data_6X2M # _model_server_result.job_id Bgt6YpJiyWSBJ-hWVyhvHw _model_server_result.datetime_utc '2024-12-22 01:24:54' _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 6x2m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 6X2M # _exptl.entry_id 6X2M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 4 _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 6X2M _cell.length_a 105.313 _cell.length_b 105.313 _cell.length_c 306.71 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6X2M _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 ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,H,I _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 metalc ? metalc1 A OG1 THR 24 A THR 24 1_555 E MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc2 A OG1 THR 42 A THR 42 1_555 E MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? metalc ? metalc3 D O3G GNP . A GNP 301 1_555 E MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc4 D O1B GNP . A GNP 301 1_555 E MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? # _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 6X2M _atom_sites.fract_transf_matrix[1][1] 0.009496 _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] 0.009496 _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] 0.00326 _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 GNP A 1 301 301 GNP GNP . E 5 MG A 1 302 302 MG MG . F 6 GOL C 1 1101 1 GOL GOL . G 7 HOH A 1 401 53 HOH HOH . G 7 HOH A 2 402 36 HOH HOH . G 7 HOH A 3 403 19 HOH HOH . G 7 HOH A 4 404 30 HOH HOH . G 7 HOH A 5 405 105 HOH HOH . G 7 HOH A 6 406 138 HOH HOH . G 7 HOH A 7 407 33 HOH HOH . G 7 HOH A 8 408 133 HOH HOH . G 7 HOH A 9 409 136 HOH HOH . G 7 HOH A 10 410 51 HOH HOH . G 7 HOH A 11 411 65 HOH HOH . G 7 HOH A 12 412 39 HOH HOH . G 7 HOH A 13 413 68 HOH HOH . G 7 HOH A 14 414 90 HOH HOH . G 7 HOH A 15 415 104 HOH HOH . G 7 HOH A 16 416 99 HOH HOH . G 7 HOH A 17 417 22 HOH HOH . G 7 HOH A 18 418 16 HOH HOH . G 7 HOH A 19 419 24 HOH HOH . G 7 HOH A 20 420 131 HOH HOH . G 7 HOH A 21 421 109 HOH HOH . G 7 HOH A 22 422 12 HOH HOH . G 7 HOH A 23 423 96 HOH HOH . G 7 HOH A 24 424 1 HOH HOH . G 7 HOH A 25 425 115 HOH HOH . H 7 HOH B 1 301 91 HOH HOH . H 7 HOH B 2 302 2 HOH HOH . H 7 HOH B 3 303 125 HOH HOH . H 7 HOH B 4 304 72 HOH HOH . H 7 HOH B 5 305 45 HOH HOH . H 7 HOH B 6 306 10 HOH HOH . H 7 HOH B 7 307 75 HOH HOH . H 7 HOH B 8 308 85 HOH HOH . I 7 HOH C 1 1201 21 HOH HOH . I 7 HOH C 2 1202 5 HOH HOH . I 7 HOH C 3 1203 49 HOH HOH . I 7 HOH C 4 1204 54 HOH HOH . I 7 HOH C 5 1205 84 HOH HOH . I 7 HOH C 6 1206 76 HOH HOH . I 7 HOH C 7 1207 4 HOH HOH . I 7 HOH C 8 1208 14 HOH HOH . I 7 HOH C 9 1209 128 HOH HOH . I 7 HOH C 10 1210 103 HOH HOH . I 7 HOH C 11 1211 63 HOH HOH . I 7 HOH C 12 1212 8 HOH HOH . I 7 HOH C 13 1213 108 HOH HOH . I 7 HOH C 14 1214 13 HOH HOH . I 7 HOH C 15 1215 134 HOH HOH . I 7 HOH C 16 1216 98 HOH HOH . I 7 HOH C 17 1217 92 HOH HOH . I 7 HOH C 18 1218 28 HOH HOH . I 7 HOH C 19 1219 29 HOH HOH . I 7 HOH C 20 1220 52 HOH HOH . I 7 HOH C 21 1221 37 HOH HOH . I 7 HOH C 22 1222 123 HOH HOH . I 7 HOH C 23 1223 34 HOH HOH . I 7 HOH C 24 1224 120 HOH HOH . I 7 HOH C 25 1225 126 HOH HOH . I 7 HOH C 26 1226 106 HOH HOH . I 7 HOH C 27 1227 59 HOH HOH . I 7 HOH C 28 1228 47 HOH HOH . I 7 HOH C 29 1229 94 HOH HOH . I 7 HOH C 30 1230 23 HOH HOH . I 7 HOH C 31 1231 80 HOH HOH . I 7 HOH C 32 1232 61 HOH HOH . I 7 HOH C 33 1233 95 HOH HOH . I 7 HOH C 34 1234 127 HOH HOH . I 7 HOH C 35 1235 97 HOH HOH . I 7 HOH C 36 1236 15 HOH HOH . I 7 HOH C 37 1237 43 HOH HOH . I 7 HOH C 38 1238 83 HOH HOH . I 7 HOH C 39 1239 42 HOH HOH . I 7 HOH C 40 1240 79 HOH HOH . I 7 HOH C 41 1241 60 HOH HOH . I 7 HOH C 42 1242 46 HOH HOH . I 7 HOH C 43 1243 88 HOH HOH . I 7 HOH C 44 1244 40 HOH HOH . I 7 HOH C 45 1245 58 HOH HOH . I 7 HOH C 46 1246 38 HOH HOH . I 7 HOH C 47 1247 118 HOH HOH . I 7 HOH C 48 1248 129 HOH HOH . I 7 HOH C 49 1249 56 HOH HOH . I 7 HOH C 50 1250 70 HOH HOH . I 7 HOH C 51 1251 77 HOH HOH . I 7 HOH C 52 1252 6 HOH HOH . I 7 HOH C 53 1253 81 HOH HOH . I 7 HOH C 54 1254 116 HOH HOH . I 7 HOH C 55 1255 25 HOH HOH . I 7 HOH C 56 1256 3 HOH HOH . I 7 HOH C 57 1257 62 HOH HOH . I 7 HOH C 58 1258 78 HOH HOH . I 7 HOH C 59 1259 67 HOH HOH . I 7 HOH C 60 1260 101 HOH HOH . I 7 HOH C 61 1261 102 HOH HOH . I 7 HOH C 62 1262 89 HOH HOH . I 7 HOH C 63 1263 100 HOH HOH . I 7 HOH C 64 1264 11 HOH HOH . I 7 HOH C 65 1265 122 HOH HOH . I 7 HOH C 66 1266 20 HOH HOH . I 7 HOH C 67 1267 66 HOH HOH . I 7 HOH C 68 1268 82 HOH HOH . I 7 HOH C 69 1269 71 HOH HOH . I 7 HOH C 70 1270 41 HOH HOH . I 7 HOH C 71 1271 44 HOH HOH . I 7 HOH C 72 1272 124 HOH HOH . I 7 HOH C 73 1273 55 HOH HOH . I 7 HOH C 74 1274 119 HOH HOH . I 7 HOH C 75 1275 137 HOH HOH . I 7 HOH C 76 1276 17 HOH HOH . I 7 HOH C 77 1277 121 HOH HOH . I 7 HOH C 78 1278 87 HOH HOH . I 7 HOH C 79 1279 130 HOH HOH . I 7 HOH C 80 1280 27 HOH HOH . I 7 HOH C 81 1281 50 HOH HOH . I 7 HOH C 82 1282 7 HOH HOH . I 7 HOH C 83 1283 111 HOH HOH . I 7 HOH C 84 1284 64 HOH HOH . I 7 HOH C 85 1285 135 HOH HOH . I 7 HOH C 86 1286 74 HOH HOH . I 7 HOH C 87 1287 35 HOH HOH . I 7 HOH C 88 1288 26 HOH HOH . I 7 HOH C 89 1289 48 HOH HOH . I 7 HOH C 90 1290 112 HOH HOH . I 7 HOH C 91 1291 32 HOH HOH . I 7 HOH C 92 1292 9 HOH HOH . I 7 HOH C 93 1293 107 HOH HOH . I 7 HOH C 94 1294 69 HOH HOH . I 7 HOH C 95 1295 18 HOH HOH . I 7 HOH C 96 1296 57 HOH HOH . I 7 HOH C 97 1297 93 HOH HOH . I 7 HOH C 98 1298 73 HOH HOH . I 7 HOH C 99 1299 114 HOH HOH . I 7 HOH C 100 1300 132 HOH HOH . I 7 HOH C 101 1301 86 HOH HOH . I 7 HOH C 102 1302 113 HOH HOH . I 7 HOH C 103 1303 110 HOH HOH . I 7 HOH C 104 1304 31 HOH HOH . I 7 HOH C 105 1305 117 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 . . . D 4 59.999 -15.031 28.029 1 19.37 ? PG GNP 301 A 1 HETATM 2 O O1G GNP . . . D 4 60.152 -16.388 27.365 1 24.35 ? O1G GNP 301 A 1 HETATM 3 O O2G GNP . . . D 4 59.671 -15.223 29.526 1 24.35 ? O2G GNP 301 A 1 HETATM 4 O O3G GNP . . . D 4 61.321 -14.238 27.882 1 24.34 ? O3G GNP 301 A 1 HETATM 5 N N3B GNP . . . D 4 58.76 -14.168 27.268 1 21.32 ? N3B GNP 301 A 1 HETATM 6 P PB GNP . . . D 4 58.242 -12.671 27.885 1 41.78 ? PB GNP 301 A 1 HETATM 7 O O1B GNP . . . D 4 59.467 -11.789 28.211 1 25.06 ? O1B GNP 301 A 1 HETATM 8 O O2B GNP . . . D 4 57.422 -12.879 29.134 1 18.33 ? O2B GNP 301 A 1 HETATM 9 O O3A GNP . . . D 4 57.315 -11.902 26.725 1 17.39 ? O3A GNP 301 A 1 HETATM 10 P PA GNP . . . D 4 57.953 -10.856 25.591 1 34.47 ? PA GNP 301 A 1 HETATM 11 O O1A GNP . . . D 4 59.291 -11.368 25.126 1 18.95 ? O1A GNP 301 A 1 HETATM 12 O O2A GNP . . . D 4 58.126 -9.471 26.215 1 18.95 ? O2A GNP 301 A 1 HETATM 13 O O5' GNP . . . D 4 56.911 -10.763 24.271 1 18.25 ? O5' GNP 301 A 1 HETATM 14 C C5' GNP . . . D 4 55.89 -11.715 24.158 1 23.69 ? C5' GNP 301 A 1 HETATM 15 C C4' GNP . . . D 4 54.911 -11.299 23.076 1 20.83 ? C4' GNP 301 A 1 HETATM 16 O O4' GNP . . . D 4 53.845 -10.73 23.622 1 22.1 ? O4' GNP 301 A 1 HETATM 17 C C3' GNP . . . D 4 55.543 -10.244 22.155 1 23.06 ? C3' GNP 301 A 1 HETATM 18 O O3' GNP . . . D 4 55.216 -10.493 20.867 1 21.44 ? O3' GNP 301 A 1 HETATM 19 C C2' GNP . . . D 4 54.918 -8.902 22.617 1 20.71 ? C2' GNP 301 A 1 HETATM 20 O O2' GNP . . . D 4 54.833 -7.93 21.446 1 22.15 ? O2' GNP 301 A 1 HETATM 21 C C1' GNP . . . D 4 53.721 -9.237 23.023 1 23.29 ? C1' GNP 301 A 1 HETATM 22 N N9 GNP . . . D 4 53.276 -8.34 24.049 1 21.94 ? N9 GNP 301 A 1 HETATM 23 C C8 GNP . . . D 4 53.882 -7.915 25.187 1 23.33 ? C8 GNP 301 A 1 HETATM 24 N N7 GNP . . . D 4 53.058 -7.093 25.8 1 23.29 ? N7 GNP 301 A 1 HETATM 25 C C5 GNP . . . D 4 51.931 -6.997 25.055 1 22.92 ? C5 GNP 301 A 1 HETATM 26 C C6 GNP . . . D 4 50.772 -6.289 25.227 1 23.94 ? C6 GNP 301 A 1 HETATM 27 O O6 GNP . . . D 4 50.636 -5.601 26.179 1 23.6 ? O6 GNP 301 A 1 HETATM 28 N N1 GNP . . . D 4 49.804 -6.375 24.327 1 23.44 ? N1 GNP 301 A 1 HETATM 29 C C2 GNP . . . D 4 49.961 -7.163 23.235 1 24.19 ? C2 GNP 301 A 1 HETATM 30 N N2 GNP . . . D 4 48.798 -7.221 22.222 1 23.74 ? N2 GNP 301 A 1 HETATM 31 N N3 GNP . . . D 4 51.095 -7.857 23.065 1 23.05 ? N3 GNP 301 A 1 HETATM 32 C C4 GNP . . . D 4 52.081 -7.77 23.982 1 24.22 ? C4 GNP 301 A 1 # _model_server_stats.io_time_ms 36 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 32 #