data_3G82 # _model_server_result.job_id qvqflOpxW5NrWM6erzv1Gg _model_server_result.datetime_utc '2024-11-24 03:22:16' _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 3g82 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":395}' # _entry.id 3G82 # _exptl.entry_id 3G82 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 539.246 _entity.id 9 _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 3G82 _cell.length_a 117.637 _cell.length_b 133.423 _cell.length_c 70.642 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3G82 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 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,K,L,M _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 9 _struct_asym.id J _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 G O2A MI3 . A MI3 100 1_555 D MN MN . A MN 581 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc2 G O1B MI3 . A MI3 100 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc3 G O3B MI3 . A MI3 100 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.692 ? metalc ? metalc4 A OD2 ASP 41 A ASP 396 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc5 A O ILE 42 A ILE 397 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc6 A OD1 ASP 85 A ASP 440 1_555 D MN MN . A MN 581 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.442 ? metalc ? metalc7 A OD2 ASP 85 A ASP 440 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc8 C OG SER 54 C SER 54 1_555 H MG MG . C MG 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc9 C OG1 THR 204 C THR 204 1_555 H MG MG . C MG 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc10 J O2G GSP . C GSP 395 1_555 H MG MG . C MG 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.722 ? metalc ? metalc11 J O2B GSP . C GSP 395 1_555 H MG MG . C MG 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.545 ? # _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 194 n n PG S1G GSP doub 195 n n PG O2G GSP sing 196 n n PG O3G GSP sing 197 n n O3B PB GSP sing 198 n n O2G HOG2 GSP sing 199 n n O3G HOG3 GSP sing 200 n n PB O1B GSP doub 201 n n PB O2B GSP sing 202 n n PB O3A GSP sing 203 n n O2B HOB2 GSP sing 204 n n PA O1A GSP doub 205 n n PA O2A GSP sing 206 n n PA O3A GSP sing 207 n n PA O5' GSP sing 208 n n O2A HOA2 GSP sing 209 n n O5' C5' GSP sing 210 n n C5' C4' GSP sing 211 n n C5' "H5'1" GSP sing 212 n n C5' "H5'2" GSP sing 213 n n C4' O4' GSP sing 214 n n C4' C3' GSP sing 215 n n C4' H4' GSP sing 216 n n O4' C1' GSP sing 217 n n C3' O3' GSP sing 218 n n C3' C2' GSP sing 219 n n C3' H3' GSP sing 220 n n O3' HO3' GSP sing 221 n n C2' O2' GSP sing 222 n n C2' C1' GSP sing 223 n n C2' H2' GSP sing 224 n n O2' HO2' GSP sing 225 n n C1' N9 GSP sing 226 n n C1' H1' GSP sing 227 n n N9 C8 GSP sing 228 n y N9 C4 GSP sing 229 n y C8 N7 GSP doub 230 n y C8 H8 GSP sing 231 n n N7 C5 GSP sing 232 n y C5 C6 GSP sing 233 n n C5 C4 GSP doub 234 n y C6 O6 GSP doub 235 n n C6 N1 GSP sing 236 n n N1 C2 GSP sing 237 n n N1 HN1 GSP sing 238 n n C2 N2 GSP sing 239 n n C2 N3 GSP doub 240 n n N2 HN21 GSP sing 241 n n N2 HN22 GSP sing 242 n n N3 C4 GSP sing 243 n n # _atom_sites.entry_id 3G82 _atom_sites.fract_transf_matrix[1][1] 0.008501 _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] 0.007495 _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] 0.014156 _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 MN A 1 581 502 MN MN . E 4 MN A 1 582 503 MN MN . F 5 FOK A 1 101 101 FOK FOK . G 6 MI3 A 1 100 100 MI3 MI3 . H 7 MG C 1 396 396 MG MG . I 8 CL C 1 397 397 CL CL . J 9 GSP C 1 395 395 GSP GSP . K 10 HOH A 1 22 22 HOH HOH . L 10 HOH B 1 28 28 HOH HOH . L 10 HOH B 2 37 37 HOH HOH . M 10 HOH C 1 398 51 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 P PG GSP . . . J 9 23.305 3.132 -41.858 1 36.88 ? PG GSP 395 C 1 HETATM 2 O O3B GSP . . . J 9 22.174 3.403 -42.837 1 31.19 ? O3B GSP 395 C 1 HETATM 3 S S1G GSP . . . J 9 24.726 4.367 -42.007 1 37.48 ? S1G GSP 395 C 1 HETATM 4 O O2G GSP . . . J 9 22.819 3.411 -40.476 1 34.77 ? O2G GSP 395 C 1 HETATM 5 O O3G GSP . . . J 9 23.867 1.791 -42.17 1 36.98 ? O3G GSP 395 C 1 HETATM 6 P PB GSP . . . J 9 20.887 2.684 -43.148 1 26.62 ? PB GSP 395 C 1 HETATM 7 O O1B GSP . . . J 9 21.173 1.57 -44.084 1 20.26 ? O1B GSP 395 C 1 HETATM 8 O O2B GSP . . . J 9 20.197 2.404 -41.877 1 25.42 ? O2B GSP 395 C 1 HETATM 9 P PA GSP . . . J 9 18.887 4.476 -43.455 1 26.67 ? PA GSP 395 C 1 HETATM 10 O O1A GSP . . . J 9 17.9 3.468 -42.993 1 24.07 ? O1A GSP 395 C 1 HETATM 11 O O2A GSP . . . J 9 19.291 5.594 -42.564 1 22.85 ? O2A GSP 395 C 1 HETATM 12 O O3A GSP . . . J 9 20.121 3.746 -43.878 1 26.61 ? O3A GSP 395 C 1 HETATM 13 O O5' GSP . . . J 9 18.328 5.122 -44.802 1 26.66 ? O5' GSP 395 C 1 HETATM 14 C C5' GSP . . . J 9 19.033 6.197 -45.448 1 27.3 ? C5' GSP 395 C 1 HETATM 15 C C4' GSP . . . J 9 18.073 7.182 -46.076 1 23.71 ? C4' GSP 395 C 1 HETATM 16 O O4' GSP . . . J 9 17.428 6.624 -47.245 1 23.64 ? O4' GSP 395 C 1 HETATM 17 C C3' GSP . . . J 9 16.943 7.644 -45.166 1 24.47 ? C3' GSP 395 C 1 HETATM 18 O O3' GSP . . . J 9 16.727 9.044 -45.369 1 25.39 ? O3' GSP 395 C 1 HETATM 19 C C2' GSP . . . J 9 15.761 6.839 -45.671 1 22.93 ? C2' GSP 395 C 1 HETATM 20 O O2' GSP . . . J 9 14.525 7.457 -45.447 1 28.07 ? O2' GSP 395 C 1 HETATM 21 C C1' GSP . . . J 9 16.027 6.774 -47.144 1 21.21 ? C1' GSP 395 C 1 HETATM 22 N N9 GSP . . . J 9 15.395 5.641 -47.813 1 21.89 ? N9 GSP 395 C 1 HETATM 23 C C8 GSP . . . J 9 15.466 4.325 -47.445 1 23.55 ? C8 GSP 395 C 1 HETATM 24 N N7 GSP . . . J 9 14.777 3.54 -48.231 1 24.83 ? N7 GSP 395 C 1 HETATM 25 C C5 GSP . . . J 9 14.219 4.392 -49.174 1 21.15 ? C5 GSP 395 C 1 HETATM 26 C C6 GSP . . . J 9 13.371 4.116 -50.266 1 19.67 ? C6 GSP 395 C 1 HETATM 27 O O6 GSP . . . J 9 12.93 3.036 -50.632 1 22.19 ? O6 GSP 395 C 1 HETATM 28 N N1 GSP . . . J 9 13.037 5.259 -50.962 1 18.96 ? N1 GSP 395 C 1 HETATM 29 C C2 GSP . . . J 9 13.466 6.514 -50.655 1 22.02 ? C2 GSP 395 C 1 HETATM 30 N N2 GSP . . . J 9 13.036 7.52 -51.464 1 17.34 ? N2 GSP 395 C 1 HETATM 31 N N3 GSP . . . J 9 14.266 6.784 -49.629 1 23.9 ? N3 GSP 395 C 1 HETATM 32 C C4 GSP . . . J 9 14.596 5.685 -48.938 1 21.15 ? C4 GSP 395 C 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #