data_1BO6 # _model_server_result.job_id sVyx8Mmerx4KxZn6wGgawQ _model_server_result.datetime_utc '2025-07-07 09:44:23' _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 1bo6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 1BO6 # _exptl.entry_id 1BO6 _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 2 _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 1BO6 _cell.length_a 96.292 _cell.length_b 78.909 _cell.length_c 80.362 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1BO6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 D O6P A3P . A A3P 301 1_555 C V VO4 . A VO4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc2 F O6P A3P . B A3P 303 1_555 E V VO4 . B VO4 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? # _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 1BO6 _atom_sites.fract_transf_matrix[1][1] 0.010385 _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] 0.012673 _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] 0.012444 _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 C 2 VO4 A 1 302 302 VO4 VO4 . D 3 A3P A 1 301 301 A3P A3P . E 2 VO4 B 1 304 304 VO4 VO4 . F 3 A3P B 1 303 303 A3P A3P . G 4 HOH A 1 303 1 HOH HOH . G 4 HOH A 2 304 2 HOH HOH . G 4 HOH A 3 305 3 HOH HOH . G 4 HOH A 4 306 4 HOH HOH . G 4 HOH A 5 307 6 HOH HOH . G 4 HOH A 6 308 7 HOH HOH . G 4 HOH A 7 309 9 HOH HOH . G 4 HOH A 8 310 10 HOH HOH . G 4 HOH A 9 311 13 HOH HOH . G 4 HOH A 10 312 15 HOH HOH . G 4 HOH A 11 313 17 HOH HOH . G 4 HOH A 12 314 18 HOH HOH . G 4 HOH A 13 315 19 HOH HOH . G 4 HOH A 14 316 22 HOH HOH . G 4 HOH A 15 317 26 HOH HOH . G 4 HOH A 16 318 27 HOH HOH . G 4 HOH A 17 319 28 HOH HOH . G 4 HOH A 18 320 30 HOH HOH . G 4 HOH A 19 321 33 HOH HOH . G 4 HOH A 20 322 35 HOH HOH . G 4 HOH A 21 323 40 HOH HOH . G 4 HOH A 22 324 41 HOH HOH . G 4 HOH A 23 325 45 HOH HOH . G 4 HOH A 24 326 46 HOH HOH . G 4 HOH A 25 327 54 HOH HOH . G 4 HOH A 26 328 56 HOH HOH . G 4 HOH A 27 329 58 HOH HOH . G 4 HOH A 28 330 60 HOH HOH . G 4 HOH A 29 331 62 HOH HOH . G 4 HOH A 30 332 63 HOH HOH . G 4 HOH A 31 333 65 HOH HOH . G 4 HOH A 32 334 66 HOH HOH . G 4 HOH A 33 335 68 HOH HOH . G 4 HOH A 34 336 69 HOH HOH . G 4 HOH A 35 337 73 HOH HOH . G 4 HOH A 36 338 74 HOH HOH . G 4 HOH A 37 339 75 HOH HOH . G 4 HOH A 38 340 77 HOH HOH . G 4 HOH A 39 341 78 HOH HOH . G 4 HOH A 40 342 81 HOH HOH . G 4 HOH A 41 343 82 HOH HOH . G 4 HOH A 42 344 83 HOH HOH . G 4 HOH A 43 345 84 HOH HOH . G 4 HOH A 44 346 85 HOH HOH . G 4 HOH A 45 347 87 HOH HOH . G 4 HOH A 46 348 88 HOH HOH . G 4 HOH A 47 349 89 HOH HOH . G 4 HOH A 48 350 90 HOH HOH . G 4 HOH A 49 351 91 HOH HOH . G 4 HOH A 50 352 92 HOH HOH . G 4 HOH A 51 353 94 HOH HOH . G 4 HOH A 52 354 95 HOH HOH . G 4 HOH A 53 355 97 HOH HOH . G 4 HOH A 54 356 99 HOH HOH . G 4 HOH A 55 357 100 HOH HOH . G 4 HOH A 56 358 102 HOH HOH . G 4 HOH A 57 359 104 HOH HOH . G 4 HOH A 58 360 105 HOH HOH . G 4 HOH A 59 361 106 HOH HOH . G 4 HOH A 60 362 107 HOH HOH . G 4 HOH A 61 363 108 HOH HOH . G 4 HOH A 62 364 109 HOH HOH . G 4 HOH A 63 365 110 HOH HOH . G 4 HOH A 64 366 111 HOH HOH . G 4 HOH A 65 367 114 HOH HOH . G 4 HOH A 66 368 116 HOH HOH . G 4 HOH A 67 369 117 HOH HOH . G 4 HOH A 68 370 118 HOH HOH . G 4 HOH A 69 371 119 HOH HOH . G 4 HOH A 70 372 120 HOH HOH . G 4 HOH A 71 373 121 HOH HOH . G 4 HOH A 72 374 122 HOH HOH . G 4 HOH A 73 375 123 HOH HOH . G 4 HOH A 74 376 124 HOH HOH . G 4 HOH A 75 377 125 HOH HOH . G 4 HOH A 76 378 126 HOH HOH . G 4 HOH A 77 379 127 HOH HOH . G 4 HOH A 78 380 128 HOH HOH . G 4 HOH A 79 381 129 HOH HOH . G 4 HOH A 80 382 130 HOH HOH . G 4 HOH A 81 383 131 HOH HOH . G 4 HOH A 82 384 132 HOH HOH . G 4 HOH A 83 385 133 HOH HOH . G 4 HOH A 84 386 134 HOH HOH . G 4 HOH A 85 387 136 HOH HOH . G 4 HOH A 86 388 143 HOH HOH . G 4 HOH A 87 389 153 HOH HOH . G 4 HOH A 88 390 154 HOH HOH . G 4 HOH A 89 391 155 HOH HOH . G 4 HOH A 90 392 156 HOH HOH . G 4 HOH A 91 393 157 HOH HOH . G 4 HOH A 92 394 158 HOH HOH . G 4 HOH A 93 395 161 HOH HOH . G 4 HOH A 94 396 162 HOH HOH . G 4 HOH A 95 397 163 HOH HOH . G 4 HOH A 96 398 164 HOH HOH . G 4 HOH A 97 399 165 HOH HOH . G 4 HOH A 98 400 166 HOH HOH . G 4 HOH A 99 401 167 HOH HOH . G 4 HOH A 100 402 168 HOH HOH . H 4 HOH B 1 305 5 HOH HOH . H 4 HOH B 2 306 8 HOH HOH . H 4 HOH B 3 307 11 HOH HOH . H 4 HOH B 4 308 12 HOH HOH . H 4 HOH B 5 309 14 HOH HOH . H 4 HOH B 6 310 16 HOH HOH . H 4 HOH B 7 311 20 HOH HOH . H 4 HOH B 8 312 21 HOH HOH . H 4 HOH B 9 313 23 HOH HOH . H 4 HOH B 10 314 24 HOH HOH . H 4 HOH B 11 315 25 HOH HOH . H 4 HOH B 12 316 29 HOH HOH . H 4 HOH B 13 317 31 HOH HOH . H 4 HOH B 14 318 32 HOH HOH . H 4 HOH B 15 319 34 HOH HOH . H 4 HOH B 16 320 36 HOH HOH . H 4 HOH B 17 321 37 HOH HOH . H 4 HOH B 18 322 38 HOH HOH . H 4 HOH B 19 323 39 HOH HOH . H 4 HOH B 20 324 42 HOH HOH . H 4 HOH B 21 325 43 HOH HOH . H 4 HOH B 22 326 44 HOH HOH . H 4 HOH B 23 327 47 HOH HOH . H 4 HOH B 24 328 48 HOH HOH . H 4 HOH B 25 329 49 HOH HOH . H 4 HOH B 26 330 50 HOH HOH . H 4 HOH B 27 331 51 HOH HOH . H 4 HOH B 28 332 52 HOH HOH . H 4 HOH B 29 333 53 HOH HOH . H 4 HOH B 30 334 55 HOH HOH . H 4 HOH B 31 335 57 HOH HOH . H 4 HOH B 32 336 59 HOH HOH . H 4 HOH B 33 337 61 HOH HOH . H 4 HOH B 34 338 64 HOH HOH . H 4 HOH B 35 339 67 HOH HOH . H 4 HOH B 36 340 70 HOH HOH . H 4 HOH B 37 341 71 HOH HOH . H 4 HOH B 38 342 72 HOH HOH . H 4 HOH B 39 343 76 HOH HOH . H 4 HOH B 40 344 79 HOH HOH . H 4 HOH B 41 345 80 HOH HOH . H 4 HOH B 42 346 86 HOH HOH . H 4 HOH B 43 347 93 HOH HOH . H 4 HOH B 44 348 96 HOH HOH . H 4 HOH B 45 349 98 HOH HOH . H 4 HOH B 46 350 101 HOH HOH . H 4 HOH B 47 351 103 HOH HOH . H 4 HOH B 48 352 112 HOH HOH . H 4 HOH B 49 353 113 HOH HOH . H 4 HOH B 50 354 115 HOH HOH . H 4 HOH B 51 355 135 HOH HOH . H 4 HOH B 52 356 137 HOH HOH . H 4 HOH B 53 357 138 HOH HOH . H 4 HOH B 54 358 139 HOH HOH . H 4 HOH B 55 359 140 HOH HOH . H 4 HOH B 56 360 141 HOH HOH . H 4 HOH B 57 361 142 HOH HOH . H 4 HOH B 58 362 144 HOH HOH . H 4 HOH B 59 363 145 HOH HOH . H 4 HOH B 60 364 146 HOH HOH . H 4 HOH B 61 365 147 HOH HOH . H 4 HOH B 62 366 148 HOH HOH . H 4 HOH B 63 367 149 HOH HOH . H 4 HOH B 64 368 150 HOH HOH . H 4 HOH B 65 369 151 HOH HOH . H 4 HOH B 66 370 152 HOH HOH . H 4 HOH B 67 371 159 HOH HOH . H 4 HOH B 68 372 160 HOH HOH . H 4 HOH B 69 373 169 HOH HOH . H 4 HOH B 70 374 170 HOH HOH . H 4 HOH B 71 375 171 HOH HOH . H 4 HOH B 72 376 172 HOH HOH . H 4 HOH B 73 377 173 HOH HOH . H 4 HOH B 74 378 174 HOH HOH . H 4 HOH B 75 379 175 HOH HOH . H 4 HOH B 76 380 176 HOH HOH . H 4 HOH B 77 381 177 HOH HOH . H 4 HOH B 78 382 178 HOH HOH . H 4 HOH B 79 383 179 HOH HOH . H 4 HOH B 80 384 180 HOH HOH . H 4 HOH B 81 385 181 HOH HOH . H 4 HOH B 82 386 182 HOH HOH . H 4 HOH B 83 387 183 HOH HOH . H 4 HOH B 84 388 184 HOH HOH . H 4 HOH B 85 389 185 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 . . . D 3 12.639 29.518 65.5 1 21.05 ? P1 A3P 301 A 1 HETATM 2 O O1P A3P . . . D 3 11.598 29.67 64.468 1 19.27 ? O1P A3P 301 A 1 HETATM 3 O O2P A3P . . . D 3 13.731 30.463 65.257 1 19.29 ? O2P A3P 301 A 1 HETATM 4 O O3P A3P . . . D 3 12.077 29.727 66.819 1 20.79 ? O3P A3P 301 A 1 HETATM 5 P P2 A3P . . . D 3 13.068 22.574 62.643 1 14.47 ? P2 A3P 301 A 1 HETATM 6 O O4P A3P . . . D 3 14.494 22.418 62.388 1 14.73 ? O4P A3P 301 A 1 HETATM 7 O O5P A3P . . . D 3 12.553 21.461 63.43 1 11.18 ? O5P A3P 301 A 1 HETATM 8 O O6P A3P . . . D 3 12.274 22.713 61.379 1 27.8 ? O6P A3P 301 A 1 HETATM 9 O O5' A3P . . . D 3 12.875 23.87 63.495 1 13.4 ? O5' A3P 301 A 1 HETATM 10 C C5' A3P . . . D 3 13.471 25.109 63.201 1 9.24 ? C5' A3P 301 A 1 HETATM 11 C C4' A3P . . . D 3 13.607 25.869 64.531 1 15.21 ? C4' A3P 301 A 1 HETATM 12 O O4' A3P . . . D 3 14.804 25.364 65.227 1 15.3 ? O4' A3P 301 A 1 HETATM 13 C C3' A3P . . . D 3 13.863 27.358 64.371 1 17.12 ? C3' A3P 301 A 1 HETATM 14 O O3' A3P . . . D 3 13.211 28.015 65.476 1 19.1 ? O3' A3P 301 A 1 HETATM 15 C C2' A3P . . . D 3 15.384 27.434 64.369 1 14.91 ? C2' A3P 301 A 1 HETATM 16 O O2' A3P . . . D 3 15.964 28.716 64.492 1 15.98 ? O2' A3P 301 A 1 HETATM 17 C C1' A3P . . . D 3 15.724 26.44 65.456 1 11.02 ? C1' A3P 301 A 1 HETATM 18 N N9 A3P . . . D 3 17.147 26.024 65.351 1 17.56 ? N9 A3P 301 A 1 HETATM 19 C C8 A3P . . . D 3 17.799 25.334 64.35 1 21.72 ? C8 A3P 301 A 1 HETATM 20 N N7 A3P . . . D 3 19.068 25.13 64.555 1 25.16 ? N7 A3P 301 A 1 HETATM 21 C C5 A3P . . . D 3 19.312 25.716 65.777 1 22.1 ? C5 A3P 301 A 1 HETATM 22 C C6 A3P . . . D 3 20.491 25.864 66.589 1 16.02 ? C6 A3P 301 A 1 HETATM 23 N N6 A3P . . . D 3 21.669 25.4 66.236 1 15.36 ? N6 A3P 301 A 1 HETATM 24 N N1 A3P . . . D 3 20.37 26.524 67.793 1 15.12 ? N1 A3P 301 A 1 HETATM 25 C C2 A3P . . . D 3 19.17 27.022 68.195 1 14.41 ? C2 A3P 301 A 1 HETATM 26 N N3 A3P . . . D 3 17.986 26.952 67.518 1 19.83 ? N3 A3P 301 A 1 HETATM 27 C C4 A3P . . . D 3 18.125 26.28 66.303 1 23.26 ? C4 A3P 301 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 370 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #