data_3OYR # _model_server_result.job_id 1ibkr_j6Dx9kuWhGcEYZXQ _model_server_result.datetime_utc '2024-11-27 09:19:41' _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 3oyr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":336}' # _entry.id 3OYR # _exptl.entry_id 3OYR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 175.959 _entity.id 2 _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 3OYR _cell.length_a 72.894 _cell.length_b 72.438 _cell.length_c 125.854 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3OYR _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 PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 2 _struct_asym.id C _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 B OD2 ASP 105 B ASP 95 1_555 E CA CA . B CA 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc2 B OD1 ASP 109 B ASP 99 1_555 E CA CA . B CA 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc3 B OD1 ASP 232 B ASP 222 1_555 F CA CA . B CA 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc4 E CA CA . B CA 337 1_555 G O2A DMA . B DMA 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc5 E CA CA . B CA 337 1_555 G O3B DMA . B DMA 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc6 E CA CA . B CA 337 1_555 I O HOH . B HOH 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc7 E CA CA . B CA 337 1_555 I O HOH . B HOH 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? metalc ? metalc8 F CA CA . B CA 338 1_555 G O2B DMA . B DMA 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc9 F CA CA . B CA 338 1_555 G O1A DMA . B DMA 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc10 F CA CA . B CA 338 1_555 I O HOH . B HOH 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc11 F CA CA . B CA 338 1_555 I O HOH . B HOH 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc12 F CA CA . B CA 338 1_555 I O HOH . B HOH 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? # _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 272 n n P1 O2 POP sing 273 n n P1 O3 POP sing 274 n n P1 O POP sing 275 n n O2 HO2 POP sing 276 n n O P2 POP sing 277 n n P2 O4 POP doub 278 n n P2 O5 POP sing 279 n n P2 O6 POP sing 280 n n O5 HO5 POP sing 281 n n # _atom_sites.entry_id 3OYR _atom_sites.fract_transf_matrix[1][1] 0.013719 _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] 0.013805 _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] 0.007946 _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 C 2 POP A 1 336 1 POP POP . D 3 DMA B 1 336 1 DMA IPE . E 4 CA B 1 337 1 CA CA . F 4 CA B 1 338 1 CA CA . G 3 DMA B 1 339 1 DMA IPE . H 5 HOH A 1 337 25 HOH HOH . H 5 HOH A 2 338 41 HOH HOH . H 5 HOH A 3 339 47 HOH HOH . H 5 HOH A 4 340 51 HOH HOH . H 5 HOH A 5 341 56 HOH HOH . H 5 HOH A 6 342 59 HOH HOH . H 5 HOH A 7 343 66 HOH HOH . H 5 HOH A 8 344 73 HOH HOH . H 5 HOH A 9 345 74 HOH HOH . H 5 HOH A 10 346 77 HOH HOH . H 5 HOH A 11 347 90 HOH HOH . H 5 HOH A 12 348 102 HOH HOH . H 5 HOH A 13 349 104 HOH HOH . H 5 HOH A 14 350 105 HOH HOH . H 5 HOH A 15 351 124 HOH HOH . H 5 HOH A 16 352 125 HOH HOH . H 5 HOH A 17 353 126 HOH HOH . H 5 HOH A 18 354 127 HOH HOH . H 5 HOH A 19 355 128 HOH HOH . H 5 HOH A 20 356 129 HOH HOH . H 5 HOH A 21 357 162 HOH HOH . H 5 HOH A 22 358 163 HOH HOH . H 5 HOH A 23 359 164 HOH HOH . H 5 HOH A 24 360 165 HOH HOH . H 5 HOH A 25 361 166 HOH HOH . H 5 HOH A 26 362 167 HOH HOH . H 5 HOH A 27 363 168 HOH HOH . H 5 HOH A 28 364 169 HOH HOH . H 5 HOH A 29 365 170 HOH HOH . H 5 HOH A 30 366 171 HOH HOH . H 5 HOH A 31 367 172 HOH HOH . H 5 HOH A 32 368 173 HOH HOH . H 5 HOH A 33 369 174 HOH HOH . H 5 HOH A 34 370 175 HOH HOH . H 5 HOH A 35 371 177 HOH HOH . H 5 HOH A 36 372 179 HOH HOH . H 5 HOH A 37 373 180 HOH HOH . H 5 HOH A 38 374 181 HOH HOH . H 5 HOH A 39 375 182 HOH HOH . H 5 HOH A 40 376 183 HOH HOH . H 5 HOH A 41 377 184 HOH HOH . H 5 HOH A 42 378 185 HOH HOH . H 5 HOH A 43 379 186 HOH HOH . H 5 HOH A 44 380 187 HOH HOH . H 5 HOH A 45 381 199 HOH HOH . H 5 HOH A 46 382 240 HOH HOH . H 5 HOH A 47 383 241 HOH HOH . H 5 HOH A 48 384 242 HOH HOH . H 5 HOH A 49 385 243 HOH HOH . H 5 HOH A 50 386 244 HOH HOH . H 5 HOH A 51 387 247 HOH HOH . H 5 HOH A 52 388 248 HOH HOH . H 5 HOH A 53 389 249 HOH HOH . H 5 HOH A 54 390 251 HOH HOH . H 5 HOH A 55 391 252 HOH HOH . H 5 HOH A 56 392 255 HOH HOH . H 5 HOH A 57 393 256 HOH HOH . H 5 HOH A 58 394 259 HOH HOH . H 5 HOH A 59 395 260 HOH HOH . I 5 HOH B 1 340 1 HOH HOH . I 5 HOH B 2 341 2 HOH HOH . I 5 HOH B 3 342 3 HOH HOH . I 5 HOH B 4 343 4 HOH HOH . I 5 HOH B 5 344 5 HOH HOH . I 5 HOH B 6 345 6 HOH HOH . I 5 HOH B 7 346 7 HOH HOH . I 5 HOH B 8 347 8 HOH HOH . I 5 HOH B 9 348 9 HOH HOH . I 5 HOH B 10 349 11 HOH HOH . I 5 HOH B 11 350 15 HOH HOH . I 5 HOH B 12 351 17 HOH HOH . I 5 HOH B 13 352 19 HOH HOH . I 5 HOH B 14 353 24 HOH HOH . I 5 HOH B 15 354 27 HOH HOH . I 5 HOH B 16 355 29 HOH HOH . I 5 HOH B 17 356 31 HOH HOH . I 5 HOH B 18 357 34 HOH HOH . I 5 HOH B 19 358 35 HOH HOH . I 5 HOH B 20 359 37 HOH HOH . I 5 HOH B 21 360 38 HOH HOH . I 5 HOH B 22 361 39 HOH HOH . I 5 HOH B 23 362 40 HOH HOH . I 5 HOH B 24 363 42 HOH HOH . I 5 HOH B 25 364 43 HOH HOH . I 5 HOH B 26 365 45 HOH HOH . I 5 HOH B 27 366 46 HOH HOH . I 5 HOH B 28 367 49 HOH HOH . I 5 HOH B 29 368 52 HOH HOH . I 5 HOH B 30 369 55 HOH HOH . I 5 HOH B 31 370 57 HOH HOH . I 5 HOH B 32 371 65 HOH HOH . I 5 HOH B 33 372 67 HOH HOH . I 5 HOH B 34 373 68 HOH HOH . I 5 HOH B 35 374 75 HOH HOH . I 5 HOH B 36 375 78 HOH HOH . I 5 HOH B 37 376 79 HOH HOH . I 5 HOH B 38 377 82 HOH HOH . I 5 HOH B 39 378 83 HOH HOH . I 5 HOH B 40 379 87 HOH HOH . I 5 HOH B 41 380 91 HOH HOH . I 5 HOH B 42 381 94 HOH HOH . I 5 HOH B 43 382 95 HOH HOH . I 5 HOH B 44 383 96 HOH HOH . I 5 HOH B 45 384 100 HOH HOH . I 5 HOH B 46 385 107 HOH HOH . I 5 HOH B 47 386 109 HOH HOH . I 5 HOH B 48 387 113 HOH HOH . I 5 HOH B 49 388 114 HOH HOH . I 5 HOH B 50 389 115 HOH HOH . I 5 HOH B 51 390 116 HOH HOH . I 5 HOH B 52 391 117 HOH HOH . I 5 HOH B 53 392 118 HOH HOH . I 5 HOH B 54 393 119 HOH HOH . I 5 HOH B 55 394 120 HOH HOH . I 5 HOH B 56 395 121 HOH HOH . I 5 HOH B 57 396 122 HOH HOH . I 5 HOH B 58 397 123 HOH HOH . I 5 HOH B 59 398 130 HOH HOH . I 5 HOH B 60 399 131 HOH HOH . I 5 HOH B 61 400 132 HOH HOH . I 5 HOH B 62 401 133 HOH HOH . I 5 HOH B 63 402 134 HOH HOH . I 5 HOH B 64 403 135 HOH HOH . I 5 HOH B 65 404 136 HOH HOH . I 5 HOH B 66 405 137 HOH HOH . I 5 HOH B 67 406 138 HOH HOH . I 5 HOH B 68 407 139 HOH HOH . I 5 HOH B 69 408 140 HOH HOH . I 5 HOH B 70 409 141 HOH HOH . I 5 HOH B 71 410 142 HOH HOH . I 5 HOH B 72 411 143 HOH HOH . I 5 HOH B 73 412 144 HOH HOH . I 5 HOH B 74 413 145 HOH HOH . I 5 HOH B 75 414 146 HOH HOH . I 5 HOH B 76 415 147 HOH HOH . I 5 HOH B 77 416 148 HOH HOH . I 5 HOH B 78 417 149 HOH HOH . I 5 HOH B 79 418 150 HOH HOH . I 5 HOH B 80 419 151 HOH HOH . I 5 HOH B 81 420 152 HOH HOH . I 5 HOH B 82 421 153 HOH HOH . I 5 HOH B 83 422 154 HOH HOH . I 5 HOH B 84 423 155 HOH HOH . I 5 HOH B 85 424 156 HOH HOH . I 5 HOH B 86 425 157 HOH HOH . I 5 HOH B 87 426 158 HOH HOH . I 5 HOH B 88 427 159 HOH HOH . I 5 HOH B 89 428 160 HOH HOH . I 5 HOH B 90 429 161 HOH HOH . I 5 HOH B 91 430 176 HOH HOH . I 5 HOH B 92 431 178 HOH HOH . I 5 HOH B 93 432 188 HOH HOH . I 5 HOH B 94 433 189 HOH HOH . I 5 HOH B 95 434 190 HOH HOH . I 5 HOH B 96 435 191 HOH HOH . I 5 HOH B 97 436 192 HOH HOH . I 5 HOH B 98 437 193 HOH HOH . I 5 HOH B 99 438 194 HOH HOH . I 5 HOH B 100 439 195 HOH HOH . I 5 HOH B 101 440 196 HOH HOH . I 5 HOH B 102 441 197 HOH HOH . I 5 HOH B 103 442 198 HOH HOH . I 5 HOH B 104 443 200 HOH HOH . I 5 HOH B 105 444 201 HOH HOH . I 5 HOH B 106 445 202 HOH HOH . I 5 HOH B 107 446 203 HOH HOH . I 5 HOH B 108 447 204 HOH HOH . I 5 HOH B 109 448 205 HOH HOH . I 5 HOH B 110 449 206 HOH HOH . I 5 HOH B 111 450 207 HOH HOH . I 5 HOH B 112 451 208 HOH HOH . I 5 HOH B 113 452 209 HOH HOH . I 5 HOH B 114 453 210 HOH HOH . I 5 HOH B 115 454 211 HOH HOH . I 5 HOH B 116 455 212 HOH HOH . I 5 HOH B 117 456 213 HOH HOH . I 5 HOH B 118 457 214 HOH HOH . I 5 HOH B 119 458 215 HOH HOH . I 5 HOH B 120 459 216 HOH HOH . I 5 HOH B 121 460 217 HOH HOH . I 5 HOH B 122 461 218 HOH HOH . I 5 HOH B 123 462 219 HOH HOH . I 5 HOH B 124 463 220 HOH HOH . I 5 HOH B 125 464 221 HOH HOH . I 5 HOH B 126 465 222 HOH HOH . I 5 HOH B 127 466 223 HOH HOH . I 5 HOH B 128 467 224 HOH HOH . I 5 HOH B 129 468 225 HOH HOH . I 5 HOH B 130 469 226 HOH HOH . I 5 HOH B 131 470 227 HOH HOH . I 5 HOH B 132 471 228 HOH HOH . I 5 HOH B 133 472 229 HOH HOH . I 5 HOH B 134 473 230 HOH HOH . I 5 HOH B 135 474 231 HOH HOH . I 5 HOH B 136 475 232 HOH HOH . I 5 HOH B 137 476 233 HOH HOH . I 5 HOH B 138 477 234 HOH HOH . I 5 HOH B 139 478 235 HOH HOH . I 5 HOH B 140 479 236 HOH HOH . I 5 HOH B 141 480 237 HOH HOH . I 5 HOH B 142 481 238 HOH HOH . I 5 HOH B 143 482 239 HOH HOH . I 5 HOH B 144 483 250 HOH HOH . I 5 HOH B 145 484 253 HOH HOH . I 5 HOH B 146 485 254 HOH HOH . I 5 HOH B 147 486 257 HOH HOH . I 5 HOH B 148 487 258 HOH HOH . I 5 HOH B 149 488 261 HOH HOH . I 5 HOH B 150 489 262 HOH HOH . I 5 HOH B 151 490 263 HOH HOH . I 5 HOH B 152 491 264 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 . . . C 2 -1.09 1.142 -14.97 1 112.13 ? P1 POP 336 A 1 HETATM 2 O O1 POP . . . C 2 -1.22 2.645 -14.879 1 108.48 ? O1 POP 336 A 1 HETATM 3 O O2 POP . . . C 2 0.354 0.778 -14.713 1 107.08 ? O2 POP 336 A 1 HETATM 4 O O3 POP . . . C 2 -1.972 0.505 -13.919 1 113.44 ? O3 POP 336 A 1 HETATM 5 O O POP . . . C 2 -1.549 0.661 -16.45 1 112.75 ? O POP 336 A 1 HETATM 6 P P2 POP . . . C 2 -2.013 -0.848 -16.829 1 116.62 ? P2 POP 336 A 1 HETATM 7 O O4 POP . . . C 2 -2.261 -0.947 -18.32 1 111.39 ? O4 POP 336 A 1 HETATM 8 O O5 POP . . . C 2 -0.941 -1.845 -16.447 1 112.03 ? O5 POP 336 A 1 HETATM 9 O O6 POP . . . C 2 -3.298 -1.166 -16.095 1 114.98 ? O6 POP 336 A 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 9 #