data_3TDH # _model_server_result.job_id QjRJysgPbj7h0C5FXPYryQ _model_server_result.datetime_utc '2025-07-03 12:12:45' _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 3tdh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":323}' # _entry.id 3TDH # _exptl.entry_id 3TDH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ADENOSINE MONOPHOSPHATE' _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 3TDH _cell.length_a 94.97 _cell.length_b 242.378 _cell.length_c 79.352 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3TDH _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 # _chem_comp.formula 'C10 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id AMP _chem_comp.mon_nstd_flag . _chem_comp.name 'ADENOSINE MONOPHOSPHATE' _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 P O1P AMP doub 13 n n P O2P AMP sing 14 n n P O3P AMP sing 15 n n P O5' AMP sing 16 n n O2P HOP2 AMP sing 17 n n O3P HOP3 AMP sing 18 n n O5' C5' AMP sing 19 n n C5' C4' AMP sing 20 n n C5' "H5'1" AMP sing 21 n n C5' "H5'2" AMP sing 22 n n C4' O4' AMP sing 23 n n C4' C3' AMP sing 24 n n C4' H4' AMP sing 25 n n O4' C1' AMP sing 26 n n C3' O3' AMP sing 27 n n C3' C2' AMP sing 28 n n C3' H3' AMP sing 29 n n O3' HO3' AMP sing 30 n n C2' O2' AMP sing 31 n n C2' C1' AMP sing 32 n n C2' H2' AMP sing 33 n n O2' HO2' AMP sing 34 n n C1' N9 AMP sing 35 n n C1' H1' AMP sing 36 n n N9 C8 AMP sing 37 n y N9 C4 AMP sing 38 n y C8 N7 AMP doub 39 n y C8 H8 AMP sing 40 n n N7 C5 AMP sing 41 n y C5 C6 AMP sing 42 n y C5 C4 AMP doub 43 n y C6 N6 AMP sing 44 n n C6 N1 AMP doub 45 n y N6 HN61 AMP sing 46 n n N6 HN62 AMP sing 47 n n N1 C2 AMP sing 48 n y C2 N3 AMP doub 49 n y C2 H2 AMP sing 50 n n N3 C4 AMP sing 51 n y # _atom_sites.entry_id 3TDH _atom_sites.fract_transf_matrix[1][1] 0.01053 _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] 0.004126 _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] 0.012602 _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 D 4 AMP C 1 323 1 AMP AMP . E 5 HOH A 1 43 43 HOH HOH . E 5 HOH A 2 47 47 HOH HOH . E 5 HOH A 3 49 49 HOH HOH . E 5 HOH A 4 57 57 HOH HOH . E 5 HOH A 5 62 62 HOH HOH . E 5 HOH A 6 67 67 HOH HOH . E 5 HOH A 7 68 68 HOH HOH . E 5 HOH A 8 70 70 HOH HOH . E 5 HOH A 9 74 74 HOH HOH . E 5 HOH A 10 75 75 HOH HOH . E 5 HOH A 11 80 80 HOH HOH . E 5 HOH A 12 83 83 HOH HOH . E 5 HOH A 13 86 86 HOH HOH . E 5 HOH A 14 92 92 HOH HOH . E 5 HOH A 15 93 93 HOH HOH . E 5 HOH A 16 106 106 HOH HOH . E 5 HOH A 17 114 114 HOH HOH . E 5 HOH A 18 116 116 HOH HOH . E 5 HOH A 19 119 119 HOH HOH . E 5 HOH A 20 122 122 HOH HOH . E 5 HOH A 21 124 124 HOH HOH . E 5 HOH A 22 134 134 HOH HOH . E 5 HOH A 23 154 154 HOH HOH . E 5 HOH A 24 156 156 HOH HOH . E 5 HOH A 25 165 165 HOH HOH . E 5 HOH A 26 178 178 HOH HOH . F 5 HOH B 1 6 6 HOH HOH . F 5 HOH B 2 14 14 HOH HOH . F 5 HOH B 3 22 22 HOH HOH . F 5 HOH B 4 24 24 HOH HOH . F 5 HOH B 5 33 33 HOH HOH . F 5 HOH B 6 36 36 HOH HOH . F 5 HOH B 7 40 40 HOH HOH . F 5 HOH B 8 42 42 HOH HOH . F 5 HOH B 9 51 51 HOH HOH . F 5 HOH B 10 55 55 HOH HOH . F 5 HOH B 11 58 58 HOH HOH . F 5 HOH B 12 72 72 HOH HOH . F 5 HOH B 13 76 76 HOH HOH . F 5 HOH B 14 82 82 HOH HOH . F 5 HOH B 15 87 87 HOH HOH . F 5 HOH B 16 97 97 HOH HOH . F 5 HOH B 17 104 104 HOH HOH . F 5 HOH B 18 107 107 HOH HOH . F 5 HOH B 19 110 110 HOH HOH . F 5 HOH B 20 112 112 HOH HOH . F 5 HOH B 21 115 115 HOH HOH . F 5 HOH B 22 127 127 HOH HOH . F 5 HOH B 23 130 130 HOH HOH . F 5 HOH B 24 137 137 HOH HOH . F 5 HOH B 25 138 138 HOH HOH . F 5 HOH B 26 140 140 HOH HOH . F 5 HOH B 27 141 141 HOH HOH . F 5 HOH B 28 151 151 HOH HOH . F 5 HOH B 29 155 155 HOH HOH . F 5 HOH B 30 157 157 HOH HOH . F 5 HOH B 31 164 164 HOH HOH . F 5 HOH B 32 172 172 HOH HOH . F 5 HOH B 33 173 173 HOH HOH . F 5 HOH B 34 176 176 HOH HOH . G 5 HOH C 1 324 1 HOH HOH . G 5 HOH C 2 325 2 HOH HOH . G 5 HOH C 3 326 3 HOH HOH . G 5 HOH C 4 327 4 HOH HOH . G 5 HOH C 5 328 5 HOH HOH . G 5 HOH C 6 329 7 HOH HOH . G 5 HOH C 7 330 8 HOH HOH . G 5 HOH C 8 331 9 HOH HOH . G 5 HOH C 9 332 11 HOH HOH . G 5 HOH C 10 333 12 HOH HOH . G 5 HOH C 11 334 13 HOH HOH . G 5 HOH C 12 335 17 HOH HOH . G 5 HOH C 13 336 18 HOH HOH . G 5 HOH C 14 337 19 HOH HOH . G 5 HOH C 15 338 20 HOH HOH . G 5 HOH C 16 339 25 HOH HOH . G 5 HOH C 17 340 26 HOH HOH . G 5 HOH C 18 341 27 HOH HOH . G 5 HOH C 19 342 29 HOH HOH . G 5 HOH C 20 343 30 HOH HOH . G 5 HOH C 21 344 31 HOH HOH . G 5 HOH C 22 345 32 HOH HOH . G 5 HOH C 23 346 34 HOH HOH . G 5 HOH C 24 347 35 HOH HOH . G 5 HOH C 25 348 37 HOH HOH . G 5 HOH C 26 349 38 HOH HOH . G 5 HOH C 27 350 39 HOH HOH . G 5 HOH C 28 351 41 HOH HOH . G 5 HOH C 29 352 44 HOH HOH . G 5 HOH C 30 353 45 HOH HOH . G 5 HOH C 31 354 46 HOH HOH . G 5 HOH C 32 355 48 HOH HOH . G 5 HOH C 33 356 50 HOH HOH . G 5 HOH C 34 357 52 HOH HOH . G 5 HOH C 35 358 53 HOH HOH . G 5 HOH C 36 359 54 HOH HOH . G 5 HOH C 37 360 59 HOH HOH . G 5 HOH C 38 361 60 HOH HOH . G 5 HOH C 39 362 61 HOH HOH . G 5 HOH C 40 363 63 HOH HOH . G 5 HOH C 41 364 64 HOH HOH . G 5 HOH C 42 365 65 HOH HOH . G 5 HOH C 43 366 66 HOH HOH . G 5 HOH C 44 367 69 HOH HOH . G 5 HOH C 45 368 71 HOH HOH . G 5 HOH C 46 369 73 HOH HOH . G 5 HOH C 47 370 77 HOH HOH . G 5 HOH C 48 371 78 HOH HOH . G 5 HOH C 49 372 79 HOH HOH . G 5 HOH C 50 373 81 HOH HOH . G 5 HOH C 51 374 84 HOH HOH . G 5 HOH C 52 375 85 HOH HOH . G 5 HOH C 53 376 88 HOH HOH . G 5 HOH C 54 377 89 HOH HOH . G 5 HOH C 55 378 90 HOH HOH . G 5 HOH C 56 379 91 HOH HOH . G 5 HOH C 57 380 94 HOH HOH . G 5 HOH C 58 381 95 HOH HOH . G 5 HOH C 59 382 96 HOH HOH . G 5 HOH C 60 383 98 HOH HOH . G 5 HOH C 61 384 99 HOH HOH . G 5 HOH C 62 385 100 HOH HOH . G 5 HOH C 63 386 101 HOH HOH . G 5 HOH C 64 387 102 HOH HOH . G 5 HOH C 65 388 103 HOH HOH . G 5 HOH C 66 389 108 HOH HOH . G 5 HOH C 67 390 109 HOH HOH . G 5 HOH C 68 391 111 HOH HOH . G 5 HOH C 69 392 113 HOH HOH . G 5 HOH C 70 393 117 HOH HOH . G 5 HOH C 71 394 118 HOH HOH . G 5 HOH C 72 395 120 HOH HOH . G 5 HOH C 73 396 121 HOH HOH . G 5 HOH C 74 397 123 HOH HOH . G 5 HOH C 75 398 125 HOH HOH . G 5 HOH C 76 399 126 HOH HOH . G 5 HOH C 77 400 128 HOH HOH . G 5 HOH C 78 401 129 HOH HOH . G 5 HOH C 79 402 131 HOH HOH . G 5 HOH C 80 403 132 HOH HOH . G 5 HOH C 81 404 135 HOH HOH . G 5 HOH C 82 405 136 HOH HOH . G 5 HOH C 83 406 139 HOH HOH . G 5 HOH C 84 407 143 HOH HOH . G 5 HOH C 85 408 145 HOH HOH . G 5 HOH C 86 409 146 HOH HOH . G 5 HOH C 87 410 147 HOH HOH . G 5 HOH C 88 411 148 HOH HOH . G 5 HOH C 89 412 149 HOH HOH . G 5 HOH C 90 413 150 HOH HOH . G 5 HOH C 91 414 152 HOH HOH . G 5 HOH C 92 415 153 HOH HOH . G 5 HOH C 93 416 158 HOH HOH . G 5 HOH C 94 417 159 HOH HOH . G 5 HOH C 95 418 160 HOH HOH . G 5 HOH C 96 419 161 HOH HOH . G 5 HOH C 97 420 162 HOH HOH . G 5 HOH C 98 421 163 HOH HOH . G 5 HOH C 99 422 166 HOH HOH . G 5 HOH C 100 423 167 HOH HOH . G 5 HOH C 101 424 168 HOH HOH . G 5 HOH C 102 425 169 HOH HOH . G 5 HOH C 103 426 170 HOH HOH . G 5 HOH C 104 427 171 HOH HOH . G 5 HOH C 105 428 175 HOH HOH . G 5 HOH C 106 429 177 HOH HOH . G 5 HOH C 107 430 179 HOH HOH . G 5 HOH C 108 431 180 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 P AMP . . . D 4 31.01 66.28 1.806 1 49.66 ? P AMP 323 C 1 HETATM 2 O O1P AMP . . . D 4 31.564 66.333 3.208 1 49.72 ? O1P AMP 323 C 1 HETATM 3 O O2P AMP . . . D 4 32.04 66.483 0.719 1 49.5 ? O2P AMP 323 C 1 HETATM 4 O O3P AMP . . . D 4 30.076 65.113 1.568 1 50.48 ? O3P AMP 323 C 1 HETATM 5 O O5' AMP . . . D 4 30.063 67.581 1.708 1 48.09 ? O5' AMP 323 C 1 HETATM 6 C C5' AMP . . . D 4 29.337 67.902 0.517 1 46.83 ? C5' AMP 323 C 1 HETATM 7 C C4' AMP . . . D 4 29.089 69.411 0.431 1 46 ? C4' AMP 323 C 1 HETATM 8 O O4' AMP . . . D 4 28.492 69.902 1.638 1 45.68 ? O4' AMP 323 C 1 HETATM 9 C C3' AMP . . . D 4 30.377 70.193 0.238 1 45.65 ? C3' AMP 323 C 1 HETATM 10 O O3' AMP . . . D 4 30.143 71.234 -0.713 1 45.04 ? O3' AMP 323 C 1 HETATM 11 C C2' AMP . . . D 4 30.695 70.771 1.606 1 45.55 ? C2' AMP 323 C 1 HETATM 12 O O2' AMP . . . D 4 31.334 72.048 1.529 1 45.85 ? O2' AMP 323 C 1 HETATM 13 C C1' AMP . . . D 4 29.337 70.859 2.288 1 45.47 ? C1' AMP 323 C 1 HETATM 14 N N9 AMP . . . D 4 29.409 70.526 3.732 1 45.66 ? N9 AMP 323 C 1 HETATM 15 C C8 AMP . . . D 4 30.153 69.561 4.31 1 45.37 ? C8 AMP 323 C 1 HETATM 16 N N7 AMP . . . D 4 29.964 69.534 5.655 1 45.94 ? N7 AMP 323 C 1 HETATM 17 C C5 AMP . . . D 4 29.075 70.5 5.954 1 46.08 ? C5 AMP 323 C 1 HETATM 18 C C6 AMP . . . D 4 28.42 71.018 7.18 1 45.91 ? C6 AMP 323 C 1 HETATM 19 N N6 AMP . . . D 4 28.689 70.488 8.392 1 46.38 ? N6 AMP 323 C 1 HETATM 20 N N1 AMP . . . D 4 27.546 72.042 7.048 1 46.42 ? N1 AMP 323 C 1 HETATM 21 C C2 AMP . . . D 4 27.261 72.588 5.849 1 45.97 ? C2 AMP 323 C 1 HETATM 22 N N3 AMP . . . D 4 27.813 72.165 4.696 1 45.79 ? N3 AMP 323 C 1 HETATM 23 C C4 AMP . . . D 4 28.71 71.148 4.682 1 45.81 ? C4 AMP 323 C 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 23 #