data_3U3R # _model_server_result.job_id dDbXcLUmIEMKd2LQkAF1kg _model_server_result.datetime_utc '2024-11-23 12:24:27' _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 3u3r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 3U3R # _exptl.entry_id 3U3R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-3'-5'-DIPHOSPHATE" _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 3U3R _cell.length_a 72.38 _cell.length_b 80.27 _cell.length_c 123.16 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3U3R _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 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,D,E _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id A3P _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-3'-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 P1 O1P A3P doub 1 n n P1 O2P A3P sing 2 n n P1 O3P A3P sing 3 n n P1 O3' A3P sing 4 n n O2P HOP2 A3P sing 5 n n O3P HOP3 A3P sing 6 n n P2 O4P A3P doub 7 n n P2 O5P A3P sing 8 n n P2 O6P A3P sing 9 n n P2 O5' A3P sing 10 n n O5P HOP5 A3P sing 11 n n O6P HOP6 A3P sing 12 n n O5' C5' A3P sing 13 n n C5' C4' A3P sing 14 n n C5' "H5'1" A3P sing 15 n n C5' "H5'2" A3P sing 16 n n C4' O4' A3P sing 17 n n C4' C3' A3P sing 18 n n C4' H4' A3P sing 19 n n O4' C1' A3P sing 20 n n C3' O3' A3P sing 21 n n C3' C2' A3P sing 22 n n C3' H3' A3P sing 23 n n C2' O2' A3P sing 24 n n C2' C1' A3P sing 25 n n C2' H2' A3P sing 26 n n O2' HO2' A3P sing 27 n n C1' N9 A3P sing 28 n n C1' H1' A3P sing 29 n n N9 C8 A3P sing 30 n y N9 C4 A3P sing 31 n y C8 N7 A3P doub 32 n y C8 H8 A3P sing 33 n n N7 C5 A3P sing 34 n y C5 C6 A3P sing 35 n y C5 C4 A3P doub 36 n y C6 N6 A3P sing 37 n n C6 N1 A3P doub 38 n y N6 HN61 A3P sing 39 n n N6 HN62 A3P sing 40 n n N1 C2 A3P sing 41 n y C2 N3 A3P doub 42 n y C2 H2 A3P sing 43 n n N3 C4 A3P sing 44 n y # _atom_sites.entry_id 3U3R _atom_sites.fract_transf_matrix[1][1] 0.013816 _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] 0.012458 _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] 0.00812 _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 NPO A 1 300 300 NPO NPO . C 3 A3P A 1 301 301 A3P A3P . D 2 NPO A 1 302 302 NPO NPO . E 4 HOH A 1 296 1 HOH HOH . E 4 HOH A 2 297 2 HOH HOH . E 4 HOH A 3 298 3 HOH HOH . E 4 HOH A 4 299 11 HOH HOH . E 4 HOH A 5 303 12 HOH HOH . E 4 HOH A 6 304 13 HOH HOH . E 4 HOH A 7 305 14 HOH HOH . E 4 HOH A 8 306 16 HOH HOH . E 4 HOH A 9 307 18 HOH HOH . E 4 HOH A 10 308 19 HOH HOH . E 4 HOH A 11 309 28 HOH HOH . E 4 HOH A 12 310 29 HOH HOH . E 4 HOH A 13 311 36 HOH HOH . E 4 HOH A 14 312 41 HOH HOH . E 4 HOH A 15 313 44 HOH HOH . E 4 HOH A 16 314 46 HOH HOH . E 4 HOH A 17 315 47 HOH HOH . E 4 HOH A 18 316 51 HOH HOH . E 4 HOH A 19 317 56 HOH HOH . E 4 HOH A 20 318 65 HOH HOH . E 4 HOH A 21 319 66 HOH HOH . E 4 HOH A 22 320 72 HOH HOH . E 4 HOH A 23 321 83 HOH HOH . E 4 HOH A 24 322 85 HOH HOH . E 4 HOH A 25 323 87 HOH HOH . E 4 HOH A 26 324 94 HOH HOH . E 4 HOH A 27 325 103 HOH HOH . E 4 HOH A 28 326 104 HOH HOH . E 4 HOH A 29 327 105 HOH HOH . E 4 HOH A 30 328 106 HOH HOH . E 4 HOH A 31 329 110 HOH HOH . E 4 HOH A 32 330 118 HOH HOH . E 4 HOH A 33 331 122 HOH HOH . E 4 HOH A 34 332 129 HOH HOH . E 4 HOH A 35 333 130 HOH HOH . E 4 HOH A 36 334 160 HOH HOH . E 4 HOH A 37 335 161 HOH HOH . E 4 HOH A 38 336 162 HOH HOH . E 4 HOH A 39 337 163 HOH HOH . E 4 HOH A 40 338 164 HOH HOH . E 4 HOH A 41 339 165 HOH HOH . E 4 HOH A 42 340 166 HOH HOH . E 4 HOH A 43 341 167 HOH HOH . E 4 HOH A 44 342 168 HOH HOH . E 4 HOH A 45 343 169 HOH HOH . E 4 HOH A 46 344 170 HOH HOH . E 4 HOH A 47 345 171 HOH HOH . E 4 HOH A 48 346 172 HOH HOH . E 4 HOH A 49 347 173 HOH HOH . E 4 HOH A 50 348 175 HOH HOH . E 4 HOH A 51 349 176 HOH HOH . E 4 HOH A 52 350 177 HOH HOH . E 4 HOH A 53 351 178 HOH HOH . E 4 HOH A 54 352 180 HOH HOH . E 4 HOH A 55 353 181 HOH HOH . E 4 HOH A 56 354 182 HOH HOH . E 4 HOH A 57 355 183 HOH HOH . E 4 HOH A 58 356 184 HOH HOH . E 4 HOH A 59 357 185 HOH HOH . E 4 HOH A 60 358 186 HOH HOH . E 4 HOH A 61 359 187 HOH HOH . E 4 HOH A 62 360 188 HOH HOH . E 4 HOH A 63 361 191 HOH HOH . E 4 HOH A 64 362 192 HOH HOH . E 4 HOH A 65 363 193 HOH HOH . E 4 HOH A 66 364 194 HOH HOH . E 4 HOH A 67 365 195 HOH HOH . E 4 HOH A 68 366 196 HOH HOH . E 4 HOH A 69 367 197 HOH HOH . E 4 HOH A 70 368 198 HOH HOH . E 4 HOH A 71 369 199 HOH HOH . E 4 HOH A 72 370 200 HOH HOH . E 4 HOH A 73 371 201 HOH HOH . E 4 HOH A 74 372 202 HOH HOH . E 4 HOH A 75 373 203 HOH HOH . E 4 HOH A 76 374 204 HOH HOH . E 4 HOH A 77 375 205 HOH HOH . E 4 HOH A 78 376 206 HOH HOH . E 4 HOH A 79 377 207 HOH HOH . E 4 HOH A 80 378 208 HOH HOH . E 4 HOH A 81 379 209 HOH HOH . E 4 HOH A 82 380 210 HOH HOH . E 4 HOH A 83 381 211 HOH HOH . E 4 HOH A 84 382 213 HOH HOH . E 4 HOH A 85 383 214 HOH HOH . E 4 HOH A 86 384 215 HOH HOH . E 4 HOH A 87 385 216 HOH HOH . E 4 HOH A 88 386 217 HOH HOH . E 4 HOH A 89 387 218 HOH HOH . E 4 HOH A 90 388 219 HOH HOH . E 4 HOH A 91 389 220 HOH HOH . E 4 HOH A 92 390 221 HOH HOH . E 4 HOH A 93 391 222 HOH HOH . E 4 HOH A 94 392 223 HOH HOH . E 4 HOH A 95 393 224 HOH HOH . E 4 HOH A 96 394 225 HOH HOH . E 4 HOH A 97 395 226 HOH HOH . E 4 HOH A 98 396 227 HOH HOH . E 4 HOH A 99 397 228 HOH HOH . E 4 HOH A 100 398 230 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 P1 A3P . . . C 3 20.115 -22.436 23.942 1 18.75 ? P1 A3P 301 A 1 HETATM 2 O O1P A3P . . . C 3 19.301 -22.903 25.097 1 21.44 ? O1P A3P 301 A 1 HETATM 3 O O2P A3P . . . C 3 20.827 -21.078 24.26 1 12.85 ? O2P A3P 301 A 1 HETATM 4 O O3P A3P . . . C 3 20.918 -23.656 23.349 1 20.67 ? O3P A3P 301 A 1 HETATM 5 P P2 A3P . . . C 3 16.866 -22.719 17.067 1 21.06 ? P2 A3P 301 A 1 HETATM 6 O O4P A3P . . . C 3 17.697 -23.943 16.741 1 22.03 ? O4P A3P 301 A 1 HETATM 7 O O5P A3P . . . C 3 15.348 -23.098 17.29 1 22.47 ? O5P A3P 301 A 1 HETATM 8 O O6P A3P . . . C 3 17.06 -21.574 16.016 1 22.33 ? O6P A3P 301 A 1 HETATM 9 O O5' A3P . . . C 3 17.297 -22.073 18.417 1 23.31 ? O5' A3P 301 A 1 HETATM 10 C C5' A3P . . . C 3 17.556 -22.943 19.436 1 20.83 ? C5' A3P 301 A 1 HETATM 11 C C4' A3P . . . C 3 17.66 -22.213 20.769 1 21.82 ? C4' A3P 301 A 1 HETATM 12 O O4' A3P . . . C 3 16.604 -21.312 21.216 1 22.74 ? O4' A3P 301 A 1 HETATM 13 C C3' A3P . . . C 3 18.271 -22.791 21.998 1 22.69 ? C3' A3P 301 A 1 HETATM 14 O O3' A3P . . . C 3 19.09 -21.958 22.781 1 24.33 ? O3' A3P 301 A 1 HETATM 15 C C2' A3P . . . C 3 16.973 -23.086 22.663 1 24.23 ? C2' A3P 301 A 1 HETATM 16 O O2' A3P . . . C 3 17.042 -23.615 23.986 1 27.41 ? O2' A3P 301 A 1 HETATM 17 C C1' A3P . . . C 3 16.209 -21.819 22.491 1 20.63 ? C1' A3P 301 A 1 HETATM 18 N N9 A3P . . . C 3 14.747 -21.786 22.623 1 24.37 ? N9 A3P 301 A 1 HETATM 19 C C8 A3P . . . C 3 13.797 -22.748 22.24 1 21.92 ? C8 A3P 301 A 1 HETATM 20 N N7 A3P . . . C 3 12.551 -22.296 22.498 1 19.93 ? N7 A3P 301 A 1 HETATM 21 C C5 A3P . . . C 3 12.73 -21.136 23.209 1 23.5 ? C5 A3P 301 A 1 HETATM 22 C C6 A3P . . . C 3 11.781 -20.317 23.945 1 21.45 ? C6 A3P 301 A 1 HETATM 23 N N6 A3P . . . C 3 10.387 -20.48 23.775 1 17.61 ? N6 A3P 301 A 1 HETATM 24 N N1 A3P . . . C 3 12.244 -19.362 24.774 1 25.75 ? N1 A3P 301 A 1 HETATM 25 C C2 A3P . . . C 3 13.627 -19.052 24.831 1 26.5 ? C2 A3P 301 A 1 HETATM 26 N N3 A3P . . . C 3 14.557 -19.841 24.089 1 22.29 ? N3 A3P 301 A 1 HETATM 27 C C4 A3P . . . C 3 14.096 -20.921 23.401 1 22.75 ? C4 A3P 301 A 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 382 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #