data_4GSP # _model_server_result.job_id C2iQDOVbg-oVWnVJUC3Oag _model_server_result.datetime_utc '2024-11-28 16:53:53' _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 4gsp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":106}' # _entry.id 4GSP # _exptl.entry_id 4GSP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 361.271 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-2',3'-CYCLOPHOSPHOROTHIOATE" _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 4GSP _cell.length_a 48.24 _cell.length_b 51.1 _cell.length_c 40.45 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4GSP _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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,E _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 4 _struct_asym.id D _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 disulf ? disulf1 A SG CYS 2 A CYS 2 1_555 A SG CYS 10 A CYS 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf2 A SG CYS 6 A CYS 6 1_555 A SG CYS 103 A CYS 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc1 A OD2 ASP 15 A ASP 15 1_555 B CA CA . A CA 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc2 A OD1 ASP 15 A ASP 15 1_555 B CA CA . A CA 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.617 ? metalc ? metalc3 B CA CA . A CA 107 1_555 E O HOH . A HOH 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc4 B CA CA . A CA 107 1_555 E O HOH . A HOH 133 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? metalc ? metalc5 B CA CA . A CA 107 1_555 E O HOH . A HOH 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc6 B CA CA . A CA 107 1_555 E O HOH . A HOH 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.973 ? metalc ? metalc7 B CA CA . A CA 107 1_555 E O HOH . A HOH 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? # _chem_comp.formula 'C10 H12 N5 O6 P S' _chem_comp.formula_weight 361.271 _chem_comp.id SGP _chem_comp.mon_nstd_flag . _chem_comp.name "GUANOSINE-2',3'-CYCLOPHOSPHOROTHIOATE" _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 P S1P SGP doub 311 n n P O1P SGP sing 312 n n P O3' SGP sing 313 n n P O2' SGP sing 314 n n O1P HOP1 SGP sing 315 n n O5' C5' SGP sing 316 n n O5' HO5' SGP sing 317 n n C5' C4' SGP sing 318 n n C5' "H5'1" SGP sing 319 n n C5' "H5'2" SGP sing 320 n n C4' O4' SGP sing 321 n n C4' C3' SGP sing 322 n n C4' H4' SGP sing 323 n n O4' C1' SGP sing 324 n n C3' O3' SGP sing 325 n n C3' C2' SGP sing 326 n n C3' H3' SGP sing 327 n n C2' O2' SGP sing 328 n n C2' C1' SGP sing 329 n n C2' H2' SGP sing 330 n n C1' N9 SGP sing 331 n n C1' H1' SGP sing 332 n n N9 C8 SGP sing 333 n y N9 C4 SGP sing 334 n y C8 N7 SGP doub 335 n y C8 H8 SGP sing 336 n n N7 C5 SGP sing 337 n y C5 C6 SGP sing 338 n n C5 C4 SGP doub 339 n y C6 O6 SGP doub 340 n n C6 N1 SGP sing 341 n n N1 C2 SGP sing 342 n n N1 HN1 SGP sing 343 n n C2 N2 SGP sing 344 n n C2 N3 SGP doub 345 n n N2 HN21 SGP sing 346 n n N2 HN22 SGP sing 347 n n N3 C4 SGP sing 348 n n # _atom_sites.entry_id 4GSP _atom_sites.fract_transf_matrix[1][1] 0.02073 _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] 0.019569 _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] 0.024722 _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 CA A 1 107 107 CA CA . C 3 3GP A 1 105 105 3GP 3GP . D 4 SGP A 1 106 106 SGP SGP . E 5 HOH A 1 108 108 HOH HOH . E 5 HOH A 2 109 109 HOH HOH . E 5 HOH A 3 110 110 HOH HOH . E 5 HOH A 4 111 111 HOH HOH . E 5 HOH A 5 112 112 HOH HOH . E 5 HOH A 6 113 113 HOH HOH . E 5 HOH A 7 114 114 HOH HOH . E 5 HOH A 8 115 115 HOH HOH . E 5 HOH A 9 116 116 HOH HOH . E 5 HOH A 10 117 117 HOH HOH . E 5 HOH A 11 118 118 HOH HOH . E 5 HOH A 12 119 119 HOH HOH . E 5 HOH A 13 120 120 HOH HOH . E 5 HOH A 14 121 121 HOH HOH . E 5 HOH A 15 122 122 HOH HOH . E 5 HOH A 16 123 123 HOH HOH . E 5 HOH A 17 124 124 HOH HOH . E 5 HOH A 18 125 125 HOH HOH . E 5 HOH A 19 126 126 HOH HOH . E 5 HOH A 20 127 127 HOH HOH . E 5 HOH A 21 128 128 HOH HOH . E 5 HOH A 22 129 129 HOH HOH . E 5 HOH A 23 130 130 HOH HOH . E 5 HOH A 24 131 131 HOH HOH . E 5 HOH A 25 132 132 HOH HOH . E 5 HOH A 26 133 133 HOH HOH . E 5 HOH A 27 134 134 HOH HOH . E 5 HOH A 28 135 135 HOH HOH . E 5 HOH A 29 136 136 HOH HOH . E 5 HOH A 30 137 137 HOH HOH . E 5 HOH A 31 138 138 HOH HOH . E 5 HOH A 32 139 139 HOH HOH . E 5 HOH A 33 140 140 HOH HOH . E 5 HOH A 34 141 141 HOH HOH . E 5 HOH A 35 142 142 HOH HOH . E 5 HOH A 36 143 143 HOH HOH . E 5 HOH A 37 144 144 HOH HOH . E 5 HOH A 38 145 145 HOH HOH . E 5 HOH A 39 146 146 HOH HOH . E 5 HOH A 40 147 147 HOH HOH . E 5 HOH A 41 148 148 HOH HOH . E 5 HOH A 42 149 149 HOH HOH . E 5 HOH A 43 150 150 HOH HOH . E 5 HOH A 44 151 151 HOH HOH . E 5 HOH A 45 152 152 HOH HOH . E 5 HOH A 46 153 153 HOH HOH . E 5 HOH A 47 154 154 HOH HOH . E 5 HOH A 48 155 155 HOH HOH . E 5 HOH A 49 156 156 HOH HOH . E 5 HOH A 50 157 157 HOH HOH . E 5 HOH A 51 158 158 HOH HOH . E 5 HOH A 52 159 159 HOH HOH . E 5 HOH A 53 160 160 HOH HOH . E 5 HOH A 54 161 161 HOH HOH . E 5 HOH A 55 162 162 HOH HOH . E 5 HOH A 56 163 163 HOH HOH . E 5 HOH A 57 164 164 HOH HOH . E 5 HOH A 58 165 165 HOH HOH . E 5 HOH A 59 166 166 HOH HOH . E 5 HOH A 60 167 167 HOH HOH . E 5 HOH A 61 168 168 HOH HOH . E 5 HOH A 62 169 169 HOH HOH . E 5 HOH A 63 170 170 HOH HOH . E 5 HOH A 64 171 171 HOH HOH . E 5 HOH A 65 172 172 HOH HOH . E 5 HOH A 66 173 173 HOH HOH . E 5 HOH A 67 174 174 HOH HOH . E 5 HOH A 68 175 175 HOH HOH . E 5 HOH A 69 176 176 HOH HOH . E 5 HOH A 70 177 177 HOH HOH . E 5 HOH A 71 178 178 HOH HOH . E 5 HOH A 72 179 179 HOH HOH . E 5 HOH A 73 180 180 HOH HOH . E 5 HOH A 74 181 181 HOH HOH . E 5 HOH A 75 182 182 HOH HOH . E 5 HOH A 76 183 183 HOH HOH . E 5 HOH A 77 184 184 HOH HOH . E 5 HOH A 78 185 185 HOH HOH . E 5 HOH A 79 186 186 HOH HOH . E 5 HOH A 80 187 187 HOH HOH . E 5 HOH A 81 188 188 HOH HOH . E 5 HOH A 82 189 189 HOH HOH . E 5 HOH A 83 190 190 HOH HOH . E 5 HOH A 84 191 191 HOH HOH . E 5 HOH A 85 192 192 HOH HOH . E 5 HOH A 86 193 193 HOH HOH . E 5 HOH A 87 194 194 HOH HOH . E 5 HOH A 88 195 195 HOH HOH . E 5 HOH A 89 196 196 HOH HOH . E 5 HOH A 90 197 197 HOH HOH . E 5 HOH A 91 198 198 HOH HOH . E 5 HOH A 92 199 199 HOH HOH . E 5 HOH A 93 200 200 HOH HOH . E 5 HOH A 94 201 201 HOH HOH . E 5 HOH A 95 202 202 HOH HOH . E 5 HOH A 96 203 203 HOH HOH . E 5 HOH A 97 204 204 HOH HOH . E 5 HOH A 98 205 205 HOH HOH . E 5 HOH A 99 206 206 HOH HOH . E 5 HOH A 100 207 207 HOH HOH . E 5 HOH A 101 208 208 HOH HOH . E 5 HOH A 102 209 209 HOH HOH . E 5 HOH A 103 210 210 HOH HOH . E 5 HOH A 104 211 211 HOH HOH . E 5 HOH A 105 212 212 HOH HOH . E 5 HOH A 106 213 213 HOH HOH . E 5 HOH A 107 214 214 HOH HOH . E 5 HOH A 108 215 215 HOH HOH . E 5 HOH A 109 216 216 HOH HOH . E 5 HOH A 110 217 217 HOH HOH . E 5 HOH A 111 218 218 HOH HOH . E 5 HOH A 112 219 219 HOH HOH . E 5 HOH A 113 220 220 HOH HOH . E 5 HOH A 114 221 221 HOH HOH . E 5 HOH A 115 222 222 HOH HOH . E 5 HOH A 116 223 223 HOH HOH . E 5 HOH A 117 224 224 HOH HOH . E 5 HOH A 118 225 225 HOH HOH . E 5 HOH A 119 226 226 HOH HOH . E 5 HOH A 120 227 227 HOH HOH . E 5 HOH A 121 228 228 HOH HOH . E 5 HOH A 122 229 229 HOH HOH . E 5 HOH A 123 230 230 HOH HOH . E 5 HOH A 124 231 231 HOH HOH . E 5 HOH A 125 232 232 HOH HOH . E 5 HOH A 126 233 233 HOH HOH . E 5 HOH A 127 234 234 HOH HOH . E 5 HOH A 128 235 235 HOH HOH . E 5 HOH A 129 236 236 HOH HOH . E 5 HOH A 130 237 237 HOH HOH . E 5 HOH A 131 238 238 HOH HOH . E 5 HOH A 132 239 239 HOH HOH . E 5 HOH A 133 240 240 HOH HOH . E 5 HOH A 134 241 241 HOH HOH . E 5 HOH A 135 242 242 HOH HOH . E 5 HOH A 136 243 243 HOH HOH . E 5 HOH A 137 244 244 HOH HOH . E 5 HOH A 138 245 245 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 P SGP . . . D 4 20.827 37.471 19.265 0.35 37.24 ? P SGP 106 A 1 HETATM 2 S S1P SGP . . . D 4 21.029 39.173 19.822 0.35 37.24 ? S1P SGP 106 A 1 HETATM 3 O O1P SGP . . . D 4 21.165 37.521 17.812 0.35 37.2 ? O1P SGP 106 A 1 HETATM 4 O O5' SGP . . . D 4 19.415 36.26 23.529 0.35 33.77 ? O5' SGP 106 A 1 HETATM 5 C C5' SGP . . . D 4 20.761 35.845 23.482 0.35 34.45 ? C5' SGP 106 A 1 HETATM 6 C C4' SGP . . . D 4 21.196 35.133 22.231 0.35 33.86 ? C4' SGP 106 A 1 HETATM 7 O O4' SGP . . . D 4 20.398 33.945 21.955 0.35 33.01 ? O4' SGP 106 A 1 HETATM 8 C C3' SGP . . . D 4 20.907 36.149 21.09 0.35 35.2 ? C3' SGP 106 A 1 HETATM 9 O O3' SGP . . . D 4 21.704 36.273 19.901 0.35 36.82 ? O3' SGP 106 A 1 HETATM 10 C C2' SGP . . . D 4 19.593 35.715 20.549 0.35 34.37 ? C2' SGP 106 A 1 HETATM 11 O O2' SGP . . . D 4 19.609 36.455 19.291 0.35 36.95 ? O2' SGP 106 A 1 HETATM 12 C C1' SGP . . . D 4 19.656 34.122 20.701 0.35 32.21 ? C1' SGP 106 A 1 HETATM 13 N N9 SGP . . . D 4 18.274 33.486 20.861 0.35 29.33 ? N9 SGP 106 A 1 HETATM 14 C C8 SGP . . . D 4 17.798 32.327 20.28 0.35 28.08 ? C8 SGP 106 A 1 HETATM 15 N N7 SGP . . . D 4 16.52 32.094 20.432 0.35 25.89 ? N7 SGP 106 A 1 HETATM 16 C C5 SGP . . . D 4 16.098 33.187 21.187 0.35 25.82 ? C5 SGP 106 A 1 HETATM 17 C C6 SGP . . . D 4 14.804 33.536 21.669 0.35 25.42 ? C6 SGP 106 A 1 HETATM 18 O O6 SGP . . . D 4 13.768 32.929 21.439 0.35 24.33 ? O6 SGP 106 A 1 HETATM 19 N N1 SGP . . . D 4 14.799 34.725 22.401 0.35 24.7 ? N1 SGP 106 A 1 HETATM 20 C C2 SGP . . . D 4 15.912 35.497 22.642 0.35 25.21 ? C2 SGP 106 A 1 HETATM 21 N N2 SGP . . . D 4 15.757 36.601 23.366 0.35 22.59 ? N2 SGP 106 A 1 HETATM 22 N N3 SGP . . . D 4 17.117 35.179 22.183 0.35 25.72 ? N3 SGP 106 A 1 HETATM 23 C C4 SGP . . . D 4 17.147 34.025 21.467 0.35 27 ? C4 SGP 106 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 23 #