data_1YXT # _model_server_result.job_id r1oQ7bGjfP0eLx1DdxN-0g _model_server_result.datetime_utc '2024-12-03 12:21:50' _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 1yxt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":322}' # _entry.id 1YXT # _exptl.entry_id 1YXT _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 120 _cell.entry_id 1YXT _cell.length_a 95.566 _cell.length_b 95.566 _cell.length_c 80.862 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YXT _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _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 _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 1YXT _atom_sites.fract_transf_matrix[1][1] 0.01046 _atom_sites.fract_transf_matrix[1][2] 0.00604 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01208 _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] 0.01237 _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 1 322 1 ANP ANP . C 3 HOH A 1 323 1 HOH HOH . C 3 HOH A 2 324 2 HOH HOH . C 3 HOH A 3 325 3 HOH HOH . C 3 HOH A 4 326 4 HOH HOH . C 3 HOH A 5 327 5 HOH HOH . C 3 HOH A 6 328 6 HOH HOH . C 3 HOH A 7 329 7 HOH HOH . C 3 HOH A 8 330 8 HOH HOH . C 3 HOH A 9 331 9 HOH HOH . C 3 HOH A 10 332 10 HOH HOH . C 3 HOH A 11 333 11 HOH HOH . C 3 HOH A 12 334 12 HOH HOH . C 3 HOH A 13 335 13 HOH HOH . C 3 HOH A 14 336 14 HOH HOH . C 3 HOH A 15 337 15 HOH HOH . C 3 HOH A 16 338 16 HOH HOH . C 3 HOH A 17 339 17 HOH HOH . C 3 HOH A 18 340 18 HOH HOH . C 3 HOH A 19 341 19 HOH HOH . C 3 HOH A 20 342 20 HOH HOH . C 3 HOH A 21 343 21 HOH HOH . C 3 HOH A 22 344 22 HOH HOH . C 3 HOH A 23 345 23 HOH HOH . C 3 HOH A 24 346 24 HOH HOH . C 3 HOH A 25 347 25 HOH HOH . C 3 HOH A 26 348 26 HOH HOH . C 3 HOH A 27 349 27 HOH HOH . C 3 HOH A 28 350 28 HOH HOH . C 3 HOH A 29 351 29 HOH HOH . C 3 HOH A 30 352 30 HOH HOH . C 3 HOH A 31 353 31 HOH HOH . C 3 HOH A 32 354 32 HOH HOH . C 3 HOH A 33 355 33 HOH HOH . C 3 HOH A 34 356 34 HOH HOH . C 3 HOH A 35 357 35 HOH HOH . C 3 HOH A 36 358 36 HOH HOH . C 3 HOH A 37 359 37 HOH HOH . C 3 HOH A 38 360 38 HOH HOH . C 3 HOH A 39 361 39 HOH HOH . C 3 HOH A 40 362 40 HOH HOH . C 3 HOH A 41 363 41 HOH HOH . C 3 HOH A 42 364 42 HOH HOH . C 3 HOH A 43 365 43 HOH HOH . C 3 HOH A 44 366 44 HOH HOH . C 3 HOH A 45 367 45 HOH HOH . C 3 HOH A 46 368 46 HOH HOH . C 3 HOH A 47 369 47 HOH HOH . C 3 HOH A 48 370 48 HOH HOH . C 3 HOH A 49 371 49 HOH HOH . C 3 HOH A 50 372 50 HOH HOH . C 3 HOH A 51 373 51 HOH HOH . C 3 HOH A 52 374 52 HOH HOH . C 3 HOH A 53 375 53 HOH HOH . C 3 HOH A 54 376 54 HOH HOH . C 3 HOH A 55 377 55 HOH HOH . C 3 HOH A 56 378 56 HOH HOH . C 3 HOH A 57 379 57 HOH HOH . C 3 HOH A 58 380 58 HOH HOH . C 3 HOH A 59 381 59 HOH HOH . C 3 HOH A 60 382 60 HOH HOH . C 3 HOH A 61 383 61 HOH HOH . C 3 HOH A 62 384 62 HOH HOH . C 3 HOH A 63 385 63 HOH HOH . C 3 HOH A 64 386 64 HOH HOH . C 3 HOH A 65 387 65 HOH HOH . C 3 HOH A 66 388 66 HOH HOH . C 3 HOH A 67 389 67 HOH HOH . C 3 HOH A 68 390 68 HOH HOH . C 3 HOH A 69 391 69 HOH HOH . C 3 HOH A 70 392 70 HOH HOH . C 3 HOH A 71 393 71 HOH HOH . C 3 HOH A 72 394 72 HOH HOH . C 3 HOH A 73 395 73 HOH HOH . C 3 HOH A 74 396 74 HOH HOH . C 3 HOH A 75 397 75 HOH HOH . C 3 HOH A 76 398 76 HOH HOH . C 3 HOH A 77 399 77 HOH HOH . C 3 HOH A 78 400 78 HOH HOH . C 3 HOH A 79 401 79 HOH HOH . C 3 HOH A 80 402 80 HOH HOH . C 3 HOH A 81 403 81 HOH HOH . C 3 HOH A 82 404 82 HOH HOH . C 3 HOH A 83 405 83 HOH HOH . C 3 HOH A 84 406 84 HOH HOH . C 3 HOH A 85 407 85 HOH HOH . C 3 HOH A 86 408 86 HOH HOH . C 3 HOH A 87 409 87 HOH HOH . C 3 HOH A 88 410 88 HOH HOH . C 3 HOH A 89 411 89 HOH HOH . C 3 HOH A 90 412 90 HOH HOH . C 3 HOH A 91 413 91 HOH HOH . C 3 HOH A 92 414 92 HOH HOH . C 3 HOH A 93 415 93 HOH HOH . C 3 HOH A 94 416 94 HOH HOH . C 3 HOH A 95 417 95 HOH HOH . C 3 HOH A 96 418 96 HOH HOH . C 3 HOH A 97 419 97 HOH HOH . C 3 HOH A 98 420 98 HOH HOH . C 3 HOH A 99 421 99 HOH HOH . C 3 HOH A 100 422 100 HOH HOH . C 3 HOH A 101 423 101 HOH HOH . C 3 HOH A 102 424 102 HOH HOH . C 3 HOH A 103 425 103 HOH HOH . C 3 HOH A 104 426 104 HOH HOH . C 3 HOH A 105 427 105 HOH HOH . C 3 HOH A 106 428 106 HOH HOH . C 3 HOH A 107 429 107 HOH HOH . C 3 HOH A 108 430 108 HOH HOH . C 3 HOH A 109 431 109 HOH HOH . C 3 HOH A 110 432 110 HOH HOH . C 3 HOH A 111 433 111 HOH HOH . C 3 HOH A 112 434 112 HOH HOH . C 3 HOH A 113 435 113 HOH HOH . C 3 HOH A 114 436 114 HOH HOH . C 3 HOH A 115 437 115 HOH HOH . C 3 HOH A 116 438 116 HOH HOH . C 3 HOH A 117 439 117 HOH HOH . C 3 HOH A 118 440 118 HOH HOH . C 3 HOH A 119 441 119 HOH HOH . C 3 HOH A 120 442 120 HOH HOH . C 3 HOH A 121 443 121 HOH HOH . C 3 HOH A 122 444 122 HOH HOH . C 3 HOH A 123 445 123 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 73.375 27.866 2.744 1 45.04 ? PG ANP 322 A 1 HETATM 2 O O1G ANP . . . B 2 72.872 26.413 3.351 1 37.7 ? O1G ANP 322 A 1 HETATM 3 O O2G ANP . . . B 2 73.027 28.008 1.278 1 41.43 ? O2G ANP 322 A 1 HETATM 4 O O3G ANP . . . B 2 72.965 29.088 3.832 1 35.91 ? O3G ANP 322 A 1 HETATM 5 P PB ANP . . . B 2 76.388 28.467 1.873 1 38.19 ? PB ANP 322 A 1 HETATM 6 O O1B ANP . . . B 2 77.369 27.587 1.04 1 37.6 ? O1B ANP 322 A 1 HETATM 7 O O2B ANP . . . B 2 77.299 29.103 3.043 1 45.01 ? O2B ANP 322 A 1 HETATM 8 N N3B ANP . . . B 2 75.145 27.592 2.705 1 37.83 ? N3B ANP 322 A 1 HETATM 9 P PA ANP . . . B 2 74.722 30.402 0.607 1 35.55 ? PA ANP 322 A 1 HETATM 10 O O1A ANP . . . B 2 74.661 30.605 -0.951 1 37.26 ? O1A ANP 322 A 1 HETATM 11 O O2A ANP . . . B 2 73.595 29.647 1.427 1 34.61 ? O2A ANP 322 A 1 HETATM 12 O O3A ANP . . . B 2 76.098 29.718 0.933 1 36.83 ? O3A ANP 322 A 1 HETATM 13 O O5' ANP . . . B 2 74.874 31.855 1.241 1 35.48 ? O5' ANP 322 A 1 HETATM 14 C C5' ANP . . . B 2 75.253 31.845 2.602 1 33.99 ? C5' ANP 322 A 1 HETATM 15 C C4' ANP . . . B 2 74.511 32.985 3.251 1 34.92 ? C4' ANP 322 A 1 HETATM 16 O O4' ANP . . . B 2 74.816 34.271 2.686 1 35.71 ? O4' ANP 322 A 1 HETATM 17 C C3' ANP . . . B 2 72.998 32.868 3.263 1 34.45 ? C3' ANP 322 A 1 HETATM 18 O O3' ANP . . . B 2 72.429 32.126 4.312 1 33.44 ? O3' ANP 322 A 1 HETATM 19 C C2' ANP . . . B 2 72.539 34.291 3.039 1 36.37 ? C2' ANP 322 A 1 HETATM 20 O O2' ANP . . . B 2 72.374 34.825 4.357 1 38.15 ? O2' ANP 322 A 1 HETATM 21 C C1' ANP . . . B 2 73.679 35.098 2.52 1 33.6 ? C1' ANP 322 A 1 HETATM 22 N N9 ANP . . . B 2 73.509 35.297 1.067 1 33.44 ? N9 ANP 322 A 1 HETATM 23 C C8 ANP . . . B 2 73.779 34.381 0.108 1 31.52 ? C8 ANP 322 A 1 HETATM 24 N N7 ANP . . . B 2 73.542 34.854 -1.158 1 30.61 ? N7 ANP 322 A 1 HETATM 25 C C5 ANP . . . B 2 73.077 36.088 -1.012 1 31.72 ? C5 ANP 322 A 1 HETATM 26 C C6 ANP . . . B 2 72.617 37.187 -1.864 1 33.93 ? C6 ANP 322 A 1 HETATM 27 N N6 ANP . . . B 2 72.589 37.001 -3.2 1 34.42 ? N6 ANP 322 A 1 HETATM 28 N N1 ANP . . . B 2 72.244 38.354 -1.297 1 33.91 ? N1 ANP 322 A 1 HETATM 29 C C2 ANP . . . B 2 72.25 38.55 0.029 1 33.75 ? C2 ANP 322 A 1 HETATM 30 N N3 ANP . . . B 2 72.646 37.612 0.915 1 35.18 ? N3 ANP 322 A 1 HETATM 31 C C4 ANP . . . B 2 73.075 36.351 0.402 1 31.84 ? C4 ANP 322 A 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #