data_3C16 # _model_server_result.job_id PW2jloQC5VpIyInDC1BVGQ _model_server_result.datetime_utc '2025-08-05 02:43:54' _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 3c16 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":395}' # _entry.id 3C16 # _exptl.entry_id 3C16 _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 3C16 _cell.length_a 118.331 _cell.length_b 133.527 _cell.length_c 70.703 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3C16 _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 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 O1B ATP . A ATP 1 1_555 D CA CA . A CA 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc2 G O3A ATP . A ATP 1 1_555 D CA CA . A CA 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc3 G O3G ATP . A ATP 1 1_555 D CA CA . A CA 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.031 ? metalc ? metalc4 G O1A ATP . A ATP 1 1_555 E CA CA . A CA 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? metalc ? metalc5 K O HOH . A HOH 2 1_555 E CA CA . A CA 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.872 ? metalc ? metalc6 D CA CA . A CA 29 1_555 A OD2 ASP 41 A ASP 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? metalc ? metalc7 D CA CA . A CA 29 1_555 A O ILE 42 A ILE 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.131 ? metalc ? metalc8 D CA CA . A CA 29 1_555 A OD2 ASP 85 A ASP 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc9 E CA CA . A CA 30 1_555 A OD2 ASP 41 A ASP 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.727 ? metalc ? metalc10 E CA CA . A CA 30 1_555 A OD1 ASP 41 A ASP 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.088 ? metalc ? metalc11 E CA CA . A CA 30 1_555 A OD1 ASP 85 A ASP 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.984 ? metalc ? metalc12 C OG SER 54 C SER 51 1_555 I MG MG . C MG 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc13 C OG1 THR 204 C THR 182 1_555 I MG MG . C MG 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.851 ? metalc ? metalc14 J O2G GSP . C GSP 395 1_555 I MG MG . C MG 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.922 ? metalc ? metalc15 J O2B GSP . C GSP 395 1_555 I MG MG . C MG 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? # _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 243 n n PG S1G GSP doub 244 n n PG O2G GSP sing 245 n n PG O3G GSP sing 246 n n O3B PB GSP sing 247 n n O2G HOG2 GSP sing 248 n n O3G HOG3 GSP sing 249 n n PB O1B GSP doub 250 n n PB O2B GSP sing 251 n n PB O3A GSP sing 252 n n O2B HOB2 GSP sing 253 n n PA O1A GSP doub 254 n n PA O2A GSP sing 255 n n PA O3A GSP sing 256 n n PA O5' GSP sing 257 n n O2A HOA2 GSP sing 258 n n O5' C5' GSP sing 259 n n C5' C4' GSP sing 260 n n C5' "H5'1" GSP sing 261 n n C5' "H5'2" GSP sing 262 n n C4' O4' GSP sing 263 n n C4' C3' GSP sing 264 n n C4' H4' GSP sing 265 n n O4' C1' GSP sing 266 n n C3' O3' GSP sing 267 n n C3' C2' GSP sing 268 n n C3' H3' GSP sing 269 n n O3' HO3' GSP sing 270 n n C2' O2' GSP sing 271 n n C2' C1' GSP sing 272 n n C2' H2' GSP sing 273 n n O2' HO2' GSP sing 274 n n C1' N9 GSP sing 275 n n C1' H1' GSP sing 276 n n N9 C8 GSP sing 277 n y N9 C4 GSP sing 278 n y C8 N7 GSP doub 279 n y C8 H8 GSP sing 280 n n N7 C5 GSP sing 281 n y C5 C6 GSP sing 282 n n C5 C4 GSP doub 283 n y C6 O6 GSP doub 284 n n C6 N1 GSP sing 285 n n N1 C2 GSP sing 286 n n N1 HN1 GSP sing 287 n n C2 N2 GSP sing 288 n n C2 N3 GSP doub 289 n n N2 HN21 GSP sing 290 n n N2 HN22 GSP sing 291 n n N3 C4 GSP sing 292 n n # _atom_sites.entry_id 3C16 _atom_sites.fract_transf_matrix[1][1] 0.008451 _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] 0.007489 _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] 0.014144 _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 CA A 1 29 29 CA CA . E 4 CA A 1 30 30 CA CA . F 5 FOK A 1 101 101 FOK FOK . G 6 ATP A 1 1 1 ATP ATP . H 7 CL C 1 397 397 CL CL . I 8 MG C 1 398 398 MG MG . J 9 GSP C 1 395 395 GSP GSP . K 10 HOH A 1 2 2 HOH HOH . K 10 HOH A 2 3 3 HOH HOH . K 10 HOH A 3 4 4 HOH HOH . K 10 HOH A 4 5 5 HOH HOH . K 10 HOH A 5 6 6 HOH HOH . K 10 HOH A 6 7 7 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 23.708 -3.218 42.061 1 22.42 ? PG GSP 395 C 1 HETATM 2 O O3B GSP . . . J 9 22.685 -3.464 43.303 1 25.69 ? O3B GSP 395 C 1 HETATM 3 S S1G GSP . . . J 9 25.028 -4.316 42.082 1 26.77 ? S1G GSP 395 C 1 HETATM 4 O O2G GSP . . . J 9 22.927 -3.336 40.716 1 18.07 ? O2G GSP 395 C 1 HETATM 5 O O3G GSP . . . J 9 24.329 -1.81 42.206 1 25.4 ? O3G GSP 395 C 1 HETATM 6 P PB GSP . . . J 9 21.201 -2.842 43.281 1 25.04 ? PB GSP 395 C 1 HETATM 7 O O1B GSP . . . J 9 21.222 -1.443 43.73 1 21.75 ? O1B GSP 395 C 1 HETATM 8 O O2B GSP . . . J 9 20.621 -2.96 41.933 1 23.45 ? O2B GSP 395 C 1 HETATM 9 P PA GSP . . . J 9 19.092 -4.546 43.858 1 22.44 ? PA GSP 395 C 1 HETATM 10 O O1A GSP . . . J 9 18.047 -3.625 43.368 1 18.62 ? O1A GSP 395 C 1 HETATM 11 O O2A GSP . . . J 9 19.482 -5.541 42.829 1 25.54 ? O2A GSP 395 C 1 HETATM 12 O O3A GSP . . . J 9 20.365 -3.7 44.337 1 24.88 ? O3A GSP 395 C 1 HETATM 13 O O5' GSP . . . J 9 18.566 -5.222 45.217 1 18.55 ? O5' GSP 395 C 1 HETATM 14 C C5' GSP . . . J 9 19.11 -6.458 45.63 1 20.63 ? C5' GSP 395 C 1 HETATM 15 C C4' GSP . . . J 9 18.009 -7.413 46.074 1 20.39 ? C4' GSP 395 C 1 HETATM 16 O O4' GSP . . . J 9 17.457 -6.978 47.307 1 21.59 ? O4' GSP 395 C 1 HETATM 17 C C3' GSP . . . J 9 16.883 -7.483 45.057 1 21.1 ? C3' GSP 395 C 1 HETATM 18 O O3' GSP . . . J 9 16.783 -8.805 44.58 1 19.48 ? O3' GSP 395 C 1 HETATM 19 C C2' GSP . . . J 9 15.645 -7.045 45.826 1 23.13 ? C2' GSP 395 C 1 HETATM 20 O O2' GSP . . . J 9 14.54 -7.895 45.641 1 32.45 ? O2' GSP 395 C 1 HETATM 21 C C1' GSP . . . J 9 16.051 -7.052 47.29 1 22.84 ? C1' GSP 395 C 1 HETATM 22 N N9 GSP . . . J 9 15.464 -5.879 47.964 1 20.03 ? N9 GSP 395 C 1 HETATM 23 C C8 GSP . . . J 9 15.532 -4.575 47.541 1 22.72 ? C8 GSP 395 C 1 HETATM 24 N N7 GSP . . . J 9 14.865 -3.803 48.425 1 24.69 ? N7 GSP 395 C 1 HETATM 25 C C5 GSP . . . J 9 14.369 -4.588 49.401 1 34.93 ? C5 GSP 395 C 1 HETATM 26 C C6 GSP . . . J 9 13.618 -4.311 50.534 1 41.85 ? C6 GSP 395 C 1 HETATM 27 O O6 GSP . . . J 9 13.285 -3.163 50.796 1 30.68 ? O6 GSP 395 C 1 HETATM 28 N N1 GSP . . . J 9 13.243 -5.329 51.375 1 18.72 ? N1 GSP 395 C 1 HETATM 29 C C2 GSP . . . J 9 13.617 -6.625 51.086 1 24.38 ? C2 GSP 395 C 1 HETATM 30 N N2 GSP . . . J 9 13.251 -7.611 51.897 1 17.92 ? N2 GSP 395 C 1 HETATM 31 N N3 GSP . . . J 9 14.364 -6.898 49.955 1 17.43 ? N3 GSP 395 C 1 HETATM 32 C C4 GSP . . . J 9 14.736 -5.896 49.124 1 26.65 ? C4 GSP 395 C 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 256 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 32 #