data_1GIL # _model_server_result.job_id nc_Yz2aXilLVTo70K1ddow _model_server_result.datetime_utc '2024-11-06 01:48:19' _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 1gil # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":355}' # _entry.id 1GIL # _exptl.entry_id 1GIL _exptl.method 'X-RAY DIFFRACTION' # _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 120 _cell.entry_id 1GIL _cell.length_a 80.5 _cell.length_b 80.5 _cell.length_c 106.55 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1GIL _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 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 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 A OG SER 46 A SER 47 1_555 B MG MG . A MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc2 A OG1 THR 180 A THR 181 1_555 B MG MG . A MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc3 C O2G GSP . A GSP 355 1_555 B MG MG . A MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc4 C O2B GSP . A GSP 355 1_555 B MG MG . A MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc5 B MG MG . A MG 356 1_555 D O HOH . A HOH 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc6 B MG MG . A MG 356 1_555 D O HOH . A HOH 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? # _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 1GIL _atom_sites.fract_transf_matrix[1][1] 0.012422 _atom_sites.fract_transf_matrix[1][2] 0.007172 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014344 _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] 0.009385 _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 MG A 1 356 356 MG MG . C 3 GSP A 1 355 355 GSP GSP . D 4 HOH A 1 401 401 HOH HOH . D 4 HOH A 2 402 402 HOH HOH . D 4 HOH A 3 403 403 HOH HOH . D 4 HOH A 4 404 404 HOH HOH . D 4 HOH A 5 405 405 HOH HOH . D 4 HOH A 6 406 406 HOH HOH . D 4 HOH A 7 407 407 HOH HOH . D 4 HOH A 8 408 408 HOH HOH . D 4 HOH A 9 409 409 HOH HOH . D 4 HOH A 10 410 410 HOH HOH . D 4 HOH A 11 411 411 HOH HOH . D 4 HOH A 12 413 413 HOH HOH . D 4 HOH A 13 414 414 HOH HOH . D 4 HOH A 14 416 416 HOH HOH . D 4 HOH A 15 417 417 HOH HOH . D 4 HOH A 16 419 419 HOH HOH . D 4 HOH A 17 421 421 HOH HOH . D 4 HOH A 18 422 422 HOH HOH . D 4 HOH A 19 423 423 HOH HOH . D 4 HOH A 20 426 426 HOH HOH . D 4 HOH A 21 427 427 HOH HOH . D 4 HOH A 22 428 428 HOH HOH . D 4 HOH A 23 430 430 HOH HOH . D 4 HOH A 24 431 431 HOH HOH . D 4 HOH A 25 433 433 HOH HOH . D 4 HOH A 26 435 435 HOH HOH . D 4 HOH A 27 436 436 HOH HOH . D 4 HOH A 28 437 437 HOH HOH . D 4 HOH A 29 439 439 HOH HOH . D 4 HOH A 30 442 442 HOH HOH . D 4 HOH A 31 444 444 HOH HOH . D 4 HOH A 32 447 447 HOH HOH . D 4 HOH A 33 448 448 HOH HOH . D 4 HOH A 34 449 449 HOH HOH . D 4 HOH A 35 452 452 HOH HOH . D 4 HOH A 36 454 454 HOH HOH . D 4 HOH A 37 456 456 HOH HOH . D 4 HOH A 38 457 457 HOH HOH . D 4 HOH A 39 458 458 HOH HOH . D 4 HOH A 40 459 459 HOH HOH . D 4 HOH A 41 460 460 HOH HOH . D 4 HOH A 42 465 465 HOH HOH . D 4 HOH A 43 468 468 HOH HOH . D 4 HOH A 44 469 469 HOH HOH . D 4 HOH A 45 471 471 HOH HOH . D 4 HOH A 46 472 472 HOH HOH . D 4 HOH A 47 473 473 HOH HOH . D 4 HOH A 48 474 474 HOH HOH . D 4 HOH A 49 475 475 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 . . . C 3 37.146 -32.587 12.449 1 6.73 ? PG GSP 355 A 1 HETATM 2 O O3B GSP . . . C 3 37.371 -31.738 11.104 1 9.59 ? O3B GSP 355 A 1 HETATM 3 S S1G GSP . . . C 3 38.866 -32.914 13.249 1 7.19 ? S1G GSP 355 A 1 HETATM 4 O O2G GSP . . . C 3 36.343 -31.631 13.258 1 10.84 ? O2G GSP 355 A 1 HETATM 5 O O3G GSP . . . C 3 36.484 -33.853 12.083 1 3.79 ? O3G GSP 355 A 1 HETATM 6 P PB GSP . . . C 3 36.439 -30.783 10.145 1 6.69 ? PB GSP 355 A 1 HETATM 7 O O1B GSP . . . C 3 35.964 -31.775 9.214 1 5.25 ? O1B GSP 355 A 1 HETATM 8 O O2B GSP . . . C 3 35.411 -29.927 10.77 1 8.12 ? O2B GSP 355 A 1 HETATM 9 P PA GSP . . . C 3 37.566 -28.359 9.578 1 2 ? PA GSP 355 A 1 HETATM 10 O O1A GSP . . . C 3 36.352 -27.655 9.161 1 7.72 ? O1A GSP 355 A 1 HETATM 11 O O2A GSP . . . C 3 38.086 -28.17 10.959 1 10.83 ? O2A GSP 355 A 1 HETATM 12 O O3A GSP . . . C 3 37.436 -29.886 9.347 1 4.17 ? O3A GSP 355 A 1 HETATM 13 O O5' GSP . . . C 3 38.656 -27.936 8.537 1 5.45 ? O5' GSP 355 A 1 HETATM 14 C C5' GSP . . . C 3 40.051 -28.14 8.861 1 7.99 ? C5' GSP 355 A 1 HETATM 15 C C4' GSP . . . C 3 40.971 -27.107 8.287 1 3.57 ? C4' GSP 355 A 1 HETATM 16 O O4' GSP . . . C 3 40.85 -27.176 6.878 1 4.75 ? O4' GSP 355 A 1 HETATM 17 C C3' GSP . . . C 3 40.605 -25.685 8.76 1 3.07 ? C3' GSP 355 A 1 HETATM 18 O O3' GSP . . . C 3 41.776 -24.914 9.181 1 6.37 ? O3' GSP 355 A 1 HETATM 19 C C2' GSP . . . C 3 39.931 -25.098 7.509 1 4.99 ? C2' GSP 355 A 1 HETATM 20 O O2' GSP . . . C 3 40.126 -23.663 7.363 1 7.81 ? O2' GSP 355 A 1 HETATM 21 C C1' GSP . . . C 3 40.616 -25.819 6.37 1 3.64 ? C1' GSP 355 A 1 HETATM 22 N N9 GSP . . . C 3 39.722 -25.86 5.201 1 5.01 ? N9 GSP 355 A 1 HETATM 23 C C8 GSP . . . C 3 38.468 -26.424 5.094 1 2 ? C8 GSP 355 A 1 HETATM 24 N N7 GSP . . . C 3 37.935 -26.416 3.906 1 2.16 ? N7 GSP 355 A 1 HETATM 25 C C5 GSP . . . C 3 38.958 -25.797 3.113 1 6.67 ? C5 GSP 355 A 1 HETATM 26 C C6 GSP . . . C 3 39.044 -25.572 1.63 1 2 ? C6 GSP 355 A 1 HETATM 27 O O6 GSP . . . C 3 38.255 -25.896 0.745 1 2 ? O6 GSP 355 A 1 HETATM 28 N N1 GSP . . . C 3 40.203 -24.948 1.281 1 2 ? N1 GSP 355 A 1 HETATM 29 C C2 GSP . . . C 3 41.185 -24.58 2.177 1 2 ? C2 GSP 355 A 1 HETATM 30 N N2 GSP . . . C 3 42.097 -23.787 1.722 1 3.31 ? N2 GSP 355 A 1 HETATM 31 N N3 GSP . . . C 3 41.225 -24.847 3.51 1 7.77 ? N3 GSP 355 A 1 HETATM 32 C C4 GSP . . . C 3 40.055 -25.477 3.917 1 5.59 ? C4 GSP 355 A 1 # _model_server_stats.io_time_ms 74 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 32 #