9 ? C6 GSP 501 B 1 HETATM 27 O O6 GSP . . . C 3 48.179 162.723 129.396 1 72.9 ? O6 GSP 501 B 1 HETATM 28 N N1 GSP . . . C 3 46.062 163.48 129.462 1 72.9 ? N1 GSP 501 B 1 HETATM 29 C C2 GSP . . . C 3 44.891 163.721 128.79 1 72.9 ? C2 GSP 501 B 1 HETATM 30 N N2 GSP . . . C 3 43.857 164.248 129.425 1 72.9 ? N2 GSP 501 B 1 HETATM 31 N N3 GSP . . . C 3 44.788 163.417 127.458 1 72.9 ? N3 GSP 501 B 1 HETATM 32 C C4 GSP . . . C 3 45.838 162.882 126.802 1 72.9 ? C4 GSP 501 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 239 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 32 #