data_3KZ1 # _model_server_result.job_id ORGLSzdGMQ7BAEr3KUMwdA _model_server_result.datetime_utc '2024-11-23 20:47:47' _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 3kz1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":538}' # _entry.id 3KZ1 # _exptl.entry_id 3KZ1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 539.246 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 3KZ1 _cell.length_a 98.166 _cell.length_b 111.836 _cell.length_c 138.39 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KZ1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,G,H,I,L 1 1 B,C,E,F,J,K 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 H N 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 C OG1 THR 20 E THR 19 1_555 E MG MG . E MG 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? metalc ? metalc2 C OG1 THR 38 E THR 37 1_555 E MG MG . E MG 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.901 ? metalc ? metalc3 F O2G GSP . E GSP 538 1_555 E MG MG . E MG 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc4 F O2B GSP . E GSP 538 1_555 E MG MG . E MG 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc5 D OG1 THR 20 F THR 19 1_555 G MG MG . F MG 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc6 D OG1 THR 38 F THR 37 1_555 G MG MG . F MG 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc7 H O2G GSP . F GSP 538 1_555 G MG MG . F MG 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc8 H O2B GSP . F GSP 538 1_555 G MG MG . F MG 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? # _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 3KZ1 _atom_sites.fract_transf_matrix[1][1] 0.010187 _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] 0.008942 _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] 0.007226 _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 E 3 MG E 1 550 550 MG MG . F 4 GSP E 1 538 538 GSP GSP . G 3 MG F 1 550 550 MG MG . H 4 GSP F 1 538 538 GSP GSP . I 5 HOH A 1 200 200 HOH HOH . I 5 HOH A 2 201 201 HOH HOH . I 5 HOH A 3 202 202 HOH HOH . I 5 HOH A 4 203 203 HOH HOH . I 5 HOH A 5 204 204 HOH HOH . I 5 HOH A 6 205 205 HOH HOH . I 5 HOH A 7 206 206 HOH HOH . I 5 HOH A 8 207 207 HOH HOH . I 5 HOH A 9 208 208 HOH HOH . I 5 HOH A 10 209 209 HOH HOH . I 5 HOH A 11 210 210 HOH HOH . I 5 HOH A 12 211 211 HOH HOH . I 5 HOH A 13 212 212 HOH HOH . I 5 HOH A 14 213 213 HOH HOH . I 5 HOH A 15 214 214 HOH HOH . I 5 HOH A 16 215 215 HOH HOH . I 5 HOH A 17 216 216 HOH HOH . I 5 HOH A 18 217 217 HOH HOH . I 5 HOH A 19 218 218 HOH HOH . I 5 HOH A 20 219 219 HOH HOH . I 5 HOH A 21 220 220 HOH HOH . I 5 HOH A 22 221 221 HOH HOH . I 5 HOH A 23 222 222 HOH HOH . I 5 HOH A 24 223 223 HOH HOH . I 5 HOH A 25 224 224 HOH HOH . I 5 HOH A 26 225 225 HOH HOH . I 5 HOH A 27 226 226 HOH HOH . I 5 HOH A 28 227 227 HOH HOH . I 5 HOH A 29 228 228 HOH HOH . I 5 HOH A 30 229 229 HOH HOH . I 5 HOH A 31 230 230 HOH HOH . I 5 HOH A 32 231 231 HOH HOH . I 5 HOH A 33 232 232 HOH HOH . I 5 HOH A 34 233 233 HOH HOH . I 5 HOH A 35 234 234 HOH HOH . I 5 HOH A 36 235 235 HOH HOH . J 5 HOH B 1 200 200 HOH HOH . J 5 HOH B 2 201 201 HOH HOH . J 5 HOH B 3 202 202 HOH HOH . J 5 HOH B 4 203 203 HOH HOH . J 5 HOH B 5 204 204 HOH HOH . J 5 HOH B 6 205 205 HOH HOH . J 5 HOH B 7 206 206 HOH HOH . J 5 HOH B 8 207 207 HOH HOH . J 5 HOH B 9 208 208 HOH HOH . J 5 HOH B 10 209 209 HOH HOH . J 5 HOH B 11 210 210 HOH HOH . J 5 HOH B 12 211 211 HOH HOH . J 5 HOH B 13 212 212 HOH HOH . J 5 HOH B 14 213 213 HOH HOH . J 5 HOH B 15 214 214 HOH HOH . J 5 HOH B 16 215 215 HOH HOH . J 5 HOH B 17 216 216 HOH HOH . J 5 HOH B 18 217 217 HOH HOH . K 5 HOH E 1 200 200 HOH HOH . K 5 HOH E 2 201 201 HOH HOH . K 5 HOH E 3 202 202 HOH HOH . K 5 HOH E 4 203 203 HOH HOH . K 5 HOH E 5 204 204 HOH HOH . K 5 HOH E 6 205 205 HOH HOH . K 5 HOH E 7 206 206 HOH HOH . K 5 HOH E 8 207 207 HOH HOH . K 5 HOH E 9 208 208 HOH HOH . K 5 HOH E 10 209 209 HOH HOH . K 5 HOH E 11 210 210 HOH HOH . K 5 HOH E 12 211 211 HOH HOH . L 5 HOH F 1 200 200 HOH HOH . L 5 HOH F 2 201 201 HOH HOH . L 5 HOH F 3 202 202 HOH HOH . L 5 HOH F 4 203 203 HOH HOH . L 5 HOH F 5 204 204 HOH HOH . L 5 HOH F 6 205 205 HOH HOH . L 5 HOH F 7 206 206 HOH HOH . L 5 HOH F 8 207 207 HOH HOH . L 5 HOH F 9 208 208 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 . . . F 4 12.902 1.966 4.867 1 60.31 ? PG GSP 538 E 1 HETATM 2 O O3B GSP . . . F 4 13.197 1.907 3.281 1 61.84 ? O3B GSP 538 E 1 HETATM 3 S S1G GSP . . . F 4 13.615 3.434 5.515 1 62.33 ? S1G GSP 538 E 1 HETATM 4 O O2G GSP . . . F 4 11.368 1.834 5.052 1 57.59 ? O2G GSP 538 E 1 HETATM 5 O O3G GSP . . . F 4 13.613 0.755 5.482 1 55.93 ? O3G GSP 538 E 1 HETATM 6 P PB GSP . . . F 4 12.739 0.713 2.293 1 61.13 ? PB GSP 538 E 1 HETATM 7 O O1B GSP . . . F 4 13.773 -0.352 2.234 1 56.43 ? O1B GSP 538 E 1 HETATM 8 O O2B GSP . . . F 4 11.422 0.167 2.721 1 58.35 ? O2B GSP 538 E 1 HETATM 9 P PA GSP . . . F 4 11.248 1.833 0.108 1 64.31 ? PA GSP 538 E 1 HETATM 10 O O1A GSP . . . F 4 10.545 0.547 -0.131 1 64.04 ? O1A GSP 538 E 1 HETATM 11 O O2A GSP . . . F 4 10.342 2.632 0.952 1 62.95 ? O2A GSP 538 E 1 HETATM 12 O O3A GSP . . . F 4 12.645 1.482 0.856 1 63.13 ? O3A GSP 538 E 1 HETATM 13 O O5' GSP . . . F 4 11.644 2.445 -1.332 1 67.3 ? O5' GSP 538 E 1 HETATM 14 C C5' GSP . . . F 4 12.647 3.441 -1.375 1 73.73 ? C5' GSP 538 E 1 HETATM 15 C C4' GSP . . . F 4 12.661 4.352 -2.609 1 78.92 ? C4' GSP 538 E 1 HETATM 16 O O4' GSP . . . F 4 13.174 3.645 -3.711 1 78.9 ? O4' GSP 538 E 1 HETATM 17 C C3' GSP . . . F 4 11.309 4.926 -3.01 1 82.44 ? C3' GSP 538 E 1 HETATM 18 O O3' GSP . . . F 4 11.442 6.317 -3.226 1 88.74 ? O3' GSP 538 E 1 HETATM 19 C C2' GSP . . . F 4 10.952 4.246 -4.315 1 82.94 ? C2' GSP 538 E 1 HETATM 20 O O2' GSP . . . F 4 10.487 5.184 -5.266 1 89.74 ? O2' GSP 538 E 1 HETATM 21 C C1' GSP . . . F 4 12.267 3.656 -4.792 1 81.21 ? C1' GSP 538 E 1 HETATM 22 N N9 GSP . . . F 4 12.068 2.313 -5.371 1 78.1 ? N9 GSP 538 E 1 HETATM 23 C C8 GSP . . . F 4 11.485 1.205 -4.809 1 73.49 ? C8 GSP 538 E 1 HETATM 24 N N7 GSP . . . F 4 11.525 0.175 -5.701 1 72.18 ? N7 GSP 538 E 1 HETATM 25 C C5 GSP . . . F 4 12.127 0.604 -6.822 1 76.98 ? C5 GSP 538 E 1 HETATM 26 C C6 GSP . . . F 4 12.432 -0.013 -8.031 1 78.79 ? C6 GSP 538 E 1 HETATM 27 O O6 GSP . . . F 4 12.125 -1.172 -8.23 1 77.54 ? O6 GSP 538 E 1 HETATM 28 N N1 GSP . . . F 4 13.093 0.687 -9.017 1 83.85 ? N1 GSP 538 E 1 HETATM 29 C C2 GSP . . . F 4 13.44 2.015 -8.802 1 86.29 ? C2 GSP 538 E 1 HETATM 30 N N2 GSP . . . F 4 14.072 2.706 -9.742 1 90.61 ? N2 GSP 538 E 1 HETATM 31 N N3 GSP . . . F 4 13.13 2.634 -7.606 1 84.46 ? N3 GSP 538 E 1 HETATM 32 C C4 GSP . . . F 4 12.48 1.943 -6.629 1 80.5 ? C4 GSP 538 E 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #