data_3PYF # _model_server_result.job_id 9HYth_d2t6iUfuKCx0gWXA _model_server_result.datetime_utc '2025-01-03 00:31:10' _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 3pyf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":307}' # _entry.id 3PYF # _exptl.entry_id 3PYF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE 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 3PYF _cell.length_a 52.96 _cell.length_b 73.485 _cell.length_c 106.333 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PYF _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 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 _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 O12 P3' _chem_comp.formula_weight 506.196 _chem_comp.id ANP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE 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 ANP doub 13 n n PG O2G ANP sing 14 n n PG O3G ANP sing 15 n n PG N3B ANP sing 16 n n O2G HOG2 ANP sing 17 n n O3G HOG3 ANP sing 18 n n PB O1B ANP doub 19 n n PB O2B ANP sing 20 n n PB N3B ANP sing 21 n n PB O3A ANP sing 22 n n O2B HOB2 ANP sing 23 n n N3B HNB1 ANP sing 24 n n PA O1A ANP doub 25 n n PA O2A ANP sing 26 n n PA O3A ANP sing 27 n n PA O5' ANP sing 28 n n O2A HOA2 ANP sing 29 n n O5' C5' ANP sing 30 n n C5' C4' ANP sing 31 n n C5' "H5'1" ANP sing 32 n n C5' "H5'2" ANP sing 33 n n C4' O4' ANP sing 34 n n C4' C3' ANP sing 35 n n C4' H4' ANP sing 36 n n O4' C1' ANP sing 37 n n C3' O3' ANP sing 38 n n C3' C2' ANP sing 39 n n C3' H3' ANP sing 40 n n O3' HO3' ANP sing 41 n n C2' O2' ANP sing 42 n n C2' C1' ANP sing 43 n n C2' H2' ANP sing 44 n n O2' HO2' ANP sing 45 n n C1' N9 ANP sing 46 n n C1' H1' ANP sing 47 n n N9 C8 ANP sing 48 n y N9 C4 ANP sing 49 n y C8 N7 ANP doub 50 n y C8 H8 ANP sing 51 n n N7 C5 ANP sing 52 n y C5 C6 ANP sing 53 n y C5 C4 ANP doub 54 n y C6 N6 ANP sing 55 n n C6 N1 ANP doub 56 n y N6 HN61 ANP sing 57 n n N6 HN62 ANP sing 58 n n N1 C2 ANP sing 59 n y C2 N3 ANP doub 60 n y C2 H2 ANP sing 61 n n N3 C4 ANP sing 62 n y # _atom_sites.entry_id 3PYF _atom_sites.fract_transf_matrix[1][1] 0.018882 _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] 0.013608 _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] 0.009404 _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 ANP A 1 307 1 ANP ANP . C 3 HOH A 1 308 1 HOH HOH . C 3 HOH A 2 309 2 HOH HOH . C 3 HOH A 3 310 3 HOH HOH . C 3 HOH A 4 311 4 HOH HOH . C 3 HOH A 5 312 5 HOH HOH . C 3 HOH A 6 313 6 HOH HOH . C 3 HOH A 7 314 7 HOH HOH . C 3 HOH A 8 315 8 HOH HOH . C 3 HOH A 9 316 9 HOH HOH . C 3 HOH A 10 317 10 HOH HOH . C 3 HOH A 11 318 11 HOH HOH . C 3 HOH A 12 319 12 HOH HOH . C 3 HOH A 13 320 13 HOH HOH . C 3 HOH A 14 321 14 HOH HOH . C 3 HOH A 15 322 15 HOH HOH . C 3 HOH A 16 323 16 HOH HOH . C 3 HOH A 17 324 17 HOH HOH . C 3 HOH A 18 325 18 HOH HOH . C 3 HOH A 19 326 19 HOH HOH . C 3 HOH A 20 327 20 HOH HOH . C 3 HOH A 21 328 21 HOH HOH . C 3 HOH A 22 329 22 HOH HOH . C 3 HOH A 23 330 24 HOH HOH . C 3 HOH A 24 331 25 HOH HOH . C 3 HOH A 25 332 26 HOH HOH . C 3 HOH A 26 333 27 HOH HOH . C 3 HOH A 27 334 28 HOH HOH . C 3 HOH A 28 335 29 HOH HOH . C 3 HOH A 29 336 30 HOH HOH . C 3 HOH A 30 337 31 HOH HOH . C 3 HOH A 31 338 32 HOH HOH . C 3 HOH A 32 339 33 HOH HOH . C 3 HOH A 33 340 34 HOH HOH . C 3 HOH A 34 341 35 HOH HOH . C 3 HOH A 35 342 36 HOH HOH . C 3 HOH A 36 343 37 HOH HOH . C 3 HOH A 37 344 38 HOH HOH . C 3 HOH A 38 345 39 HOH HOH . C 3 HOH A 39 346 40 HOH HOH . C 3 HOH A 40 347 41 HOH HOH . C 3 HOH A 41 348 42 HOH HOH . C 3 HOH A 42 349 44 HOH HOH . C 3 HOH A 43 350 45 HOH HOH . C 3 HOH A 44 351 46 HOH HOH . C 3 HOH A 45 352 47 HOH HOH . C 3 HOH A 46 353 48 HOH HOH . C 3 HOH A 47 354 49 HOH HOH . C 3 HOH A 48 355 50 HOH HOH . C 3 HOH A 49 356 51 HOH HOH . C 3 HOH A 50 357 52 HOH HOH . C 3 HOH A 51 358 53 HOH HOH . C 3 HOH A 52 359 54 HOH HOH . C 3 HOH A 53 360 55 HOH HOH . C 3 HOH A 54 361 56 HOH HOH . C 3 HOH A 55 362 57 HOH HOH . C 3 HOH A 56 363 58 HOH HOH . C 3 HOH A 57 364 59 HOH HOH . C 3 HOH A 58 365 60 HOH HOH . C 3 HOH A 59 366 61 HOH HOH . C 3 HOH A 60 367 62 HOH HOH . C 3 HOH A 61 368 63 HOH HOH . C 3 HOH A 62 369 64 HOH HOH . C 3 HOH A 63 370 65 HOH HOH . C 3 HOH A 64 371 66 HOH HOH . C 3 HOH A 65 372 67 HOH HOH . C 3 HOH A 66 373 68 HOH HOH . C 3 HOH A 67 374 69 HOH HOH . C 3 HOH A 68 375 70 HOH HOH . C 3 HOH A 69 376 71 HOH HOH . C 3 HOH A 70 377 72 HOH HOH . C 3 HOH A 71 378 73 HOH HOH . C 3 HOH A 72 379 74 HOH HOH . C 3 HOH A 73 380 75 HOH HOH . C 3 HOH A 74 381 76 HOH HOH . C 3 HOH A 75 382 77 HOH HOH . C 3 HOH A 76 383 78 HOH HOH . C 3 HOH A 77 384 79 HOH HOH . C 3 HOH A 78 385 80 HOH HOH . C 3 HOH A 79 386 81 HOH HOH . C 3 HOH A 80 387 84 HOH HOH . C 3 HOH A 81 388 85 HOH HOH . C 3 HOH A 82 389 86 HOH HOH . C 3 HOH A 83 390 87 HOH HOH . C 3 HOH A 84 391 88 HOH HOH . C 3 HOH A 85 392 89 HOH HOH . C 3 HOH A 86 393 90 HOH HOH . C 3 HOH A 87 394 91 HOH HOH . C 3 HOH A 88 395 92 HOH HOH . C 3 HOH A 89 396 93 HOH HOH . C 3 HOH A 90 397 94 HOH HOH . C 3 HOH A 91 398 95 HOH HOH . C 3 HOH A 92 399 96 HOH HOH . C 3 HOH A 93 400 98 HOH HOH . C 3 HOH A 94 401 99 HOH HOH . C 3 HOH A 95 402 100 HOH HOH . C 3 HOH A 96 403 101 HOH HOH . C 3 HOH A 97 404 102 HOH HOH . C 3 HOH A 98 405 103 HOH HOH . C 3 HOH A 99 406 104 HOH HOH . C 3 HOH A 100 407 106 HOH HOH . C 3 HOH A 101 408 107 HOH HOH . C 3 HOH A 102 409 108 HOH HOH . C 3 HOH A 103 410 109 HOH HOH . C 3 HOH A 104 411 110 HOH HOH . C 3 HOH A 105 412 111 HOH HOH . C 3 HOH A 106 413 112 HOH HOH . C 3 HOH A 107 414 113 HOH HOH . C 3 HOH A 108 415 114 HOH HOH . C 3 HOH A 109 416 115 HOH HOH . C 3 HOH A 110 417 116 HOH HOH . C 3 HOH A 111 418 117 HOH HOH . C 3 HOH A 112 419 119 HOH HOH . C 3 HOH A 113 420 120 HOH HOH . C 3 HOH A 114 421 121 HOH HOH . C 3 HOH A 115 422 123 HOH HOH . C 3 HOH A 116 423 129 HOH HOH . C 3 HOH A 117 424 131 HOH HOH . C 3 HOH A 118 425 132 HOH HOH . C 3 HOH A 119 426 133 HOH HOH . C 3 HOH A 120 427 135 HOH HOH . C 3 HOH A 121 428 136 HOH HOH . C 3 HOH A 122 429 142 HOH HOH . C 3 HOH A 123 430 143 HOH HOH . C 3 HOH A 124 431 144 HOH HOH . C 3 HOH A 125 432 147 HOH HOH . C 3 HOH A 126 433 148 HOH HOH . C 3 HOH A 127 434 150 HOH HOH . C 3 HOH A 128 435 154 HOH HOH . C 3 HOH A 129 436 155 HOH HOH . C 3 HOH A 130 437 156 HOH HOH . C 3 HOH A 131 438 157 HOH HOH . C 3 HOH A 132 439 160 HOH HOH . C 3 HOH A 133 440 161 HOH HOH . C 3 HOH A 134 441 173 HOH HOH . C 3 HOH A 135 442 175 HOH HOH . C 3 HOH A 136 443 177 HOH HOH . C 3 HOH A 137 444 180 HOH HOH . C 3 HOH A 138 445 200 HOH HOH . C 3 HOH A 139 446 205 HOH HOH . C 3 HOH A 140 447 212 HOH HOH . C 3 HOH A 141 448 213 HOH HOH . C 3 HOH A 142 449 215 HOH HOH . C 3 HOH A 143 450 222 HOH HOH . C 3 HOH A 144 451 227 HOH HOH . C 3 HOH A 145 452 229 HOH HOH . C 3 HOH A 146 453 233 HOH HOH . C 3 HOH A 147 454 245 HOH HOH . C 3 HOH A 148 455 246 HOH HOH . C 3 HOH A 149 456 247 HOH HOH . C 3 HOH A 150 457 248 HOH HOH . C 3 HOH A 151 458 249 HOH HOH . C 3 HOH A 152 459 250 HOH HOH . C 3 HOH A 153 460 251 HOH HOH . C 3 HOH A 154 461 252 HOH HOH . C 3 HOH A 155 462 253 HOH HOH . C 3 HOH A 156 463 255 HOH HOH . C 3 HOH A 157 464 258 HOH HOH . C 3 HOH A 158 465 265 HOH HOH . C 3 HOH A 159 466 266 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 ANP . . . B 2 -10.803 -15.473 10.142 1 51.94 ? PG ANP 307 A 1 HETATM 2 O O1G ANP . . . B 2 -10.469 -14.474 11.302 1 55.55 ? O1G ANP 307 A 1 HETATM 3 O O2G ANP . . . B 2 -10.193 -16.856 10.414 1 53.04 ? O2G ANP 307 A 1 HETATM 4 O O3G ANP . . . B 2 -12.295 -15.457 9.742 1 55 ? O3G ANP 307 A 1 HETATM 5 P PB ANP . . . B 2 -10.09 -13.669 7.668 1 27.51 ? PB ANP 307 A 1 HETATM 6 O O1B ANP . . . B 2 -11.01 -12.743 8.472 1 28.84 ? O1B ANP 307 A 1 HETATM 7 O O2B ANP . . . B 2 -10.679 -14.1 6.273 1 23.8 ? O2B ANP 307 A 1 HETATM 8 N N3B ANP . . . B 2 -9.88 -15.003 8.688 1 26.21 ? N3B ANP 307 A 1 HETATM 9 P PA ANP . . . B 2 -9.229 -11.335 7.104 1 43.69 ? PA ANP 307 A 1 HETATM 10 O O1A ANP . . . B 2 -9.434 -10.618 8.505 1 44.35 ? O1A ANP 307 A 1 HETATM 11 O O2A ANP . . . B 2 -8.684 -10.755 5.837 1 27.32 ? O2A ANP 307 A 1 HETATM 12 O O3A ANP . . . B 2 -8.722 -12.854 7.416 1 28.34 ? O3A ANP 307 A 1 HETATM 13 O O5' ANP . . . B 2 -10.787 -11.593 6.568 1 47.27 ? O5' ANP 307 A 1 HETATM 14 C C5' ANP . . . B 2 -11.739 -10.675 5.895 1 51.77 ? C5' ANP 307 A 1 HETATM 15 C C4' ANP . . . B 2 -13.05 -10.473 6.716 1 51.89 ? C4' ANP 307 A 1 HETATM 16 O O4' ANP . . . B 2 -12.664 -9.924 8.011 1 55.4 ? O4' ANP 307 A 1 HETATM 17 C C3' ANP . . . B 2 -13.983 -9.393 6.115 1 49.24 ? C3' ANP 307 A 1 HETATM 18 O O3' ANP . . . B 2 -15.387 -9.47 6.485 1 33.85 ? O3' ANP 307 A 1 HETATM 19 C C2' ANP . . . B 2 -13.292 -8.092 6.588 1 51.5 ? C2' ANP 307 A 1 HETATM 20 O O2' ANP . . . B 2 -14.1 -6.907 6.69 1 46.87 ? O2' ANP 307 A 1 HETATM 21 C C1' ANP . . . B 2 -12.593 -8.463 7.909 1 54.23 ? C1' ANP 307 A 1 HETATM 22 N N9 ANP . . . B 2 -11.221 -7.788 7.955 1 54.91 ? N9 ANP 307 A 1 HETATM 23 C C8 ANP . . . B 2 -10.214 -7.723 7.027 1 55.22 ? C8 ANP 307 A 1 HETATM 24 N N7 ANP . . . B 2 -9.124 -6.973 7.445 1 56.34 ? N7 ANP 307 A 1 HETATM 25 C C5 ANP . . . B 2 -9.392 -6.511 8.691 1 46.15 ? C5 ANP 307 A 1 HETATM 26 C C6 ANP . . . B 2 -8.622 -5.687 9.723 1 42.16 ? C6 ANP 307 A 1 HETATM 27 N N6 ANP . . . B 2 -7.228 -5.047 9.558 1 17.84 ? N6 ANP 307 A 1 HETATM 28 N N1 ANP . . . B 2 -9.568 -5.655 10.841 1 42.05 ? N1 ANP 307 A 1 HETATM 29 C C2 ANP . . . B 2 -10.832 -6.256 11.119 1 16.88 ? C2 ANP 307 A 1 HETATM 30 N N3 ANP . . . B 2 -11.464 -6.902 10.205 1 48.08 ? N3 ANP 307 A 1 HETATM 31 C C4 ANP . . . B 2 -10.793 -7.075 9.012 1 51 ? C4 ANP 307 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 31 #