data_4NYJ # _model_server_result.job_id tXqF1hz5VvD1j4eGiV9csQ _model_server_result.datetime_utc '2024-12-09 13:39:26' _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 4nyj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":202}' # _entry.id 4NYJ # _exptl.entry_id 4NYJ _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 4NYJ _cell.length_a 185.338 _cell.length_b 185.338 _cell.length_c 179.535 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NYJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 4 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 OG SER 17 Q SER 17 1_555 D MG MG . Q MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc2 A OG1 THR 35 Q THR 35 1_555 D MG MG . Q MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc3 D MG MG . Q MG 201 1_555 E O1G GNP . Q GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? metalc ? metalc4 D MG MG . Q MG 201 1_555 E O1B GNP . Q GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc5 D MG MG . Q MG 201 1_555 G O HOH . Q HOH 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? metalc ? metalc6 D MG MG . Q MG 201 1_555 G O HOH . Q HOH 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? # _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 174 n n PG O2G GNP sing 175 n n PG O3G GNP sing 176 n n PG N3B GNP sing 177 n n O2G HOG2 GNP sing 178 n n O3G HOG3 GNP sing 179 n n N3B PB GNP sing 180 n n N3B HNB3 GNP sing 181 n n PB O1B GNP doub 182 n n PB O2B GNP sing 183 n n PB O3A GNP sing 184 n n O2B HOB2 GNP sing 185 n n O3A PA GNP sing 186 n n PA O1A GNP doub 187 n n PA O2A GNP sing 188 n n PA O5' GNP sing 189 n n O2A HOA2 GNP sing 190 n n O5' C5' GNP sing 191 n n C5' C4' GNP sing 192 n n C5' "H5'2" GNP sing 193 n n C5' "H5'1" GNP sing 194 n n C4' O4' GNP sing 195 n n C4' C3' GNP sing 196 n n C4' H4' GNP sing 197 n n O4' C1' GNP sing 198 n n C3' O3' GNP sing 199 n n C3' C2' GNP sing 200 n n C3' H3' GNP sing 201 n n O3' HO3' GNP sing 202 n n C2' O2' GNP sing 203 n n C2' C1' GNP sing 204 n n C2' H2' GNP sing 205 n n O2' HO2' GNP sing 206 n n C1' N9 GNP sing 207 n n C1' H1' GNP sing 208 n n N9 C8 GNP sing 209 n y N9 C4 GNP sing 210 n y C8 N7 GNP doub 211 n y C8 H8 GNP sing 212 n n N7 C5 GNP sing 213 n y C5 C6 GNP sing 214 n y C5 C4 GNP doub 215 n y C6 O6 GNP doub 216 n n C6 N1 GNP sing 217 n y N1 C2 GNP sing 218 n y N1 HN1 GNP sing 219 n n C2 N2 GNP sing 220 n n C2 N3 GNP doub 221 n y N2 HN21 GNP sing 222 n n N2 HN22 GNP sing 223 n n N3 C4 GNP sing 224 n y # _atom_sites.entry_id 4NYJ _atom_sites.fract_transf_matrix[1][1] 0.005396 _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] 0.005396 _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] 0.00557 _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 MG Q 1 201 201 MG MG . E 5 GNP Q 1 202 202 GNP GNP . F 6 2PZ S 1 1101 1101 2PZ 2PZ . G 7 HOH Q 1 301 1 HOH HOH . G 7 HOH Q 2 302 2 HOH HOH . G 7 HOH Q 3 303 3 HOH HOH . G 7 HOH Q 4 304 4 HOH HOH . G 7 HOH Q 5 305 5 HOH HOH . G 7 HOH Q 6 306 6 HOH HOH . G 7 HOH Q 7 307 8 HOH HOH . G 7 HOH Q 8 308 9 HOH HOH . G 7 HOH Q 9 309 90 HOH HOH . G 7 HOH Q 10 310 93 HOH HOH . G 7 HOH Q 11 311 100 HOH HOH . G 7 HOH Q 12 312 110 HOH HOH . G 7 HOH Q 13 313 115 HOH HOH . G 7 HOH Q 14 314 119 HOH HOH . H 7 HOH R 1 201 11 HOH HOH . H 7 HOH R 2 202 12 HOH HOH . H 7 HOH R 3 203 13 HOH HOH . H 7 HOH R 4 204 14 HOH HOH . H 7 HOH R 5 205 15 HOH HOH . H 7 HOH R 6 206 16 HOH HOH . H 7 HOH R 7 207 17 HOH HOH . H 7 HOH R 8 208 18 HOH HOH . H 7 HOH R 9 209 19 HOH HOH . H 7 HOH R 10 210 20 HOH HOH . H 7 HOH R 11 211 21 HOH HOH . H 7 HOH R 12 212 22 HOH HOH . H 7 HOH R 13 213 23 HOH HOH . H 7 HOH R 14 214 24 HOH HOH . H 7 HOH R 15 215 26 HOH HOH . H 7 HOH R 16 216 96 HOH HOH . H 7 HOH R 17 217 114 HOH HOH . H 7 HOH R 18 218 117 HOH HOH . H 7 HOH R 19 219 121 HOH HOH . H 7 HOH R 20 220 123 HOH HOH . H 7 HOH R 21 221 127 HOH HOH . H 7 HOH R 22 222 134 HOH HOH . H 7 HOH R 23 223 137 HOH HOH . I 7 HOH S 1 1201 7 HOH HOH . I 7 HOH S 2 1202 27 HOH HOH . I 7 HOH S 3 1203 28 HOH HOH . I 7 HOH S 4 1204 29 HOH HOH . I 7 HOH S 5 1205 30 HOH HOH . I 7 HOH S 6 1206 31 HOH HOH . I 7 HOH S 7 1207 32 HOH HOH . I 7 HOH S 8 1208 33 HOH HOH . I 7 HOH S 9 1209 34 HOH HOH . I 7 HOH S 10 1210 35 HOH HOH . I 7 HOH S 11 1211 38 HOH HOH . I 7 HOH S 12 1212 39 HOH HOH . I 7 HOH S 13 1213 40 HOH HOH . I 7 HOH S 14 1214 41 HOH HOH . I 7 HOH S 15 1215 42 HOH HOH . I 7 HOH S 16 1216 43 HOH HOH . I 7 HOH S 17 1217 45 HOH HOH . I 7 HOH S 18 1218 46 HOH HOH . I 7 HOH S 19 1219 48 HOH HOH . I 7 HOH S 20 1220 49 HOH HOH . I 7 HOH S 21 1221 50 HOH HOH . I 7 HOH S 22 1222 51 HOH HOH . I 7 HOH S 23 1223 52 HOH HOH . I 7 HOH S 24 1224 53 HOH HOH . I 7 HOH S 25 1225 55 HOH HOH . I 7 HOH S 26 1226 56 HOH HOH . I 7 HOH S 27 1227 58 HOH HOH . I 7 HOH S 28 1228 59 HOH HOH . I 7 HOH S 29 1229 60 HOH HOH . I 7 HOH S 30 1230 61 HOH HOH . I 7 HOH S 31 1231 62 HOH HOH . I 7 HOH S 32 1232 63 HOH HOH . I 7 HOH S 33 1233 64 HOH HOH . I 7 HOH S 34 1234 65 HOH HOH . I 7 HOH S 35 1235 66 HOH HOH . I 7 HOH S 36 1236 67 HOH HOH . I 7 HOH S 37 1237 68 HOH HOH . I 7 HOH S 38 1238 69 HOH HOH . I 7 HOH S 39 1239 70 HOH HOH . I 7 HOH S 40 1240 71 HOH HOH . I 7 HOH S 41 1241 72 HOH HOH . I 7 HOH S 42 1242 73 HOH HOH . I 7 HOH S 43 1243 74 HOH HOH . I 7 HOH S 44 1244 75 HOH HOH . I 7 HOH S 45 1245 76 HOH HOH . I 7 HOH S 46 1246 77 HOH HOH . I 7 HOH S 47 1247 78 HOH HOH . I 7 HOH S 48 1248 79 HOH HOH . I 7 HOH S 49 1249 80 HOH HOH . I 7 HOH S 50 1250 81 HOH HOH . I 7 HOH S 51 1251 82 HOH HOH . I 7 HOH S 52 1252 84 HOH HOH . I 7 HOH S 53 1253 85 HOH HOH . I 7 HOH S 54 1254 86 HOH HOH . I 7 HOH S 55 1255 87 HOH HOH . I 7 HOH S 56 1256 88 HOH HOH . I 7 HOH S 57 1257 89 HOH HOH . I 7 HOH S 58 1258 91 HOH HOH . I 7 HOH S 59 1259 92 HOH HOH . I 7 HOH S 60 1260 94 HOH HOH . I 7 HOH S 61 1261 95 HOH HOH . I 7 HOH S 62 1262 97 HOH HOH . I 7 HOH S 63 1263 98 HOH HOH . I 7 HOH S 64 1264 99 HOH HOH . I 7 HOH S 65 1265 102 HOH HOH . I 7 HOH S 66 1266 103 HOH HOH . I 7 HOH S 67 1267 104 HOH HOH . I 7 HOH S 68 1268 105 HOH HOH . I 7 HOH S 69 1269 106 HOH HOH . I 7 HOH S 70 1270 107 HOH HOH . I 7 HOH S 71 1271 108 HOH HOH . I 7 HOH S 72 1272 109 HOH HOH . I 7 HOH S 73 1273 112 HOH HOH . I 7 HOH S 74 1274 116 HOH HOH . I 7 HOH S 75 1275 118 HOH HOH . I 7 HOH S 76 1276 122 HOH HOH . I 7 HOH S 77 1277 124 HOH HOH . I 7 HOH S 78 1278 125 HOH HOH . I 7 HOH S 79 1279 126 HOH HOH . I 7 HOH S 80 1280 128 HOH HOH . I 7 HOH S 81 1281 129 HOH HOH . I 7 HOH S 82 1282 131 HOH HOH . I 7 HOH S 83 1283 132 HOH HOH . I 7 HOH S 84 1284 133 HOH HOH . I 7 HOH S 85 1285 135 HOH HOH . I 7 HOH S 86 1286 136 HOH HOH . I 7 HOH S 87 1287 138 HOH HOH . I 7 HOH S 88 1288 139 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 -51.434 15.019 -19.282 1 33.69 ? PG GNP 202 Q 1 HETATM 2 O O1G GNP . . . E 5 -50.266 15.264 -20.2 1 38.48 ? O1G GNP 202 Q 1 HETATM 3 O O2G GNP . . . E 5 -51.343 13.762 -18.471 1 42.64 ? O2G GNP 202 Q 1 HETATM 4 O O3G GNP . . . E 5 -51.521 16.26 -18.451 1 36.43 ? O3G GNP 202 Q 1 HETATM 5 N N3B GNP . . . E 5 -52.782 14.91 -20.143 1 28.68 ? N3B GNP 202 Q 1 HETATM 6 P PB GNP . . . E 5 -53.126 15.739 -21.48 1 31.88 ? PB GNP 202 Q 1 HETATM 7 O O1B GNP . . . E 5 -51.921 16.044 -22.271 1 30.07 ? O1B GNP 202 Q 1 HETATM 8 O O2B GNP . . . E 5 -53.9 16.911 -21.062 1 32.71 ? O2B GNP 202 Q 1 HETATM 9 O O3A GNP . . . E 5 -54.069 14.872 -22.314 1 27.08 ? O3A GNP 202 Q 1 HETATM 10 P PA GNP . . . E 5 -53.736 14.13 -23.61 1 31.66 ? PA GNP 202 Q 1 HETATM 11 O O1A GNP . . . E 5 -53.5 15.104 -24.684 1 27.15 ? O1A GNP 202 Q 1 HETATM 12 O O2A GNP . . . E 5 -52.7 13.094 -23.429 1 29.73 ? O2A GNP 202 Q 1 HETATM 13 O O5' GNP . . . E 5 -55.05 13.403 -24.039 1 28.11 ? O5' GNP 202 Q 1 HETATM 14 C C5' GNP . . . E 5 -55.711 12.535 -23.165 1 28.93 ? C5' GNP 202 Q 1 HETATM 15 C C4' GNP . . . E 5 -56.65 11.623 -23.934 1 37.34 ? C4' GNP 202 Q 1 HETATM 16 O O4' GNP . . . E 5 -57.739 12.411 -24.454 1 33.65 ? O4' GNP 202 Q 1 HETATM 17 C C3' GNP . . . E 5 -56.077 10.883 -25.133 1 37.27 ? C3' GNP 202 Q 1 HETATM 18 O O3' GNP . . . E 5 -56.659 9.59 -25.21 1 39.91 ? O3' GNP 202 Q 1 HETATM 19 C C2' GNP . . . E 5 -56.522 11.747 -26.3 1 35.45 ? C2' GNP 202 Q 1 HETATM 20 O O2' GNP . . . E 5 -56.595 11 -27.49 1 41.41 ? O2' GNP 202 Q 1 HETATM 21 C C1' GNP . . . E 5 -57.898 12.213 -25.832 1 34.76 ? C1' GNP 202 Q 1 HETATM 22 N N9 GNP . . . E 5 -58.311 13.499 -26.391 1 37.95 ? N9 GNP 202 Q 1 HETATM 23 C C8 GNP . . . E 5 -57.612 14.675 -26.314 1 36.13 ? C8 GNP 202 Q 1 HETATM 24 N N7 GNP . . . E 5 -58.206 15.669 -26.909 1 35.24 ? N7 GNP 202 Q 1 HETATM 25 C C5 GNP . . . E 5 -59.377 15.122 -27.407 1 33.05 ? C5 GNP 202 Q 1 HETATM 26 C C6 GNP . . . E 5 -60.422 15.717 -28.146 1 37.47 ? C6 GNP 202 Q 1 HETATM 27 O O6 GNP . . . E 5 -60.526 16.885 -28.521 1 40.33 ? O6 GNP 202 Q 1 HETATM 28 N N1 GNP . . . E 5 -61.422 14.814 -28.458 1 36.79 ? N1 GNP 202 Q 1 HETATM 29 C C2 GNP . . . E 5 -61.414 13.497 -28.099 1 36.09 ? C2 GNP 202 Q 1 HETATM 30 N N2 GNP . . . E 5 -62.468 12.767 -28.483 1 38.38 ? N2 GNP 202 Q 1 HETATM 31 N N3 GNP . . . E 5 -60.442 12.929 -27.411 1 40.75 ? N3 GNP 202 Q 1 HETATM 32 C C4 GNP . . . E 5 -59.455 13.792 -27.098 1 34.7 ? C4 GNP 202 Q 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 250 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 32 #