data_1DAG # _model_server_result.job_id tXw0VZhdbK4SwTNtJjvnrA _model_server_result.datetime_utc '2024-12-04 02:42:36' _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 1dag # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":226}' # _entry.id 1DAG # _exptl.entry_id 1DAG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 3 _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 107.1 _cell.angle_gamma 90 _cell.entry_id 1DAG _cell.length_a 73.2 _cell.length_b 49.2 _cell.length_c 61.8 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DAG _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA,PQS _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 _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' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 1DAG _atom_sites.fract_transf_matrix[1][1] 0.013661 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004203 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020325 _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] 0.01693 _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 DSD A 1 225 225 DSD DSD . C 3 ACP A 1 226 226 ACP ACP . D 4 HOH A 1 227 227 HOH HOH . D 4 HOH A 2 228 228 HOH HOH . D 4 HOH A 3 229 229 HOH HOH . D 4 HOH A 4 230 230 HOH HOH . D 4 HOH A 5 231 231 HOH HOH . D 4 HOH A 6 232 232 HOH HOH . D 4 HOH A 7 233 233 HOH HOH . D 4 HOH A 8 234 234 HOH HOH . D 4 HOH A 9 235 235 HOH HOH . D 4 HOH A 10 236 236 HOH HOH . D 4 HOH A 11 237 237 HOH HOH . D 4 HOH A 12 238 238 HOH HOH . D 4 HOH A 13 239 239 HOH HOH . D 4 HOH A 14 240 240 HOH HOH . D 4 HOH A 15 241 241 HOH HOH . D 4 HOH A 16 242 242 HOH HOH . D 4 HOH A 17 243 243 HOH HOH . D 4 HOH A 18 244 244 HOH HOH . D 4 HOH A 19 245 245 HOH HOH . D 4 HOH A 20 246 246 HOH HOH . D 4 HOH A 21 247 247 HOH HOH . D 4 HOH A 22 248 248 HOH HOH . D 4 HOH A 23 249 249 HOH HOH . D 4 HOH A 24 250 250 HOH HOH . D 4 HOH A 25 251 251 HOH HOH . D 4 HOH A 26 252 252 HOH HOH . D 4 HOH A 27 253 253 HOH HOH . D 4 HOH A 28 254 254 HOH HOH . D 4 HOH A 29 255 255 HOH HOH . D 4 HOH A 30 256 256 HOH HOH . D 4 HOH A 31 257 257 HOH HOH . D 4 HOH A 32 258 258 HOH HOH . D 4 HOH A 33 259 259 HOH HOH . D 4 HOH A 34 260 260 HOH HOH . D 4 HOH A 35 261 261 HOH HOH . D 4 HOH A 36 262 262 HOH HOH . D 4 HOH A 37 263 263 HOH HOH . D 4 HOH A 38 264 264 HOH HOH . D 4 HOH A 39 265 265 HOH HOH . D 4 HOH A 40 266 266 HOH HOH . D 4 HOH A 41 267 267 HOH HOH . D 4 HOH A 42 268 268 HOH HOH . D 4 HOH A 43 269 269 HOH HOH . D 4 HOH A 44 270 270 HOH HOH . D 4 HOH A 45 271 271 HOH HOH . D 4 HOH A 46 272 272 HOH HOH . D 4 HOH A 47 273 273 HOH HOH . D 4 HOH A 48 274 274 HOH HOH . D 4 HOH A 49 275 275 HOH HOH . D 4 HOH A 50 276 276 HOH HOH . D 4 HOH A 51 277 277 HOH HOH . D 4 HOH A 52 278 278 HOH HOH . D 4 HOH A 53 279 279 HOH HOH . D 4 HOH A 54 280 280 HOH HOH . D 4 HOH A 55 281 281 HOH HOH . D 4 HOH A 56 282 282 HOH HOH . D 4 HOH A 57 283 283 HOH HOH . D 4 HOH A 58 284 284 HOH HOH . D 4 HOH A 59 285 285 HOH HOH . D 4 HOH A 60 286 286 HOH HOH . D 4 HOH A 61 287 287 HOH HOH . D 4 HOH A 62 288 288 HOH HOH . D 4 HOH A 63 289 289 HOH HOH . D 4 HOH A 64 290 290 HOH HOH . D 4 HOH A 65 291 291 HOH HOH . D 4 HOH A 66 292 292 HOH HOH . D 4 HOH A 67 293 293 HOH HOH . D 4 HOH A 68 294 294 HOH HOH . D 4 HOH A 69 295 295 HOH HOH . D 4 HOH A 70 296 296 HOH HOH . D 4 HOH A 71 297 297 HOH HOH . D 4 HOH A 72 298 298 HOH HOH . D 4 HOH A 73 299 299 HOH HOH . D 4 HOH A 74 300 300 HOH HOH . D 4 HOH A 75 301 301 HOH HOH . D 4 HOH A 76 302 302 HOH HOH . D 4 HOH A 77 303 303 HOH HOH . D 4 HOH A 78 304 304 HOH HOH . D 4 HOH A 79 305 305 HOH HOH . D 4 HOH A 80 306 306 HOH HOH . D 4 HOH A 81 307 307 HOH HOH . D 4 HOH A 82 308 308 HOH HOH . D 4 HOH A 83 309 309 HOH HOH . D 4 HOH A 84 310 310 HOH HOH . D 4 HOH A 85 311 311 HOH HOH . D 4 HOH A 86 312 312 HOH HOH . D 4 HOH A 87 313 313 HOH HOH . D 4 HOH A 88 314 314 HOH HOH . D 4 HOH A 89 315 315 HOH HOH . D 4 HOH A 90 316 316 HOH HOH . D 4 HOH A 91 317 317 HOH HOH . D 4 HOH A 92 318 318 HOH HOH . D 4 HOH A 93 319 319 HOH HOH . D 4 HOH A 94 320 320 HOH HOH . D 4 HOH A 95 321 321 HOH HOH . D 4 HOH A 96 322 322 HOH HOH . D 4 HOH A 97 323 323 HOH HOH . D 4 HOH A 98 324 324 HOH HOH . D 4 HOH A 99 325 325 HOH HOH . D 4 HOH A 100 326 326 HOH HOH . D 4 HOH A 101 327 327 HOH HOH . D 4 HOH A 102 328 328 HOH HOH . D 4 HOH A 103 329 329 HOH HOH . D 4 HOH A 104 330 330 HOH HOH . D 4 HOH A 105 331 331 HOH HOH . D 4 HOH A 106 332 332 HOH HOH . D 4 HOH A 107 333 333 HOH HOH . D 4 HOH A 108 334 334 HOH HOH . D 4 HOH A 109 335 335 HOH HOH . D 4 HOH A 110 336 336 HOH HOH . D 4 HOH A 111 337 337 HOH HOH . D 4 HOH A 112 338 338 HOH HOH . D 4 HOH A 113 339 339 HOH HOH . D 4 HOH A 114 340 340 HOH HOH . D 4 HOH A 115 341 341 HOH HOH . D 4 HOH A 116 342 342 HOH HOH . D 4 HOH A 117 343 343 HOH HOH . D 4 HOH A 118 344 344 HOH HOH . D 4 HOH A 119 345 345 HOH HOH . D 4 HOH A 120 346 346 HOH HOH . D 4 HOH A 121 347 347 HOH HOH . D 4 HOH A 122 348 348 HOH HOH . D 4 HOH A 123 349 349 HOH HOH . D 4 HOH A 124 350 350 HOH HOH . D 4 HOH A 125 351 351 HOH HOH . D 4 HOH A 126 352 352 HOH HOH . D 4 HOH A 127 353 353 HOH HOH . D 4 HOH A 128 354 354 HOH HOH . D 4 HOH A 129 355 355 HOH HOH . D 4 HOH A 130 356 356 HOH HOH . D 4 HOH A 131 357 357 HOH HOH . D 4 HOH A 132 358 358 HOH HOH . D 4 HOH A 133 359 359 HOH HOH . D 4 HOH A 134 360 360 HOH HOH . D 4 HOH A 135 361 361 HOH HOH . D 4 HOH A 136 362 362 HOH HOH . D 4 HOH A 137 363 363 HOH HOH . D 4 HOH A 138 364 364 HOH HOH . D 4 HOH A 139 365 365 HOH HOH . D 4 HOH A 140 366 366 HOH HOH . D 4 HOH A 141 367 367 HOH HOH . D 4 HOH A 142 368 368 HOH HOH . D 4 HOH A 143 369 369 HOH HOH . D 4 HOH A 144 370 370 HOH HOH . D 4 HOH A 145 371 371 HOH HOH . D 4 HOH A 146 372 372 HOH HOH . D 4 HOH A 147 373 373 HOH HOH . D 4 HOH A 148 374 374 HOH HOH . D 4 HOH A 149 375 375 HOH HOH . D 4 HOH A 150 376 376 HOH HOH . D 4 HOH A 151 377 377 HOH HOH . D 4 HOH A 152 378 378 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 . . . C 3 0.62 23.642 12.169 1 37.99 ? PG ACP 226 A 1 HETATM 2 O O1G ACP . . . C 3 0.273 24.273 10.873 1 35.81 ? O1G ACP 226 A 1 HETATM 3 O O2G ACP . . . C 3 1.066 24.819 13.185 1 36.86 ? O2G ACP 226 A 1 HETATM 4 O O3G ACP . . . C 3 -0.48 22.815 12.72 1 38.75 ? O3G ACP 226 A 1 HETATM 5 P PB ACP . . . C 3 3.786 23.037 11.636 1 37.11 ? PB ACP 226 A 1 HETATM 6 O O1B ACP . . . C 3 4.255 23.669 12.903 1 36.07 ? O1B ACP 226 A 1 HETATM 7 O O2B ACP . . . C 3 3.827 23.958 10.446 1 35.7 ? O2B ACP 226 A 1 HETATM 8 C C3B ACP . . . C 3 2.057 22.519 11.941 1 37.23 ? C3B ACP 226 A 1 HETATM 9 P PA ACP . . . C 3 5.441 20.633 12.146 1 36.87 ? PA ACP 226 A 1 HETATM 10 O O1A ACP . . . C 3 4.635 19.987 13.185 1 36.65 ? O1A ACP 226 A 1 HETATM 11 O O2A ACP . . . C 3 6.686 21.211 12.697 1 36.52 ? O2A ACP 226 A 1 HETATM 12 O O3A ACP . . . C 3 4.605 21.727 11.331 1 37.83 ? O3A ACP 226 A 1 HETATM 13 O O5' ACP . . . C 3 5.749 19.614 10.953 1 38.93 ? O5' ACP 226 A 1 HETATM 14 C C5' ACP . . . C 3 4.654 19.131 10.142 1 37.66 ? C5' ACP 226 A 1 HETATM 15 C C4' ACP . . . C 3 5.025 17.72 9.713 1 39.98 ? C4' ACP 226 A 1 HETATM 16 O O4' ACP . . . C 3 6.18 17.789 8.844 1 40.3 ? O4' ACP 226 A 1 HETATM 17 C C3' ACP . . . C 3 5.411 16.843 10.914 1 41.14 ? C3' ACP 226 A 1 HETATM 18 O O3' ACP . . . C 3 4.898 15.51 10.777 1 44.2 ? O3' ACP 226 A 1 HETATM 19 C C2' ACP . . . C 3 6.933 16.867 10.936 1 39.48 ? C2' ACP 226 A 1 HETATM 20 O O2' ACP . . . C 3 7.507 15.686 11.533 1 38.65 ? O2' ACP 226 A 1 HETATM 21 C C1' ACP . . . C 3 7.277 17.051 9.455 1 39.9 ? C1' ACP 226 A 1 HETATM 22 N N9 ACP . . . C 3 8.597 17.742 9.263 1 39.32 ? N9 ACP 226 A 1 HETATM 23 C C8 ACP . . . C 3 8.828 19.051 9.496 1 36.34 ? C8 ACP 226 A 1 HETATM 24 N N7 ACP . . . C 3 10.117 19.305 9.298 1 36.42 ? N7 ACP 226 A 1 HETATM 25 C C5 ACP . . . C 3 10.72 18.169 8.929 1 37.5 ? C5 ACP 226 A 1 HETATM 26 C C6 ACP . . . C 3 12.023 17.842 8.596 1 38.22 ? C6 ACP 226 A 1 HETATM 27 N N6 ACP . . . C 3 13.016 18.723 8.66 1 34.15 ? N6 ACP 226 A 1 HETATM 28 N N1 ACP . . . C 3 12.28 16.556 8.236 1 37.15 ? N1 ACP 226 A 1 HETATM 29 C C2 ACP . . . C 3 11.31 15.615 8.218 1 38.02 ? C2 ACP 226 A 1 HETATM 30 N N3 ACP . . . C 3 10.072 15.93 8.559 1 37.85 ? N3 ACP 226 A 1 HETATM 31 C C4 ACP . . . C 3 9.727 17.21 8.913 1 38.01 ? C4 ACP 226 A 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #