data_3L8Y # _model_server_result.job_id X8KRQ6Q7_mYPQ2cz7NcYFQ _model_server_result.datetime_utc '2025-07-10 04:20:48' _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 3l8y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 3L8Y # _exptl.entry_id 3L8Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 2 _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 3L8Y _cell.length_a 88 _cell.length_b 88 _cell.length_c 134 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3L8Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 3L8Y _atom_sites.fract_transf_matrix[1][1] 0.011364 _atom_sites.fract_transf_matrix[1][2] 0.006561 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013122 _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] 0.007463 _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 GNP A 1 201 201 GNP GNP . C 3 MG A 1 202 202 MG MG . D 4 CA A 1 203 203 CA CA . E 4 CA A 1 204 204 CA CA . F 4 CA A 1 205 205 CA CA . G 4 CA A 1 206 206 CA CA . H 5 YCN A 1 300 300 YCN UNK . I 6 ZN A 1 301 300 ZN UNK . J 7 HOH A 1 167 2 HOH HOH . J 7 HOH A 2 168 168 HOH HOH . J 7 HOH A 3 169 169 HOH HOH . J 7 HOH A 4 170 3 HOH HOH . J 7 HOH A 5 171 4 HOH HOH . J 7 HOH A 6 172 172 HOH HOH . J 7 HOH A 7 173 173 HOH HOH . J 7 HOH A 8 174 5 HOH HOH . J 7 HOH A 9 175 175 HOH HOH . J 7 HOH A 10 176 6 HOH HOH . J 7 HOH A 11 177 177 HOH HOH . J 7 HOH A 12 178 7 HOH HOH . J 7 HOH A 13 179 179 HOH HOH . J 7 HOH A 14 180 180 HOH HOH . J 7 HOH A 15 181 8 HOH HOH . J 7 HOH A 16 182 182 HOH HOH . J 7 HOH A 17 183 183 HOH HOH . J 7 HOH A 18 184 184 HOH HOH . J 7 HOH A 19 185 9 HOH HOH . J 7 HOH A 20 186 10 HOH HOH . J 7 HOH A 21 187 11 HOH HOH . J 7 HOH A 22 188 12 HOH HOH . J 7 HOH A 23 189 13 HOH HOH . J 7 HOH A 24 190 14 HOH HOH . J 7 HOH A 25 191 15 HOH HOH . J 7 HOH A 26 192 16 HOH HOH . J 7 HOH A 27 193 17 HOH HOH . J 7 HOH A 28 194 18 HOH HOH . J 7 HOH A 29 195 19 HOH HOH . J 7 HOH A 30 196 20 HOH HOH . J 7 HOH A 31 197 21 HOH HOH . J 7 HOH A 32 198 22 HOH HOH . J 7 HOH A 33 199 23 HOH HOH . J 7 HOH A 34 200 24 HOH HOH . J 7 HOH A 35 207 25 HOH HOH . J 7 HOH A 36 208 26 HOH HOH . J 7 HOH A 37 209 27 HOH HOH . J 7 HOH A 38 210 28 HOH HOH . J 7 HOH A 39 211 29 HOH HOH . J 7 HOH A 40 212 30 HOH HOH . J 7 HOH A 41 213 31 HOH HOH . J 7 HOH A 42 214 32 HOH HOH . J 7 HOH A 43 215 33 HOH HOH . J 7 HOH A 44 216 34 HOH HOH . J 7 HOH A 45 217 35 HOH HOH . J 7 HOH A 46 218 36 HOH HOH . J 7 HOH A 47 219 37 HOH HOH . J 7 HOH A 48 220 38 HOH HOH . J 7 HOH A 49 221 39 HOH HOH . J 7 HOH A 50 222 40 HOH HOH . J 7 HOH A 51 223 42 HOH HOH . J 7 HOH A 52 224 43 HOH HOH . J 7 HOH A 53 225 44 HOH HOH . J 7 HOH A 54 226 45 HOH HOH . J 7 HOH A 55 227 46 HOH HOH . J 7 HOH A 56 228 47 HOH HOH . J 7 HOH A 57 229 48 HOH HOH . J 7 HOH A 58 230 49 HOH HOH . J 7 HOH A 59 231 50 HOH HOH . J 7 HOH A 60 232 51 HOH HOH . J 7 HOH A 61 233 52 HOH HOH . J 7 HOH A 62 234 53 HOH HOH . J 7 HOH A 63 235 54 HOH HOH . J 7 HOH A 64 236 58 HOH HOH . J 7 HOH A 65 237 59 HOH HOH . J 7 HOH A 66 238 62 HOH HOH . J 7 HOH A 67 239 63 HOH HOH . J 7 HOH A 68 240 64 HOH HOH . J 7 HOH A 69 241 71 HOH HOH . J 7 HOH A 70 242 72 HOH HOH . J 7 HOH A 71 243 73 HOH HOH . J 7 HOH A 72 244 74 HOH HOH . J 7 HOH A 73 245 75 HOH HOH . J 7 HOH A 74 246 76 HOH HOH . J 7 HOH A 75 247 77 HOH HOH . J 7 HOH A 76 248 78 HOH HOH . J 7 HOH A 77 249 79 HOH HOH . J 7 HOH A 78 250 80 HOH HOH . J 7 HOH A 79 251 81 HOH HOH . J 7 HOH A 80 252 82 HOH HOH . J 7 HOH A 81 253 84 HOH HOH . J 7 HOH A 82 254 85 HOH HOH . J 7 HOH A 83 255 86 HOH HOH . J 7 HOH A 84 256 87 HOH HOH . J 7 HOH A 85 257 88 HOH HOH . J 7 HOH A 86 258 89 HOH HOH . J 7 HOH A 87 259 90 HOH HOH . J 7 HOH A 88 260 91 HOH HOH . J 7 HOH A 89 261 92 HOH HOH . J 7 HOH A 90 262 93 HOH HOH . J 7 HOH A 91 263 94 HOH HOH . J 7 HOH A 92 264 95 HOH HOH . J 7 HOH A 93 265 96 HOH HOH . J 7 HOH A 94 266 97 HOH HOH . J 7 HOH A 95 267 98 HOH HOH . J 7 HOH A 96 268 99 HOH HOH . J 7 HOH A 97 269 100 HOH HOH . J 7 HOH A 98 270 101 HOH HOH . J 7 HOH A 99 271 102 HOH HOH . J 7 HOH A 100 272 103 HOH HOH . J 7 HOH A 101 273 104 HOH HOH . J 7 HOH A 102 274 105 HOH HOH . J 7 HOH A 103 275 106 HOH HOH . J 7 HOH A 104 276 107 HOH HOH . J 7 HOH A 105 277 108 HOH HOH . J 7 HOH A 106 278 109 HOH HOH . J 7 HOH A 107 279 110 HOH HOH . J 7 HOH A 108 280 111 HOH HOH . J 7 HOH A 109 281 112 HOH HOH . J 7 HOH A 110 282 113 HOH HOH . J 7 HOH A 111 283 114 HOH HOH . J 7 HOH A 112 284 116 HOH HOH . J 7 HOH A 113 285 117 HOH HOH . J 7 HOH A 114 286 118 HOH HOH . J 7 HOH A 115 287 119 HOH HOH . J 7 HOH A 116 288 120 HOH HOH . J 7 HOH A 117 289 121 HOH HOH . J 7 HOH A 118 290 122 HOH HOH . J 7 HOH A 119 291 123 HOH HOH . J 7 HOH A 120 292 124 HOH HOH . J 7 HOH A 121 293 125 HOH HOH . J 7 HOH A 122 294 126 HOH HOH . J 7 HOH A 123 295 127 HOH HOH . J 7 HOH A 124 296 129 HOH HOH . J 7 HOH A 125 297 131 HOH HOH . J 7 HOH A 126 298 133 HOH HOH . J 7 HOH A 127 299 137 HOH HOH . J 7 HOH A 128 302 139 HOH HOH . J 7 HOH A 129 303 142 HOH HOH . J 7 HOH A 130 304 143 HOH HOH . J 7 HOH A 131 305 147 HOH HOH . J 7 HOH A 132 306 149 HOH HOH . J 7 HOH A 133 307 150 HOH HOH . J 7 HOH A 134 308 153 HOH HOH . J 7 HOH A 135 309 154 HOH HOH . J 7 HOH A 136 310 155 HOH HOH . J 7 HOH A 137 311 158 HOH HOH . J 7 HOH A 138 312 159 HOH HOH . J 7 HOH A 139 313 161 HOH HOH . J 7 HOH A 140 314 162 HOH HOH . J 7 HOH A 141 315 164 HOH HOH . J 7 HOH A 142 316 166 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 . . . B 2 -6.607 -15.342 -22.223 1 11.35 ? PG GNP 201 A 1 HETATM 2 O O1G GNP . . . B 2 -6.686 -14.316 -21.118 1 11.32 ? O1G GNP 201 A 1 HETATM 3 O O2G GNP . . . B 2 -7.039 -16.725 -21.813 1 10.55 ? O2G GNP 201 A 1 HETATM 4 O O3G GNP . . . B 2 -5.204 -15.247 -22.749 1 11.38 ? O3G GNP 201 A 1 HETATM 5 N N3B GNP . . . B 2 -7.576 -14.861 -23.398 1 10.88 ? N3B GNP 201 A 1 HETATM 6 P PB GNP . . . B 2 -7.825 -15.584 -24.803 1 10.75 ? PB GNP 201 A 1 HETATM 7 O O1B GNP . . . B 2 -6.703 -15.317 -25.738 1 10.14 ? O1B GNP 201 A 1 HETATM 8 O O2B GNP . . . B 2 -8.14 -16.999 -24.543 1 10.34 ? O2B GNP 201 A 1 HETATM 9 O O3A GNP . . . B 2 -9.039 -14.867 -25.415 1 9.22 ? O3A GNP 201 A 1 HETATM 10 P PA GNP . . . B 2 -10.509 -15.324 -25.431 1 10.47 ? PA GNP 201 A 1 HETATM 11 O O1A GNP . . . B 2 -10.679 -16.503 -26.303 1 9.64 ? O1A GNP 201 A 1 HETATM 12 O O2A GNP . . . B 2 -11.084 -15.413 -24.057 1 9 ? O2A GNP 201 A 1 HETATM 13 O O5' GNP . . . B 2 -11.252 -14.16 -26.181 1 9.24 ? O5' GNP 201 A 1 HETATM 14 C C5' GNP . . . B 2 -11.253 -12.832 -25.651 1 10.8 ? C5' GNP 201 A 1 HETATM 15 C C4' GNP . . . B 2 -12.45 -12.077 -26.192 1 10.12 ? C4' GNP 201 A 1 HETATM 16 O O4' GNP . . . B 2 -12.301 -11.965 -27.628 1 10.6 ? O4' GNP 201 A 1 HETATM 17 C C3' GNP . . . B 2 -13.801 -12.749 -25.948 1 10.7 ? C3' GNP 201 A 1 HETATM 18 O O3' GNP . . . B 2 -14.751 -11.759 -25.591 1 11.7 ? O3' GNP 201 A 1 HETATM 19 C C2' GNP . . . B 2 -14.114 -13.418 -27.29 1 10.39 ? C2' GNP 201 A 1 HETATM 20 O O2' GNP . . . B 2 -15.494 -13.525 -27.568 1 9.65 ? O2' GNP 201 A 1 HETATM 21 C C1' GNP . . . B 2 -13.44 -12.473 -28.283 1 10.41 ? C1' GNP 201 A 1 HETATM 22 N N9 GNP . . . B 2 -13.004 -13.143 -29.503 1 10.25 ? N9 GNP 201 A 1 HETATM 23 C C8 GNP . . . B 2 -12.152 -14.215 -29.608 1 10.18 ? C8 GNP 201 A 1 HETATM 24 N N7 GNP . . . B 2 -11.951 -14.609 -30.829 1 9.65 ? N7 GNP 201 A 1 HETATM 25 C C5 GNP . . . B 2 -12.717 -13.74 -31.59 1 10.05 ? C5 GNP 201 A 1 HETATM 26 C C6 GNP . . . B 2 -12.9 -13.671 -32.993 1 10.2 ? C6 GNP 201 A 1 HETATM 27 O O6 GNP . . . B 2 -12.398 -14.396 -33.862 1 10.33 ? O6 GNP 201 A 1 HETATM 28 N N1 GNP . . . B 2 -13.76 -12.634 -33.363 1 10.47 ? N1 GNP 201 A 1 HETATM 29 C C2 GNP . . . B 2 -14.371 -11.771 -32.472 1 10.57 ? C2 GNP 201 A 1 HETATM 30 N N2 GNP . . . B 2 -15.176 -10.833 -32.99 1 10.24 ? N2 GNP 201 A 1 HETATM 31 N N3 GNP . . . B 2 -14.205 -11.827 -31.156 1 10.11 ? N3 GNP 201 A 1 HETATM 32 C C4 GNP . . . B 2 -13.37 -12.829 -30.788 1 9.88 ? C4 GNP 201 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #