data_3AF2 # _model_server_result.job_id AKFER5hEePS0FE_N-0PUtg _model_server_result.datetime_utc '2024-10-11 17:29:14' _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 3af2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":313}' # _entry.id 3AF2 # _exptl.entry_id 3AF2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC 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 120 _cell.entry_id 3AF2 _cell.length_a 103.27 _cell.length_b 103.27 _cell.length_c 91.53 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3AF2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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,J,K,L,M,N _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 6_555 -x,-x+y,-z+1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 30.51 # _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 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id ACP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE" # 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 ACP doub 1 n n PG O2G ACP sing 2 n n PG O3G ACP sing 3 n n PG C3B ACP sing 4 n n O2G HOG2 ACP sing 5 n n O3G HOG3 ACP sing 6 n n PB O1B ACP doub 7 n n PB O2B ACP sing 8 n n PB C3B ACP sing 9 n n PB O3A ACP sing 10 n n O2B HOB2 ACP sing 11 n n C3B H3B1 ACP sing 12 n n C3B H3B2 ACP sing 13 n n PA O1A ACP doub 14 n n PA O2A ACP sing 15 n n PA O3A ACP sing 16 n n PA O5' ACP sing 17 n n O2A HOA2 ACP sing 18 n n O5' C5' ACP sing 19 n n C5' C4' ACP sing 20 n n C5' "H5'1" ACP sing 21 n n C5' "H5'2" ACP sing 22 n n C4' O4' ACP sing 23 n n C4' C3' ACP sing 24 n n C4' H4' ACP sing 25 n n O4' C1' ACP sing 26 n n C3' O3' ACP sing 27 n n C3' C2' ACP sing 28 n n C3' H3' ACP sing 29 n n O3' HO3' ACP sing 30 n n C2' O2' ACP sing 31 n n C2' C1' ACP sing 32 n n C2' H2' ACP sing 33 n n O2' HO2' ACP sing 34 n n C1' N9 ACP sing 35 n n C1' H1' ACP sing 36 n n N9 C8 ACP sing 37 n y N9 C4 ACP sing 38 n y C8 N7 ACP doub 39 n y C8 H8 ACP sing 40 n n N7 C5 ACP sing 41 n y C5 C6 ACP sing 42 n y C5 C4 ACP doub 43 n y C6 N6 ACP sing 44 n n C6 N1 ACP doub 45 n y N6 HN61 ACP sing 46 n n N6 HN62 ACP sing 47 n n N1 C2 ACP sing 48 n y C2 N3 ACP doub 49 n y C2 H2 ACP sing 50 n n N3 C4 ACP sing 51 n y # _atom_sites.entry_id 3AF2 _atom_sites.fract_transf_matrix[1][1] 0.009683 _atom_sites.fract_transf_matrix[1][2] 0.005591 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011181 _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] 0.010925 _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 ACP A 1 313 1 ACP ACP . C 3 GOL A 1 314 1 GOL GOL . D 3 GOL A 1 315 2 GOL GOL . E 3 GOL A 1 316 3 GOL GOL . F 3 GOL A 1 317 4 GOL GOL . G 3 GOL A 1 318 5 GOL GOL . H 3 GOL A 1 319 7 GOL GOL . I 3 GOL A 1 320 8 GOL GOL . J 3 GOL A 1 321 9 GOL GOL . K 3 GOL A 1 322 10 GOL GOL . L 3 GOL A 1 323 11 GOL GOL . M 3 GOL A 1 324 12 GOL GOL . N 4 HOH A 1 325 1 HOH HOH . N 4 HOH A 2 326 2 HOH HOH . N 4 HOH A 3 327 3 HOH HOH . N 4 HOH A 4 328 4 HOH HOH . N 4 HOH A 5 329 5 HOH HOH . N 4 HOH A 6 330 6 HOH HOH . N 4 HOH A 7 331 7 HOH HOH . N 4 HOH A 8 332 8 HOH HOH . N 4 HOH A 9 333 9 HOH HOH . N 4 HOH A 10 334 10 HOH HOH . N 4 HOH A 11 335 11 HOH HOH . N 4 HOH A 12 336 12 HOH HOH . N 4 HOH A 13 337 13 HOH HOH . N 4 HOH A 14 338 14 HOH HOH . N 4 HOH A 15 339 15 HOH HOH . N 4 HOH A 16 340 16 HOH HOH . N 4 HOH A 17 341 17 HOH HOH . N 4 HOH A 18 342 18 HOH HOH . N 4 HOH A 19 343 19 HOH HOH . N 4 HOH A 20 344 20 HOH HOH . N 4 HOH A 21 345 21 HOH HOH . N 4 HOH A 22 346 22 HOH HOH . N 4 HOH A 23 347 23 HOH HOH . N 4 HOH A 24 348 24 HOH HOH . N 4 HOH A 25 349 25 HOH HOH . N 4 HOH A 26 350 26 HOH HOH . N 4 HOH A 27 351 28 HOH HOH . N 4 HOH A 28 352 29 HOH HOH . N 4 HOH A 29 353 30 HOH HOH . N 4 HOH A 30 354 31 HOH HOH . N 4 HOH A 31 355 32 HOH HOH . N 4 HOH A 32 356 33 HOH HOH . N 4 HOH A 33 357 34 HOH HOH . N 4 HOH A 34 358 35 HOH HOH . N 4 HOH A 35 359 36 HOH HOH . N 4 HOH A 36 360 37 HOH HOH . N 4 HOH A 37 361 38 HOH HOH . N 4 HOH A 38 362 39 HOH HOH . N 4 HOH A 39 363 40 HOH HOH . N 4 HOH A 40 364 41 HOH HOH . N 4 HOH A 41 365 42 HOH HOH . N 4 HOH A 42 366 43 HOH HOH . N 4 HOH A 43 367 44 HOH HOH . N 4 HOH A 44 368 45 HOH HOH . N 4 HOH A 45 369 46 HOH HOH . N 4 HOH A 46 370 47 HOH HOH . N 4 HOH A 47 371 48 HOH HOH . N 4 HOH A 48 372 49 HOH HOH . N 4 HOH A 49 373 50 HOH HOH . N 4 HOH A 50 374 51 HOH HOH . N 4 HOH A 51 375 52 HOH HOH . N 4 HOH A 52 376 53 HOH HOH . N 4 HOH A 53 377 54 HOH HOH . N 4 HOH A 54 378 55 HOH HOH . N 4 HOH A 55 379 56 HOH HOH . N 4 HOH A 56 380 57 HOH HOH . N 4 HOH A 57 381 58 HOH HOH . N 4 HOH A 58 382 59 HOH HOH . N 4 HOH A 59 383 60 HOH HOH . N 4 HOH A 60 384 61 HOH HOH . N 4 HOH A 61 385 62 HOH HOH . N 4 HOH A 62 386 63 HOH HOH . N 4 HOH A 63 387 64 HOH HOH . N 4 HOH A 64 388 65 HOH HOH . N 4 HOH A 65 389 66 HOH HOH . N 4 HOH A 66 390 67 HOH HOH . N 4 HOH A 67 391 68 HOH HOH . N 4 HOH A 68 392 69 HOH HOH . N 4 HOH A 69 393 70 HOH HOH . N 4 HOH A 70 394 71 HOH HOH . N 4 HOH A 71 395 72 HOH HOH . N 4 HOH A 72 396 73 HOH HOH . N 4 HOH A 73 397 74 HOH HOH . N 4 HOH A 74 398 75 HOH HOH . N 4 HOH A 75 399 76 HOH HOH . N 4 HOH A 76 400 77 HOH HOH . N 4 HOH A 77 401 78 HOH HOH . N 4 HOH A 78 402 79 HOH HOH . N 4 HOH A 79 403 80 HOH HOH . N 4 HOH A 80 404 81 HOH HOH . N 4 HOH A 81 405 82 HOH HOH . N 4 HOH A 82 406 83 HOH HOH . N 4 HOH A 83 407 84 HOH HOH . N 4 HOH A 84 408 85 HOH HOH . N 4 HOH A 85 409 86 HOH HOH . N 4 HOH A 86 410 87 HOH HOH . N 4 HOH A 87 411 89 HOH HOH . N 4 HOH A 88 412 90 HOH HOH . N 4 HOH A 89 413 91 HOH HOH . N 4 HOH A 90 414 92 HOH HOH . N 4 HOH A 91 415 93 HOH HOH . N 4 HOH A 92 416 94 HOH HOH . N 4 HOH A 93 417 95 HOH HOH . N 4 HOH A 94 418 96 HOH HOH . N 4 HOH A 95 419 97 HOH HOH . N 4 HOH A 96 420 98 HOH HOH . N 4 HOH A 97 421 99 HOH HOH . N 4 HOH A 98 422 100 HOH HOH . N 4 HOH A 99 423 101 HOH HOH . N 4 HOH A 100 424 102 HOH HOH . N 4 HOH A 101 425 103 HOH HOH . N 4 HOH A 102 426 104 HOH HOH . N 4 HOH A 103 427 105 HOH HOH . N 4 HOH A 104 428 106 HOH HOH . N 4 HOH A 105 429 107 HOH HOH . N 4 HOH A 106 430 108 HOH HOH . N 4 HOH A 107 431 109 HOH HOH . N 4 HOH A 108 432 110 HOH HOH . N 4 HOH A 109 433 111 HOH HOH . N 4 HOH A 110 434 112 HOH HOH . N 4 HOH A 111 435 113 HOH HOH . N 4 HOH A 112 436 114 HOH HOH . N 4 HOH A 113 437 115 HOH HOH . N 4 HOH A 114 438 116 HOH HOH . N 4 HOH A 115 439 117 HOH HOH . N 4 HOH A 116 440 118 HOH HOH . N 4 HOH A 117 441 119 HOH HOH . N 4 HOH A 118 442 120 HOH HOH . N 4 HOH A 119 443 121 HOH HOH . N 4 HOH A 120 444 122 HOH HOH . N 4 HOH A 121 445 123 HOH HOH . N 4 HOH A 122 446 124 HOH HOH . N 4 HOH A 123 447 125 HOH HOH . N 4 HOH A 124 448 126 HOH HOH . N 4 HOH A 125 449 127 HOH HOH . N 4 HOH A 126 450 128 HOH HOH . N 4 HOH A 127 451 129 HOH HOH . N 4 HOH A 128 452 130 HOH HOH . N 4 HOH A 129 453 131 HOH HOH . N 4 HOH A 130 454 132 HOH HOH . N 4 HOH A 131 455 133 HOH HOH . N 4 HOH A 132 456 135 HOH HOH . N 4 HOH A 133 457 136 HOH HOH . N 4 HOH A 134 458 137 HOH HOH . N 4 HOH A 135 459 138 HOH HOH . N 4 HOH A 136 460 139 HOH HOH . N 4 HOH A 137 461 140 HOH HOH . N 4 HOH A 138 462 141 HOH HOH . N 4 HOH A 139 463 142 HOH HOH . N 4 HOH A 140 464 143 HOH HOH . N 4 HOH A 141 465 144 HOH HOH . N 4 HOH A 142 466 145 HOH HOH . N 4 HOH A 143 467 146 HOH HOH . N 4 HOH A 144 468 147 HOH HOH . N 4 HOH A 145 469 148 HOH HOH . N 4 HOH A 146 470 149 HOH HOH . N 4 HOH A 147 471 150 HOH HOH . N 4 HOH A 148 472 151 HOH HOH . N 4 HOH A 149 473 152 HOH HOH . N 4 HOH A 150 474 153 HOH HOH . N 4 HOH A 151 475 154 HOH HOH . N 4 HOH A 152 476 155 HOH HOH . N 4 HOH A 153 477 156 HOH HOH . N 4 HOH A 154 478 157 HOH HOH . N 4 HOH A 155 479 158 HOH HOH . N 4 HOH A 156 480 159 HOH HOH . N 4 HOH A 157 481 160 HOH HOH . N 4 HOH A 158 482 161 HOH HOH . N 4 HOH A 159 483 162 HOH HOH . N 4 HOH A 160 484 163 HOH HOH . N 4 HOH A 161 485 164 HOH HOH . N 4 HOH A 162 486 165 HOH HOH . N 4 HOH A 163 487 166 HOH HOH . N 4 HOH A 164 488 167 HOH HOH . N 4 HOH A 165 489 168 HOH HOH . N 4 HOH A 166 490 169 HOH HOH . N 4 HOH A 167 491 171 HOH HOH . N 4 HOH A 168 492 172 HOH HOH . N 4 HOH A 169 493 173 HOH HOH . N 4 HOH A 170 494 174 HOH HOH . N 4 HOH A 171 495 175 HOH HOH . N 4 HOH A 172 496 176 HOH HOH . N 4 HOH A 173 497 177 HOH HOH . N 4 HOH A 174 498 178 HOH HOH . N 4 HOH A 175 499 179 HOH HOH . N 4 HOH A 176 500 180 HOH HOH . N 4 HOH A 177 501 181 HOH HOH . N 4 HOH A 178 502 182 HOH HOH . N 4 HOH A 179 503 183 HOH HOH . N 4 HOH A 180 504 184 HOH HOH . N 4 HOH A 181 505 185 HOH HOH . N 4 HOH A 182 506 186 HOH HOH . N 4 HOH A 183 507 187 HOH HOH . N 4 HOH A 184 508 188 HOH HOH . N 4 HOH A 185 509 189 HOH HOH . N 4 HOH A 186 510 190 HOH HOH . N 4 HOH A 187 511 191 HOH HOH . N 4 HOH A 188 512 192 HOH HOH . N 4 HOH A 189 513 193 HOH HOH . N 4 HOH A 190 514 194 HOH HOH . N 4 HOH A 191 515 195 HOH HOH . N 4 HOH A 192 516 196 HOH HOH . N 4 HOH A 193 517 197 HOH HOH . N 4 HOH A 194 518 198 HOH HOH . N 4 HOH A 195 519 199 HOH HOH . N 4 HOH A 196 520 200 HOH HOH . N 4 HOH A 197 521 201 HOH HOH . N 4 HOH A 198 522 202 HOH HOH . N 4 HOH A 199 523 204 HOH HOH . N 4 HOH A 200 524 205 HOH HOH . N 4 HOH A 201 525 206 HOH HOH . N 4 HOH A 202 526 207 HOH HOH . N 4 HOH A 203 527 208 HOH HOH . N 4 HOH A 204 528 209 HOH HOH . N 4 HOH A 205 529 210 HOH HOH . N 4 HOH A 206 530 211 HOH HOH . N 4 HOH A 207 531 212 HOH HOH . N 4 HOH A 208 532 213 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 ACP . . . B 2 -37.462 28.307 -4.09 1 59.26 ? PG ACP 313 A 1 HETATM 2 O O1G ACP . . . B 2 -37.614 29.009 -5.545 1 64.49 ? O1G ACP 313 A 1 HETATM 3 O O2G ACP . . . B 2 -35.854 28.183 -3.949 1 59.56 ? O2G ACP 313 A 1 HETATM 4 O O3G ACP . . . B 2 -38.126 26.988 -3.983 1 59.59 ? O3G ACP 313 A 1 HETATM 5 P PB ACP . . . B 2 -36.783 30.805 -2.403 1 52.44 ? PB ACP 313 A 1 HETATM 6 O O1B ACP . . . B 2 -36.469 31.759 -3.488 1 51.46 ? O1B ACP 313 A 1 HETATM 7 O O2B ACP . . . B 2 -35.674 30.04 -1.799 1 66.51 ? O2B ACP 313 A 1 HETATM 8 C C3B ACP . . . B 2 -38.078 29.58 -2.899 1 54.21 ? C3B ACP 313 A 1 HETATM 9 P PA ACP . . . B 2 -38.841 32.493 -1.212 1 55.28 ? PA ACP 313 A 1 HETATM 10 O O1A ACP . . . B 2 -38.939 33.112 -2.552 1 58.17 ? O1A ACP 313 A 1 HETATM 11 O O2A ACP . . . B 2 -38.818 33.384 -0.02 1 63.53 ? O2A ACP 313 A 1 HETATM 12 O O3A ACP . . . B 2 -37.481 31.602 -1.16 1 63.51 ? O3A ACP 313 A 1 HETATM 13 O O5' ACP . . . B 2 -40.027 31.399 -0.945 1 55.64 ? O5' ACP 313 A 1 HETATM 14 C C5' ACP . . . B 2 -41.339 31.703 -1.4 1 66.86 ? C5' ACP 313 A 1 HETATM 15 C C4' ACP . . . B 2 -42.428 30.811 -0.779 1 81.07 ? C4' ACP 313 A 1 HETATM 16 O O4' ACP . . . B 2 -43.624 31.621 -0.598 1 87.49 ? O4' ACP 313 A 1 HETATM 17 C C3' ACP . . . B 2 -42.89 29.661 -1.688 1 85.34 ? C3' ACP 313 A 1 HETATM 18 O O3' ACP . . . B 2 -43.313 28.54 -0.89 1 84.7 ? O3' ACP 313 A 1 HETATM 19 C C2' ACP . . . B 2 -44.051 30.257 -2.511 1 84.51 ? C2' ACP 313 A 1 HETATM 20 O O2' ACP . . . B 2 -45.19 29.397 -2.459 1 79.28 ? O2' ACP 313 A 1 HETATM 21 C C1' ACP . . . B 2 -44.431 31.576 -1.823 1 88.77 ? C1' ACP 313 A 1 HETATM 22 N N9 ACP . . . B 2 -44.369 32.821 -2.673 1 93.98 ? N9 ACP 313 A 1 HETATM 23 C C8 ACP . . . B 2 -43.388 33.093 -3.535 1 97.06 ? C8 ACP 313 A 1 HETATM 24 N N7 ACP . . . B 2 -43.554 34.305 -4.07 1 97.43 ? N7 ACP 313 A 1 HETATM 25 C C5 ACP . . . B 2 -44.671 34.819 -3.568 1 99.02 ? C5 ACP 313 A 1 HETATM 26 C C6 ACP . . . B 2 -45.339 36.022 -3.777 1 99.16 ? C6 ACP 313 A 1 HETATM 27 N N6 ACP . . . B 2 -44.858 36.871 -4.676 1 99.43 ? N6 ACP 313 A 1 HETATM 28 N N1 ACP . . . B 2 -46.458 36.302 -3.086 1 95.78 ? N1 ACP 313 A 1 HETATM 29 C C2 ACP . . . B 2 -46.923 35.402 -2.233 1 96.82 ? C2 ACP 313 A 1 HETATM 30 N N3 ACP . . . B 2 -46.326 34.232 -2.032 1 96.6 ? N3 ACP 313 A 1 HETATM 31 C C4 ACP . . . B 2 -45.186 33.89 -2.667 1 98.91 ? C4 ACP 313 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 31 #