data_3C15 # _model_server_result.job_id nN27GjqDh226rQ8EmXuvZA _model_server_result.datetime_utc '2024-11-23 11:14:32' _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 3c15 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":404}' # _entry.id 3C15 # _exptl.entry_id 3C15 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 539.246 _entity.id 8 _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 3C15 _cell.length_a 117.51 _cell.length_b 133.08 _cell.length_c 70.108 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3C15 _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 _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 8 _struct_asym.id H _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 F O3 POP . A POP 1 1_555 D MG MG . A MG 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.755 ? metalc ? metalc2 D MG MG . A MG 29 1_555 A OD2 ASP 41 A ASP 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc3 D MG MG . A MG 29 1_555 A O ILE 42 A ILE 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? metalc ? metalc4 D MG MG . A MG 29 1_555 A OD2 ASP 85 A ASP 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.841 ? # _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 3C15 _atom_sites.fract_transf_matrix[1][1] 0.00851 _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] 0.007514 _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] 0.014264 _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 MG A 1 29 29 MG MG . E 5 FOK A 1 101 101 FOK FOK . F 6 POP A 1 1 1 POP POP . G 7 CL C 1 403 397 CL CL . H 8 GSP C 1 404 395 GSP GSP . I 9 HOH A 1 8 8 HOH HOH . I 9 HOH A 2 20 20 HOH HOH . I 9 HOH A 3 30 30 HOH HOH . J 9 HOH B 1 19 19 HOH HOH . J 9 HOH B 2 24 24 HOH HOH . J 9 HOH B 3 46 46 HOH HOH . J 9 HOH B 4 50 50 HOH HOH . J 9 HOH B 5 51 51 HOH HOH . J 9 HOH B 6 59 59 HOH HOH . K 9 HOH C 1 405 13 HOH HOH . K 9 HOH C 2 406 23 HOH HOH . K 9 HOH C 3 407 55 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 . . . H 8 35.927 -2.913 -6.526 1 40.53 ? PG GSP 404 C 1 HETATM 2 O O3B GSP . . . H 8 36.497 -3.094 -8.013 1 33.8 ? O3B GSP 404 C 1 HETATM 3 S S1G GSP . . . H 8 34.475 -3.833 -6.398 1 44.88 ? S1G GSP 404 C 1 HETATM 4 O O2G GSP . . . H 8 37.099 -3.34 -5.59 1 36.18 ? O2G GSP 404 C 1 HETATM 5 O O3G GSP . . . H 8 35.61 -1.429 -6.25 1 43.51 ? O3G GSP 404 C 1 HETATM 6 P PB GSP . . . H 8 37.982 -2.571 -8.21 1 33.15 ? PB GSP 404 C 1 HETATM 7 O O1B GSP . . . H 8 37.896 -1.342 -9.033 1 29.86 ? O1B GSP 404 C 1 HETATM 8 O O2B GSP . . . H 8 38.575 -2.329 -6.873 1 31.56 ? O2B GSP 404 C 1 HETATM 9 P PA GSP . . . H 8 40.022 -4.415 -8.428 1 30.55 ? PA GSP 404 C 1 HETATM 10 O O1A GSP . . . H 8 40.986 -3.326 -8.178 1 36.73 ? O1A GSP 404 C 1 HETATM 11 O O2A GSP . . . H 8 39.688 -5.212 -7.218 1 33.65 ? O2A GSP 404 C 1 HETATM 12 O O3A GSP . . . H 8 38.694 -3.754 -9.01 1 32.99 ? O3A GSP 404 C 1 HETATM 13 O O5' GSP . . . H 8 40.558 -5.308 -9.641 1 36.66 ? O5' GSP 404 C 1 HETATM 14 C C5' GSP . . . H 8 39.882 -6.489 -9.95 1 38.74 ? C5' GSP 404 C 1 HETATM 15 C C4' GSP . . . H 8 40.831 -7.331 -10.776 1 38.5 ? C4' GSP 404 C 1 HETATM 16 O O4' GSP . . . H 8 41.365 -6.541 -11.818 1 39.7 ? O4' GSP 404 C 1 HETATM 17 C C3' GSP . . . H 8 42.003 -7.825 -9.942 1 39.21 ? C3' GSP 404 C 1 HETATM 18 O O3' GSP . . . H 8 42 -9.235 -9.973 1 37.59 ? O3' GSP 404 C 1 HETATM 19 C C2' GSP . . . H 8 43.234 -7.255 -10.621 1 41.24 ? C2' GSP 404 C 1 HETATM 20 O O2' GSP . . . H 8 44.244 -8.218 -10.774 1 50.56 ? O2' GSP 404 C 1 HETATM 21 C C1' GSP . . . H 8 42.726 -6.854 -11.99 1 40.95 ? C1' GSP 404 C 1 HETATM 22 N N9 GSP . . . H 8 43.438 -5.685 -12.514 1 38.14 ? N9 GSP 404 C 1 HETATM 23 C C8 GSP . . . H 8 43.407 -4.415 -12.006 1 30.83 ? C8 GSP 404 C 1 HETATM 24 N N7 GSP . . . H 8 44.184 -3.627 -12.775 1 32.8 ? N7 GSP 404 C 1 HETATM 25 C C5 GSP . . . H 8 44.697 -4.383 -13.77 1 33.04 ? C5 GSP 404 C 1 HETATM 26 C C6 GSP . . . H 8 45.548 -4.08 -14.827 1 29.96 ? C6 GSP 404 C 1 HETATM 27 O O6 GSP . . . H 8 45.967 -2.932 -14.969 1 28.79 ? O6 GSP 404 C 1 HETATM 28 N N1 GSP . . . H 8 45.922 -5.065 -15.713 1 26.83 ? N1 GSP 404 C 1 HETATM 29 C C2 GSP . . . H 8 45.453 -6.348 -15.547 1 32.49 ? C2 GSP 404 C 1 HETATM 30 N N2 GSP . . . H 8 45.839 -7.282 -16.408 1 26.03 ? N2 GSP 404 C 1 HETATM 31 N N3 GSP . . . H 8 44.606 -6.656 -14.496 1 35.54 ? N3 GSP 404 C 1 HETATM 32 C C4 GSP . . . H 8 44.237 -5.683 -13.62 1 34.76 ? C4 GSP 404 C 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 32 #