data_1P2U # _model_server_result.job_id lJT5fJQHCOzWAaqkx0TlBw _model_server_result.datetime_utc '2024-12-01 09:37:13' _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 1p2u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":167}' # _entry.id 1P2U # _exptl.entry_id 1P2U _exptl.method 'X-RAY DIFFRACTION' # _entity.details 'non-hydrolyzable GTP analog' _entity.formula_weight 522.196 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' _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 1P2U _cell.length_a 40.077 _cell.length_b 40.077 _cell.length_c 161.856 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1P2U _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,E,F,G _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 17 A SER 17 1_555 B MG MG . A MG 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc2 A OG1 THR 35 A THR 35 1_555 B MG MG . A MG 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc3 C O2G GNP . A GNP 167 1_555 B MG MG . A MG 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc4 C O2B GNP . A GNP 167 1_555 B MG MG . A MG 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc5 B MG MG . A MG 168 1_555 G O HOH . A HOH 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc6 B MG MG . A MG 168 1_555 G O HOH . A HOH 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? # _chem_comp.formula 'C10 H17 N6 O13 P3' _chem_comp.formula_weight 522.196 _chem_comp.id GNP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' _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 O1G GNP doub 129 n n PG O2G GNP sing 130 n n PG O3G GNP sing 131 n n PG N3B GNP sing 132 n n O2G HOG2 GNP sing 133 n n O3G HOG3 GNP sing 134 n n N3B PB GNP sing 135 n n N3B HNB3 GNP sing 136 n n PB O1B GNP doub 137 n n PB O2B GNP sing 138 n n PB O3A GNP sing 139 n n O2B HOB2 GNP sing 140 n n O3A PA GNP sing 141 n n PA O1A GNP doub 142 n n PA O2A GNP sing 143 n n PA O5' GNP sing 144 n n O2A HOA2 GNP sing 145 n n O5' C5' GNP sing 146 n n C5' C4' GNP sing 147 n n C5' "H5'2" GNP sing 148 n n C5' "H5'1" GNP sing 149 n n C4' O4' GNP sing 150 n n C4' C3' GNP sing 151 n n C4' H4' GNP sing 152 n n O4' C1' GNP sing 153 n n C3' O3' GNP sing 154 n n C3' C2' GNP sing 155 n n C3' H3' GNP sing 156 n n O3' HO3' GNP sing 157 n n C2' O2' GNP sing 158 n n C2' C1' GNP sing 159 n n C2' H2' GNP sing 160 n n O2' HO2' GNP sing 161 n n C1' N9 GNP sing 162 n n C1' H1' GNP sing 163 n n N9 C8 GNP sing 164 n y N9 C4 GNP sing 165 n y C8 N7 GNP doub 166 n y C8 H8 GNP sing 167 n n N7 C5 GNP sing 168 n y C5 C6 GNP sing 169 n y C5 C4 GNP doub 170 n y C6 O6 GNP doub 171 n n C6 N1 GNP sing 172 n y N1 C2 GNP sing 173 n y N1 HN1 GNP sing 174 n n C2 N2 GNP sing 175 n n C2 N3 GNP doub 176 n y N2 HN21 GNP sing 177 n n N2 HN22 GNP sing 178 n n N3 C4 GNP sing 179 n y # _atom_sites.entry_id 1P2U _atom_sites.fract_transf_matrix[1][1] 0.024952 _atom_sites.fract_transf_matrix[1][2] 0.014406 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.028812 _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] 0.006178 _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 1 168 168 MG MG . C 3 GNP A 1 167 167 GNP GNP . D 4 IPA A 1 171 171 IPA ISO . E 4 IPA A 1 172 172 IPA ISO . F 4 IPA A 1 173 173 IPA ISO . G 5 HOH A 1 201 201 HOH HOH . G 5 HOH A 2 202 202 HOH HOH . G 5 HOH A 3 203 203 HOH HOH . G 5 HOH A 4 204 204 HOH HOH . G 5 HOH A 5 205 205 HOH HOH . G 5 HOH A 6 206 206 HOH HOH . G 5 HOH A 7 207 207 HOH HOH . G 5 HOH A 8 208 208 HOH HOH . G 5 HOH A 9 209 209 HOH HOH . G 5 HOH A 10 210 210 HOH HOH . G 5 HOH A 11 211 211 HOH HOH . G 5 HOH A 12 212 212 HOH HOH . G 5 HOH A 13 213 213 HOH HOH . G 5 HOH A 14 214 214 HOH HOH . G 5 HOH A 15 215 215 HOH HOH . G 5 HOH A 16 216 216 HOH HOH . G 5 HOH A 17 217 217 HOH HOH . G 5 HOH A 18 218 218 HOH HOH . G 5 HOH A 19 219 219 HOH HOH . G 5 HOH A 20 220 220 HOH HOH . G 5 HOH A 21 221 221 HOH HOH . G 5 HOH A 22 222 222 HOH HOH . G 5 HOH A 23 223 223 HOH HOH . G 5 HOH A 24 224 224 HOH HOH . G 5 HOH A 25 225 225 HOH HOH . G 5 HOH A 26 226 226 HOH HOH . G 5 HOH A 27 227 227 HOH HOH . G 5 HOH A 28 228 228 HOH HOH . G 5 HOH A 29 229 229 HOH HOH . G 5 HOH A 30 230 230 HOH HOH . G 5 HOH A 31 231 231 HOH HOH . G 5 HOH A 32 232 232 HOH HOH . G 5 HOH A 33 233 233 HOH HOH . G 5 HOH A 34 234 234 HOH HOH . G 5 HOH A 35 235 235 HOH HOH . G 5 HOH A 36 236 236 HOH HOH . G 5 HOH A 37 237 237 HOH HOH . G 5 HOH A 38 238 238 HOH HOH . G 5 HOH A 39 239 239 HOH HOH . G 5 HOH A 40 240 240 HOH HOH . G 5 HOH A 41 241 241 HOH HOH . G 5 HOH A 42 242 242 HOH HOH . G 5 HOH A 43 243 243 HOH HOH . G 5 HOH A 44 244 244 HOH HOH . G 5 HOH A 45 245 245 HOH HOH . G 5 HOH A 46 246 246 HOH HOH . G 5 HOH A 47 247 247 HOH HOH . G 5 HOH A 48 248 248 HOH HOH . G 5 HOH A 49 249 249 HOH HOH . G 5 HOH A 50 250 250 HOH HOH . G 5 HOH A 51 251 251 HOH HOH . G 5 HOH A 52 252 252 HOH HOH . G 5 HOH A 53 253 253 HOH HOH . G 5 HOH A 54 254 254 HOH HOH . G 5 HOH A 55 255 255 HOH HOH . G 5 HOH A 56 256 256 HOH HOH . G 5 HOH A 57 257 257 HOH HOH . G 5 HOH A 58 258 258 HOH HOH . G 5 HOH A 59 259 259 HOH HOH . G 5 HOH A 60 260 260 HOH HOH . G 5 HOH A 61 261 261 HOH HOH . G 5 HOH A 62 262 262 HOH HOH . G 5 HOH A 63 263 263 HOH HOH . G 5 HOH A 64 264 264 HOH HOH . G 5 HOH A 65 265 265 HOH HOH . G 5 HOH A 66 266 266 HOH HOH . G 5 HOH A 67 267 267 HOH HOH . G 5 HOH A 68 268 268 HOH HOH . G 5 HOH A 69 269 269 HOH HOH . G 5 HOH A 70 270 270 HOH HOH . G 5 HOH A 71 271 271 HOH HOH . G 5 HOH A 72 272 272 HOH HOH . G 5 HOH A 73 274 274 HOH HOH . G 5 HOH A 74 275 275 HOH HOH . G 5 HOH A 75 276 276 HOH HOH . G 5 HOH A 76 277 277 HOH HOH . G 5 HOH A 77 278 278 HOH HOH . G 5 HOH A 78 279 279 HOH HOH . G 5 HOH A 79 280 280 HOH HOH . G 5 HOH A 80 281 281 HOH HOH . G 5 HOH A 81 282 282 HOH HOH . G 5 HOH A 82 283 283 HOH HOH . G 5 HOH A 83 286 286 HOH HOH . G 5 HOH A 84 288 288 HOH HOH . G 5 HOH A 85 289 289 HOH HOH . G 5 HOH A 86 290 290 HOH HOH . G 5 HOH A 87 291 291 HOH HOH . G 5 HOH A 88 292 292 HOH HOH . G 5 HOH A 89 293 293 HOH HOH . G 5 HOH A 90 294 294 HOH HOH . G 5 HOH A 91 295 295 HOH HOH . G 5 HOH A 92 296 296 HOH HOH . G 5 HOH A 93 297 297 HOH HOH . G 5 HOH A 94 298 298 HOH HOH . G 5 HOH A 95 299 299 HOH HOH . G 5 HOH A 96 300 300 HOH HOH . G 5 HOH A 97 301 301 HOH HOH . G 5 HOH A 98 302 302 HOH HOH . G 5 HOH A 99 303 303 HOH HOH . G 5 HOH A 100 304 304 HOH HOH . G 5 HOH A 101 305 305 HOH HOH . G 5 HOH A 102 306 306 HOH HOH . G 5 HOH A 103 307 307 HOH HOH . G 5 HOH A 104 308 308 HOH HOH . G 5 HOH A 105 309 309 HOH HOH . G 5 HOH A 106 310 310 HOH HOH . G 5 HOH A 107 311 311 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 GNP . . . C 3 29.989 11.919 48.952 1 13.71 ? PG GNP 167 A 1 HETATM 2 O O1G GNP . . . C 3 30.206 12.341 50.353 1 12.74 ? O1G GNP 167 A 1 HETATM 3 O O2G GNP . . . C 3 30.067 13.06 48.107 1 16.97 ? O2G GNP 167 A 1 HETATM 4 O O3G GNP . . . C 3 28.511 11.566 48.802 1 17.22 ? O3G GNP 167 A 1 HETATM 5 N N3B GNP . . . C 3 30.905 10.62 48.571 1 14.82 ? N3B GNP 167 A 1 HETATM 6 P PB GNP . . . C 3 30.965 9.874 47.097 1 15.3 ? PB GNP 167 A 1 HETATM 7 O O1B GNP . . . C 3 29.833 8.976 46.82 1 13.28 ? O1B GNP 167 A 1 HETATM 8 O O2B GNP . . . C 3 31.271 10.697 45.956 1 14.91 ? O2B GNP 167 A 1 HETATM 9 O O3A GNP . . . C 3 32.25 8.953 47.234 1 13.88 ? O3A GNP 167 A 1 HETATM 10 P PA GNP . . . C 3 33.782 9.249 46.751 1 15.34 ? PA GNP 167 A 1 HETATM 11 O O1A GNP . . . C 3 33.839 9.232 45.266 1 15.89 ? O1A GNP 167 A 1 HETATM 12 O O2A GNP . . . C 3 34.358 10.42 47.452 1 15.26 ? O2A GNP 167 A 1 HETATM 13 O O5' GNP . . . C 3 34.466 7.901 47.247 1 16.83 ? O5' GNP 167 A 1 HETATM 14 C C5' GNP . . . C 3 34.569 7.623 48.676 1 19.43 ? C5' GNP 167 A 1 HETATM 15 C C4' GNP . . . C 3 35.728 6.635 48.946 1 20.97 ? C4' GNP 167 A 1 HETATM 16 O O4' GNP . . . C 3 35.484 5.42 48.185 1 18.01 ? O4' GNP 167 A 1 HETATM 17 C C3' GNP . . . C 3 37.112 7.159 48.48 1 20.52 ? C3' GNP 167 A 1 HETATM 18 O O3' GNP . . . C 3 38.177 6.798 49.394 1 21.77 ? O3' GNP 167 A 1 HETATM 19 C C2' GNP . . . C 3 37.254 6.531 47.102 1 22.59 ? C2' GNP 167 A 1 HETATM 20 O O2' GNP . . . C 3 38.601 6.296 46.671 1 19.13 ? O2' GNP 167 A 1 HETATM 21 C C1' GNP . . . C 3 36.58 5.173 47.305 1 18.98 ? C1' GNP 167 A 1 HETATM 22 N N9 GNP . . . C 3 36.069 4.626 46.037 1 19.44 ? N9 GNP 167 A 1 HETATM 23 C C8 GNP . . . C 3 35.183 5.185 45.114 1 17.72 ? C8 GNP 167 A 1 HETATM 24 N N7 GNP . . . C 3 34.93 4.44 44.088 1 18.46 ? N7 GNP 167 A 1 HETATM 25 C C5 GNP . . . C 3 35.697 3.274 44.325 1 17.6 ? C5 GNP 167 A 1 HETATM 26 C C6 GNP . . . C 3 35.859 2.05 43.552 1 18.75 ? C6 GNP 167 A 1 HETATM 27 O O6 GNP . . . C 3 35.337 1.739 42.475 1 19.22 ? O6 GNP 167 A 1 HETATM 28 N N1 GNP . . . C 3 36.734 1.136 44.167 1 19.19 ? N1 GNP 167 A 1 HETATM 29 C C2 GNP . . . C 3 37.401 1.339 45.384 1 21 ? C2 GNP 167 A 1 HETATM 30 N N2 GNP . . . C 3 38.21 0.36 45.835 1 19.46 ? N2 GNP 167 A 1 HETATM 31 N N3 GNP . . . C 3 37.252 2.48 46.106 1 20.83 ? N3 GNP 167 A 1 HETATM 32 C C4 GNP . . . C 3 36.396 3.398 45.529 1 20.44 ? C4 GNP 167 A 1 # _model_server_stats.io_time_ms 75 _model_server_stats.parse_time_ms 52 _model_server_stats.create_model_time_ms 40 _model_server_stats.query_time_ms 820 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 32 #