data_6X2R # _model_server_result.job_id cK3Kq3t0DI_ufSjG7w_H6Q _model_server_result.datetime_utc '2024-10-20 12:31:25' _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 6x2r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 6X2R # _exptl.entry_id 6X2R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 5 _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 90 _cell.entry_id 6X2R _cell.length_a 106.602 _cell.length_b 106.602 _cell.length_c 303.674 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6X2R _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,L _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 5 _struct_asym.id E _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 OG1 THR 24 A THR 24 1_555 F MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc2 A OG1 THR 42 A THR 42 1_555 F MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? metalc ? metalc3 E O2G GNP . A GNP 301 1_555 F MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc4 E O1B GNP . A GNP 301 1_555 F MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? # _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 6X2R _atom_sites.fract_transf_matrix[1][1] 0.009381 _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] 0.009381 _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] 0.003293 _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 5 GNP A 1 301 301 GNP GNP . F 6 MG A 1 302 302 MG MG . G 7 GOL A 1 303 303 GOL GOL . H 7 GOL C 1 1101 1101 GOL GOL . I 7 GOL C 1 1102 1102 GOL GOL . J 8 HOH A 1 401 164 HOH HOH . J 8 HOH A 2 402 129 HOH HOH . J 8 HOH A 3 403 26 HOH HOH . J 8 HOH A 4 404 46 HOH HOH . J 8 HOH A 5 405 161 HOH HOH . J 8 HOH A 6 406 116 HOH HOH . J 8 HOH A 7 407 119 HOH HOH . J 8 HOH A 8 408 23 HOH HOH . J 8 HOH A 9 409 13 HOH HOH . J 8 HOH A 10 410 37 HOH HOH . J 8 HOH A 11 411 77 HOH HOH . J 8 HOH A 12 412 54 HOH HOH . J 8 HOH A 13 413 126 HOH HOH . J 8 HOH A 14 414 162 HOH HOH . J 8 HOH A 15 415 5 HOH HOH . J 8 HOH A 16 416 150 HOH HOH . J 8 HOH A 17 417 30 HOH HOH . J 8 HOH A 18 418 43 HOH HOH . J 8 HOH A 19 419 94 HOH HOH . J 8 HOH A 20 420 143 HOH HOH . J 8 HOH A 21 421 41 HOH HOH . J 8 HOH A 22 422 71 HOH HOH . J 8 HOH A 23 423 20 HOH HOH . J 8 HOH A 24 424 42 HOH HOH . J 8 HOH A 25 425 78 HOH HOH . J 8 HOH A 26 426 115 HOH HOH . J 8 HOH A 27 427 123 HOH HOH . J 8 HOH A 28 428 160 HOH HOH . K 8 HOH B 1 301 127 HOH HOH . K 8 HOH B 2 302 151 HOH HOH . K 8 HOH B 3 303 125 HOH HOH . L 8 HOH C 1 1201 84 HOH HOH . L 8 HOH C 2 1202 9 HOH HOH . L 8 HOH C 3 1203 159 HOH HOH . L 8 HOH C 4 1204 157 HOH HOH . L 8 HOH C 5 1205 100 HOH HOH . L 8 HOH C 6 1206 138 HOH HOH . L 8 HOH C 7 1207 95 HOH HOH . L 8 HOH C 8 1208 163 HOH HOH . L 8 HOH C 9 1209 118 HOH HOH . L 8 HOH C 10 1210 99 HOH HOH . L 8 HOH C 11 1211 103 HOH HOH . L 8 HOH C 12 1212 142 HOH HOH . L 8 HOH C 13 1213 120 HOH HOH . L 8 HOH C 14 1214 59 HOH HOH . L 8 HOH C 15 1215 56 HOH HOH . L 8 HOH C 16 1216 102 HOH HOH . L 8 HOH C 17 1217 131 HOH HOH . L 8 HOH C 18 1218 35 HOH HOH . L 8 HOH C 19 1219 72 HOH HOH . L 8 HOH C 20 1220 24 HOH HOH . L 8 HOH C 21 1221 124 HOH HOH . L 8 HOH C 22 1222 53 HOH HOH . L 8 HOH C 23 1223 101 HOH HOH . L 8 HOH C 24 1224 111 HOH HOH . L 8 HOH C 25 1225 17 HOH HOH . L 8 HOH C 26 1226 44 HOH HOH . L 8 HOH C 27 1227 70 HOH HOH . L 8 HOH C 28 1228 86 HOH HOH . L 8 HOH C 29 1229 14 HOH HOH . L 8 HOH C 30 1230 63 HOH HOH . L 8 HOH C 31 1231 98 HOH HOH . L 8 HOH C 32 1232 48 HOH HOH . L 8 HOH C 33 1233 50 HOH HOH . L 8 HOH C 34 1234 25 HOH HOH . L 8 HOH C 35 1235 11 HOH HOH . L 8 HOH C 36 1236 170 HOH HOH . L 8 HOH C 37 1237 107 HOH HOH . L 8 HOH C 38 1238 47 HOH HOH . L 8 HOH C 39 1239 6 HOH HOH . L 8 HOH C 40 1240 88 HOH HOH . L 8 HOH C 41 1241 133 HOH HOH . L 8 HOH C 42 1242 40 HOH HOH . L 8 HOH C 43 1243 52 HOH HOH . L 8 HOH C 44 1244 158 HOH HOH . L 8 HOH C 45 1245 153 HOH HOH . L 8 HOH C 46 1246 22 HOH HOH . L 8 HOH C 47 1247 27 HOH HOH . L 8 HOH C 48 1248 10 HOH HOH . L 8 HOH C 49 1249 45 HOH HOH . L 8 HOH C 50 1250 2 HOH HOH . L 8 HOH C 51 1251 1 HOH HOH . L 8 HOH C 52 1252 73 HOH HOH . L 8 HOH C 53 1253 18 HOH HOH . L 8 HOH C 54 1254 16 HOH HOH . L 8 HOH C 55 1255 19 HOH HOH . L 8 HOH C 56 1256 36 HOH HOH . L 8 HOH C 57 1257 31 HOH HOH . L 8 HOH C 58 1258 4 HOH HOH . L 8 HOH C 59 1259 134 HOH HOH . L 8 HOH C 60 1260 130 HOH HOH . L 8 HOH C 61 1261 135 HOH HOH . L 8 HOH C 62 1262 15 HOH HOH . L 8 HOH C 63 1263 169 HOH HOH . L 8 HOH C 64 1264 7 HOH HOH . L 8 HOH C 65 1265 92 HOH HOH . L 8 HOH C 66 1266 12 HOH HOH . L 8 HOH C 67 1267 109 HOH HOH . L 8 HOH C 68 1268 39 HOH HOH . L 8 HOH C 69 1269 58 HOH HOH . L 8 HOH C 70 1270 28 HOH HOH . L 8 HOH C 71 1271 29 HOH HOH . L 8 HOH C 72 1272 105 HOH HOH . L 8 HOH C 73 1273 110 HOH HOH . L 8 HOH C 74 1274 122 HOH HOH . L 8 HOH C 75 1275 65 HOH HOH . L 8 HOH C 76 1276 106 HOH HOH . L 8 HOH C 77 1277 66 HOH HOH . L 8 HOH C 78 1278 51 HOH HOH . L 8 HOH C 79 1279 34 HOH HOH . L 8 HOH C 80 1280 141 HOH HOH . L 8 HOH C 81 1281 57 HOH HOH . L 8 HOH C 82 1282 83 HOH HOH . L 8 HOH C 83 1283 32 HOH HOH . L 8 HOH C 84 1284 38 HOH HOH . L 8 HOH C 85 1285 75 HOH HOH . L 8 HOH C 86 1286 21 HOH HOH . L 8 HOH C 87 1287 61 HOH HOH . L 8 HOH C 88 1288 121 HOH HOH . L 8 HOH C 89 1289 104 HOH HOH . L 8 HOH C 90 1290 3 HOH HOH . L 8 HOH C 91 1291 97 HOH HOH . L 8 HOH C 92 1292 33 HOH HOH . L 8 HOH C 93 1293 68 HOH HOH . L 8 HOH C 94 1294 80 HOH HOH . L 8 HOH C 95 1295 62 HOH HOH . L 8 HOH C 96 1296 55 HOH HOH . L 8 HOH C 97 1297 91 HOH HOH . L 8 HOH C 98 1298 81 HOH HOH . L 8 HOH C 99 1299 117 HOH HOH . L 8 HOH C 100 1300 69 HOH HOH . L 8 HOH C 101 1301 82 HOH HOH . L 8 HOH C 102 1302 137 HOH HOH . L 8 HOH C 103 1303 79 HOH HOH . L 8 HOH C 104 1304 67 HOH HOH . L 8 HOH C 105 1305 149 HOH HOH . L 8 HOH C 106 1306 76 HOH HOH . L 8 HOH C 107 1307 96 HOH HOH . L 8 HOH C 108 1308 8 HOH HOH . L 8 HOH C 109 1309 89 HOH HOH . L 8 HOH C 110 1310 113 HOH HOH . L 8 HOH C 111 1311 166 HOH HOH . L 8 HOH C 112 1312 156 HOH HOH . L 8 HOH C 113 1313 85 HOH HOH . L 8 HOH C 114 1314 168 HOH HOH . L 8 HOH C 115 1315 136 HOH HOH . L 8 HOH C 116 1316 60 HOH HOH . L 8 HOH C 117 1317 145 HOH HOH . L 8 HOH C 118 1318 167 HOH HOH . L 8 HOH C 119 1319 108 HOH HOH . L 8 HOH C 120 1320 49 HOH HOH . L 8 HOH C 121 1321 90 HOH HOH . L 8 HOH C 122 1322 132 HOH HOH . L 8 HOH C 123 1323 146 HOH HOH . L 8 HOH C 124 1324 154 HOH HOH . L 8 HOH C 125 1325 165 HOH HOH . L 8 HOH C 126 1326 148 HOH HOH . L 8 HOH C 127 1327 93 HOH HOH . L 8 HOH C 128 1328 64 HOH HOH . L 8 HOH C 129 1329 128 HOH HOH . L 8 HOH C 130 1330 147 HOH HOH . L 8 HOH C 131 1331 155 HOH HOH . L 8 HOH C 132 1332 144 HOH HOH . L 8 HOH C 133 1333 152 HOH HOH . L 8 HOH C 134 1334 87 HOH HOH . L 8 HOH C 135 1335 114 HOH HOH . L 8 HOH C 136 1336 112 HOH HOH . L 8 HOH C 137 1337 140 HOH HOH . L 8 HOH C 138 1338 139 HOH HOH . L 8 HOH C 139 1339 74 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 . . . E 5 6.708 37.464 28.328 1 50.07 ? PG GNP 301 A 1 HETATM 2 O O1G GNP . . . E 5 7.008 36.175 27.583 1 51.42 ? O1G GNP 301 A 1 HETATM 3 O O2G GNP . . . E 5 7.998 38.295 28.459 1 51.86 ? O2G GNP 301 A 1 HETATM 4 O O3G GNP . . . E 5 6.156 37.148 29.741 1 48.86 ? O3G GNP 301 A 1 HETATM 5 N N3B GNP . . . E 5 5.579 38.368 27.458 1 49.49 ? N3B GNP 301 A 1 HETATM 6 P PB GNP . . . E 5 5.026 39.859 28.049 1 48.91 ? PB GNP 301 A 1 HETATM 7 O O1B GNP . . . E 5 6.235 40.752 28.406 1 50.41 ? O1B GNP 301 A 1 HETATM 8 O O2B GNP . . . E 5 4.172 39.646 29.274 1 47.34 ? O2B GNP 301 A 1 HETATM 9 O O3A GNP . . . E 5 4.132 40.595 26.842 1 49.76 ? O3A GNP 301 A 1 HETATM 10 P PA GNP . . . E 5 4.807 41.612 25.701 1 51.05 ? PA GNP 301 A 1 HETATM 11 O O1A GNP . . . E 5 6.126 41.044 25.247 1 53.24 ? O1A GNP 301 A 1 HETATM 12 O O2A GNP . . . E 5 5.037 42.987 26.327 1 50.98 ? O2A GNP 301 A 1 HETATM 13 O O5' GNP . . . E 5 3.784 41.753 24.368 1 52.25 ? O5' GNP 301 A 1 HETATM 14 C C5' GNP . . . E 5 2.855 40.737 24.115 1 51.68 ? C5' GNP 301 A 1 HETATM 15 C C4' GNP . . . E 5 1.936 41.149 22.981 1 52.51 ? C4' GNP 301 A 1 HETATM 16 O O4' GNP . . . E 5 0.85 41.73 23.47 1 51.48 ? O4' GNP 301 A 1 HETATM 17 C C3' GNP . . . E 5 2.622 42.186 22.077 1 54.87 ? C3' GNP 301 A 1 HETATM 18 O O3' GNP . . . E 5 2.404 41.887 20.776 1 55.95 ? O3' GNP 301 A 1 HETATM 19 C C2' GNP . . . E 5 1.953 43.539 22.434 1 53.89 ? C2' GNP 301 A 1 HETATM 20 O O2' GNP . . . E 5 1.866 44.425 21.197 1 55.92 ? O2' GNP 301 A 1 HETATM 21 C C1' GNP . . . E 5 0.754 43.215 22.843 1 52.5 ? C1' GNP 301 A 1 HETATM 22 N N9 GNP . . . E 5 0.306 44.129 23.853 1 51.64 ? N9 GNP 301 A 1 HETATM 23 C C8 GNP . . . E 5 0.866 44.521 25.026 1 50.91 ? C8 GNP 301 A 1 HETATM 24 N N7 GNP . . . E 5 0.049 45.382 25.595 1 50.08 ? N7 GNP 301 A 1 HETATM 25 C C5 GNP . . . E 5 -1.028 45.534 24.786 1 50.55 ? C5 GNP 301 A 1 HETATM 26 C C6 GNP . . . E 5 -2.162 46.296 24.89 1 50.67 ? C6 GNP 301 A 1 HETATM 27 O O6 GNP . . . E 5 -2.325 46.989 25.833 1 49.74 ? O6 GNP 301 A 1 HETATM 28 N N1 GNP . . . E 5 -3.075 46.254 23.932 1 52.96 ? N1 GNP 301 A 1 HETATM 29 C C2 GNP . . . E 5 -2.885 45.458 22.852 1 53.98 ? C2 GNP 301 A 1 HETATM 30 N N2 GNP . . . E 5 -3.972 45.445 21.762 1 56.52 ? N2 GNP 301 A 1 HETATM 31 N N3 GNP . . . E 5 -1.779 44.713 22.748 1 52.96 ? N3 GNP 301 A 1 HETATM 32 C C4 GNP . . . E 5 -0.851 44.756 23.722 1 51.51 ? C4 GNP 301 A 1 # _model_server_stats.io_time_ms 76 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 45 _model_server_stats.query_time_ms 369 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #