data_2PNY # _model_server_result.job_id 9XTUybRyHjXnhkDVKYbbNA _model_server_result.datetime_utc '2024-12-08 08:44:17' _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 2pny # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":230}' # _entry.id 2PNY # _exptl.entry_id 2PNY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 175.959 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PYROPHOSPHATE 2-' _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 2PNY _cell.length_a 50.897 _cell.length_b 52.815 _cell.length_c 96.391 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2PNY _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,H _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 NE2 HIS 59 A HIS 40 1_555 C MN MN . A MN 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc2 A NE2 HIS 70 A HIS 51 1_555 C MN MN . A MN 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc3 A O SER 105 A SER 86 1_555 B CA CA . A CA 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc4 A NE2 HIS 107 A HIS 88 1_555 C MN MN . A MN 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc5 A OE2 GLU 134 A GLU 115 1_555 B CA CA . A CA 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc6 A OE1 GLU 165 A GLU 146 1_555 C MN MN . A MN 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc7 A OE2 GLU 165 A GLU 146 1_555 C MN MN . A MN 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc8 A OE2 GLU 167 A GLU 148 1_555 C MN MN . A MN 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? metalc ? metalc9 B CA CA . A CA 228 1_555 D O5 POP . A POP 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc10 B CA CA . A CA 228 1_555 D O3 POP . A POP 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc11 B CA CA . A CA 228 1_555 D O POP . A POP 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.398 ? metalc ? metalc12 B CA CA . A CA 228 1_555 H O HOH . A HOH 270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc13 B CA CA . A CA 228 1_555 H O HOH . A HOH 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? # _chem_comp.formula 'H2 O7 P2 -2' _chem_comp.formula_weight 175.959 _chem_comp.id POP _chem_comp.mon_nstd_flag . _chem_comp.name 'PYROPHOSPHATE 2-' _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 P1 O1 POP doub 273 n n P1 O2 POP sing 274 n n P1 O3 POP sing 275 n n P1 O POP sing 276 n n O2 HO2 POP sing 277 n n O P2 POP sing 278 n n P2 O4 POP doub 279 n n P2 O5 POP sing 280 n n P2 O6 POP sing 281 n n O5 HO5 POP sing 282 n n # _atom_sites.entry_id 2PNY _atom_sites.fract_transf_matrix[1][1] 0.019648 _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] 0.018934 _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] 0.010374 _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 CA A 1 228 1 CA CA . C 3 MN A 1 229 2 MN MN . D 4 POP A 1 230 3 POP POP . E 5 GOL A 1 231 4 GOL GOL . F 5 GOL A 1 232 5 GOL GOL . G 5 GOL A 1 233 6 GOL GOL . H 6 HOH A 1 234 7 HOH HOH . H 6 HOH A 2 235 8 HOH HOH . H 6 HOH A 3 236 9 HOH HOH . H 6 HOH A 4 237 10 HOH HOH . H 6 HOH A 5 238 11 HOH HOH . H 6 HOH A 6 239 12 HOH HOH . H 6 HOH A 7 240 13 HOH HOH . H 6 HOH A 8 241 14 HOH HOH . H 6 HOH A 9 242 15 HOH HOH . H 6 HOH A 10 243 16 HOH HOH . H 6 HOH A 11 244 18 HOH HOH . H 6 HOH A 12 245 19 HOH HOH . H 6 HOH A 13 246 20 HOH HOH . H 6 HOH A 14 247 21 HOH HOH . H 6 HOH A 15 248 22 HOH HOH . H 6 HOH A 16 249 23 HOH HOH . H 6 HOH A 17 250 24 HOH HOH . H 6 HOH A 18 251 25 HOH HOH . H 6 HOH A 19 252 26 HOH HOH . H 6 HOH A 20 253 27 HOH HOH . H 6 HOH A 21 254 29 HOH HOH . H 6 HOH A 22 255 31 HOH HOH . H 6 HOH A 23 256 32 HOH HOH . H 6 HOH A 24 257 33 HOH HOH . H 6 HOH A 25 258 34 HOH HOH . H 6 HOH A 26 259 35 HOH HOH . H 6 HOH A 27 260 36 HOH HOH . H 6 HOH A 28 261 37 HOH HOH . H 6 HOH A 29 262 38 HOH HOH . H 6 HOH A 30 263 39 HOH HOH . H 6 HOH A 31 264 40 HOH HOH . H 6 HOH A 32 265 41 HOH HOH . H 6 HOH A 33 266 43 HOH HOH . H 6 HOH A 34 267 44 HOH HOH . H 6 HOH A 35 268 46 HOH HOH . H 6 HOH A 36 269 48 HOH HOH . H 6 HOH A 37 270 49 HOH HOH . H 6 HOH A 38 271 50 HOH HOH . H 6 HOH A 39 272 52 HOH HOH . H 6 HOH A 40 273 53 HOH HOH . H 6 HOH A 41 274 54 HOH HOH . H 6 HOH A 42 275 55 HOH HOH . H 6 HOH A 43 276 56 HOH HOH . H 6 HOH A 44 277 57 HOH HOH . H 6 HOH A 45 278 58 HOH HOH . H 6 HOH A 46 279 59 HOH HOH . H 6 HOH A 47 280 60 HOH HOH . H 6 HOH A 48 281 61 HOH HOH . H 6 HOH A 49 282 63 HOH HOH . H 6 HOH A 50 283 64 HOH HOH . H 6 HOH A 51 284 65 HOH HOH . H 6 HOH A 52 285 66 HOH HOH . H 6 HOH A 53 286 67 HOH HOH . H 6 HOH A 54 287 68 HOH HOH . H 6 HOH A 55 288 69 HOH HOH . H 6 HOH A 56 289 70 HOH HOH . H 6 HOH A 57 290 72 HOH HOH . H 6 HOH A 58 291 73 HOH HOH . H 6 HOH A 59 292 74 HOH HOH . H 6 HOH A 60 293 75 HOH HOH . H 6 HOH A 61 294 76 HOH HOH . H 6 HOH A 62 295 78 HOH HOH . H 6 HOH A 63 296 79 HOH HOH . H 6 HOH A 64 297 80 HOH HOH . H 6 HOH A 65 298 81 HOH HOH . H 6 HOH A 66 299 82 HOH HOH . H 6 HOH A 67 300 83 HOH HOH . H 6 HOH A 68 301 84 HOH HOH . H 6 HOH A 69 302 85 HOH HOH . H 6 HOH A 70 303 86 HOH HOH . H 6 HOH A 71 304 89 HOH HOH . H 6 HOH A 72 305 90 HOH HOH . H 6 HOH A 73 306 92 HOH HOH . H 6 HOH A 74 307 93 HOH HOH . H 6 HOH A 75 308 94 HOH HOH . H 6 HOH A 76 309 95 HOH HOH . H 6 HOH A 77 310 96 HOH HOH . H 6 HOH A 78 311 97 HOH HOH . H 6 HOH A 79 312 98 HOH HOH . H 6 HOH A 80 313 99 HOH HOH . H 6 HOH A 81 314 100 HOH HOH . H 6 HOH A 82 315 101 HOH HOH . H 6 HOH A 83 316 102 HOH HOH . H 6 HOH A 84 317 104 HOH HOH . H 6 HOH A 85 318 105 HOH HOH . H 6 HOH A 86 319 106 HOH HOH . H 6 HOH A 87 320 107 HOH HOH . H 6 HOH A 88 321 108 HOH HOH . H 6 HOH A 89 322 109 HOH HOH . H 6 HOH A 90 323 110 HOH HOH . H 6 HOH A 91 324 111 HOH HOH . H 6 HOH A 92 325 112 HOH HOH . H 6 HOH A 93 326 113 HOH HOH . H 6 HOH A 94 327 114 HOH HOH . H 6 HOH A 95 328 115 HOH HOH . H 6 HOH A 96 329 116 HOH HOH . H 6 HOH A 97 330 117 HOH HOH . H 6 HOH A 98 331 118 HOH HOH . H 6 HOH A 99 332 119 HOH HOH . H 6 HOH A 100 333 121 HOH HOH . H 6 HOH A 101 334 122 HOH HOH . H 6 HOH A 102 335 123 HOH HOH . H 6 HOH A 103 336 125 HOH HOH . H 6 HOH A 104 337 126 HOH HOH . H 6 HOH A 105 338 127 HOH HOH . H 6 HOH A 106 339 128 HOH HOH . H 6 HOH A 107 340 129 HOH HOH . H 6 HOH A 108 341 130 HOH HOH . H 6 HOH A 109 342 132 HOH HOH . H 6 HOH A 110 343 135 HOH HOH . H 6 HOH A 111 344 136 HOH HOH . H 6 HOH A 112 345 137 HOH HOH . H 6 HOH A 113 346 140 HOH HOH . H 6 HOH A 114 347 141 HOH HOH . H 6 HOH A 115 348 143 HOH HOH . H 6 HOH A 116 349 144 HOH HOH . H 6 HOH A 117 350 146 HOH HOH . H 6 HOH A 118 351 148 HOH HOH . H 6 HOH A 119 352 149 HOH HOH . H 6 HOH A 120 353 150 HOH HOH . H 6 HOH A 121 354 151 HOH HOH . H 6 HOH A 122 355 153 HOH HOH . H 6 HOH A 123 356 154 HOH HOH . H 6 HOH A 124 357 155 HOH HOH . H 6 HOH A 125 358 157 HOH HOH . H 6 HOH A 126 359 158 HOH HOH . H 6 HOH A 127 360 159 HOH HOH . H 6 HOH A 128 361 160 HOH HOH . H 6 HOH A 129 362 161 HOH HOH . H 6 HOH A 130 363 162 HOH HOH . H 6 HOH A 131 364 163 HOH HOH . H 6 HOH A 132 365 165 HOH HOH . H 6 HOH A 133 366 166 HOH HOH . H 6 HOH A 134 367 167 HOH HOH . H 6 HOH A 135 368 168 HOH HOH . H 6 HOH A 136 369 169 HOH HOH . H 6 HOH A 137 370 170 HOH HOH . H 6 HOH A 138 371 171 HOH HOH . H 6 HOH A 139 372 173 HOH HOH . H 6 HOH A 140 373 174 HOH HOH . H 6 HOH A 141 374 176 HOH HOH . H 6 HOH A 142 375 177 HOH HOH . H 6 HOH A 143 376 178 HOH HOH . H 6 HOH A 144 377 179 HOH HOH . H 6 HOH A 145 378 181 HOH HOH . H 6 HOH A 146 379 182 HOH HOH . H 6 HOH A 147 380 183 HOH HOH . H 6 HOH A 148 381 185 HOH HOH . H 6 HOH A 149 382 189 HOH HOH . H 6 HOH A 150 383 190 HOH HOH . H 6 HOH A 151 384 192 HOH HOH . H 6 HOH A 152 385 194 HOH HOH . H 6 HOH A 153 386 196 HOH HOH . H 6 HOH A 154 387 198 HOH HOH . H 6 HOH A 155 388 199 HOH HOH . H 6 HOH A 156 389 200 HOH HOH . H 6 HOH A 157 390 201 HOH HOH . H 6 HOH A 158 391 202 HOH HOH . H 6 HOH A 159 392 204 HOH HOH . H 6 HOH A 160 393 205 HOH HOH . H 6 HOH A 161 394 206 HOH HOH . H 6 HOH A 162 395 207 HOH HOH . H 6 HOH A 163 396 208 HOH HOH . H 6 HOH A 164 397 209 HOH HOH . H 6 HOH A 165 398 210 HOH HOH . H 6 HOH A 166 399 211 HOH HOH . H 6 HOH A 167 400 212 HOH HOH . H 6 HOH A 168 401 213 HOH HOH . H 6 HOH A 169 402 214 HOH HOH . H 6 HOH A 170 403 215 HOH HOH . H 6 HOH A 171 404 216 HOH HOH . H 6 HOH A 172 405 217 HOH HOH . H 6 HOH A 173 406 218 HOH HOH . H 6 HOH A 174 407 220 HOH HOH . H 6 HOH A 175 408 221 HOH HOH . H 6 HOH A 176 409 222 HOH HOH . H 6 HOH A 177 410 223 HOH HOH . H 6 HOH A 178 411 224 HOH HOH . H 6 HOH A 179 412 225 HOH HOH . H 6 HOH A 180 413 226 HOH HOH . H 6 HOH A 181 414 227 HOH HOH . H 6 HOH A 182 415 229 HOH HOH . H 6 HOH A 183 416 231 HOH HOH . H 6 HOH A 184 417 232 HOH HOH . H 6 HOH A 185 418 234 HOH HOH . H 6 HOH A 186 419 235 HOH HOH . H 6 HOH A 187 420 236 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 P1 POP . . . D 4 25.572 24.981 13.537 1 20.87 ? P1 POP 230 A 1 HETATM 2 O O1 POP . . . D 4 25.932 24.976 15.023 1 20.46 ? O1 POP 230 A 1 HETATM 3 O O2 POP . . . D 4 26.855 24.997 12.721 1 18.23 ? O2 POP 230 A 1 HETATM 4 O O3 POP . . . D 4 24.779 26.201 13.187 1 18.7 ? O3 POP 230 A 1 HETATM 5 O O POP . . . D 4 24.807 23.596 13.137 1 19.32 ? O POP 230 A 1 HETATM 6 P P2 POP . . . D 4 23.227 23.303 13.216 1 20.75 ? P2 POP 230 A 1 HETATM 7 O O4 POP . . . D 4 22.979 21.901 12.674 1 20.43 ? O4 POP 230 A 1 HETATM 8 O O5 POP . . . D 4 22.387 24.166 12.373 1 19.24 ? O5 POP 230 A 1 HETATM 9 O O6 POP . . . D 4 22.805 23.423 14.692 1 20.06 ? O6 POP 230 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 9 #