data_6WGS # _model_server_result.job_id kz3jzzWcPIZgDH06T0Jj8g _model_server_result.datetime_utc '2025-01-10 20:58:27' _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 6wgs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 6WGS # _exptl.entry_id 6WGS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 251.242 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-DEOXYADENOSINE" _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 6WGS _cell.length_a 87.157 _cell.length_b 87.157 _cell.length_c 46.819 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6WGS _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3 2 1' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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_565 -y,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -43.5785 75.480176 0 3 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -87.157 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 'C10 H13 N5 O3' _chem_comp.formula_weight 251.242 _chem_comp.id 5AD _chem_comp.mon_nstd_flag . _chem_comp.name "5'-DEOXYADENOSINE" _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 N1 C2 5AD doub 1 n y N1 C6 5AD sing 2 n y C2 N3 5AD sing 3 n y C2 H2 5AD sing 4 n n N3 C4 5AD doub 5 n y C4 N9 5AD sing 6 n y C4 C5 5AD sing 7 n y N9 C8 5AD sing 8 n y N9 C1' 5AD sing 9 n n C8 N7 5AD doub 10 n y C8 H8 5AD sing 11 n n N7 C5 5AD sing 12 n y C5 C6 5AD doub 13 n y C6 N6 5AD sing 14 n n N6 HN61 5AD sing 15 n n N6 HN62 5AD sing 16 n n C1' C2' 5AD sing 17 n n C1' O4' 5AD sing 18 n n C1' H1' 5AD sing 19 n n C2' C3' 5AD sing 20 n n C2' O2' 5AD sing 21 n n C2' H2' 5AD sing 22 n n C3' C4' 5AD sing 23 n n C3' O3' 5AD sing 24 n n C3' H3' 5AD sing 25 n n C4' C5' 5AD sing 26 n n C4' O4' 5AD sing 27 n n C4' H4' 5AD sing 28 n n C5' "H5'1" 5AD sing 29 n n C5' "H5'2" 5AD sing 30 n n C5' "H5'3" 5AD sing 31 n n O2' HO2' 5AD sing 32 n n O3' HO3' 5AD sing 33 n n # _atom_sites.entry_id 6WGS _atom_sites.fract_transf_matrix[1][1] 0.011474 _atom_sites.fract_transf_matrix[1][2] 0.006624 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013248 _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] 0.021359 _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 B12 A 1 201 201 B12 B12 . C 3 5AD A 1 202 301 5AD 5AD . D 4 HOH A 1 301 168 HOH HOH . D 4 HOH A 2 302 45 HOH HOH . D 4 HOH A 3 303 42 HOH HOH . D 4 HOH A 4 304 110 HOH HOH . D 4 HOH A 5 305 171 HOH HOH . D 4 HOH A 6 306 95 HOH HOH . D 4 HOH A 7 307 48 HOH HOH . D 4 HOH A 8 308 58 HOH HOH . D 4 HOH A 9 309 112 HOH HOH . D 4 HOH A 10 310 28 HOH HOH . D 4 HOH A 11 311 20 HOH HOH . D 4 HOH A 12 312 62 HOH HOH . D 4 HOH A 13 313 135 HOH HOH . D 4 HOH A 14 314 164 HOH HOH . D 4 HOH A 15 315 69 HOH HOH . D 4 HOH A 16 316 51 HOH HOH . D 4 HOH A 17 317 139 HOH HOH . D 4 HOH A 18 318 77 HOH HOH . D 4 HOH A 19 319 55 HOH HOH . D 4 HOH A 20 320 27 HOH HOH . D 4 HOH A 21 321 125 HOH HOH . D 4 HOH A 22 322 14 HOH HOH . D 4 HOH A 23 323 71 HOH HOH . D 4 HOH A 24 324 11 HOH HOH . D 4 HOH A 25 325 130 HOH HOH . D 4 HOH A 26 326 25 HOH HOH . D 4 HOH A 27 327 2 HOH HOH . D 4 HOH A 28 328 115 HOH HOH . D 4 HOH A 29 329 65 HOH HOH . D 4 HOH A 30 330 122 HOH HOH . D 4 HOH A 31 331 120 HOH HOH . D 4 HOH A 32 332 4 HOH HOH . D 4 HOH A 33 333 72 HOH HOH . D 4 HOH A 34 334 33 HOH HOH . D 4 HOH A 35 335 3 HOH HOH . D 4 HOH A 36 336 84 HOH HOH . D 4 HOH A 37 337 9 HOH HOH . D 4 HOH A 38 338 12 HOH HOH . D 4 HOH A 39 339 26 HOH HOH . D 4 HOH A 40 340 50 HOH HOH . D 4 HOH A 41 341 78 HOH HOH . D 4 HOH A 42 342 40 HOH HOH . D 4 HOH A 43 343 10 HOH HOH . D 4 HOH A 44 344 16 HOH HOH . D 4 HOH A 45 345 100 HOH HOH . D 4 HOH A 46 346 29 HOH HOH . D 4 HOH A 47 347 89 HOH HOH . D 4 HOH A 48 348 32 HOH HOH . D 4 HOH A 49 349 37 HOH HOH . D 4 HOH A 50 350 5 HOH HOH . D 4 HOH A 51 351 6 HOH HOH . D 4 HOH A 52 352 38 HOH HOH . D 4 HOH A 53 353 19 HOH HOH . D 4 HOH A 54 354 23 HOH HOH . D 4 HOH A 55 355 146 HOH HOH . D 4 HOH A 56 356 99 HOH HOH . D 4 HOH A 57 357 1 HOH HOH . D 4 HOH A 58 358 64 HOH HOH . D 4 HOH A 59 359 101 HOH HOH . D 4 HOH A 60 360 155 HOH HOH . D 4 HOH A 61 361 94 HOH HOH . D 4 HOH A 62 362 41 HOH HOH . D 4 HOH A 63 363 8 HOH HOH . D 4 HOH A 64 364 15 HOH HOH . D 4 HOH A 65 365 82 HOH HOH . D 4 HOH A 66 366 36 HOH HOH . D 4 HOH A 67 367 131 HOH HOH . D 4 HOH A 68 368 63 HOH HOH . D 4 HOH A 69 369 39 HOH HOH . D 4 HOH A 70 370 17 HOH HOH . D 4 HOH A 71 371 87 HOH HOH . D 4 HOH A 72 372 172 HOH HOH . D 4 HOH A 73 373 67 HOH HOH . D 4 HOH A 74 374 30 HOH HOH . D 4 HOH A 75 375 31 HOH HOH . D 4 HOH A 76 376 116 HOH HOH . D 4 HOH A 77 377 46 HOH HOH . D 4 HOH A 78 378 53 HOH HOH . D 4 HOH A 79 379 149 HOH HOH . D 4 HOH A 80 380 126 HOH HOH . D 4 HOH A 81 381 44 HOH HOH . D 4 HOH A 82 382 22 HOH HOH . D 4 HOH A 83 383 34 HOH HOH . D 4 HOH A 84 384 79 HOH HOH . D 4 HOH A 85 385 96 HOH HOH . D 4 HOH A 86 386 35 HOH HOH . D 4 HOH A 87 387 66 HOH HOH . D 4 HOH A 88 388 18 HOH HOH . D 4 HOH A 89 389 56 HOH HOH . D 4 HOH A 90 390 85 HOH HOH . D 4 HOH A 91 391 144 HOH HOH . D 4 HOH A 92 392 98 HOH HOH . D 4 HOH A 93 393 109 HOH HOH . D 4 HOH A 94 394 90 HOH HOH . D 4 HOH A 95 395 113 HOH HOH . D 4 HOH A 96 396 151 HOH HOH . D 4 HOH A 97 397 128 HOH HOH . D 4 HOH A 98 398 102 HOH HOH . D 4 HOH A 99 399 83 HOH HOH . D 4 HOH A 100 400 75 HOH HOH . D 4 HOH A 101 401 92 HOH HOH . D 4 HOH A 102 402 88 HOH HOH . D 4 HOH A 103 403 148 HOH HOH . D 4 HOH A 104 404 57 HOH HOH . D 4 HOH A 105 405 80 HOH HOH . D 4 HOH A 106 406 134 HOH HOH . D 4 HOH A 107 407 93 HOH HOH . D 4 HOH A 108 408 86 HOH HOH . D 4 HOH A 109 409 169 HOH HOH . D 4 HOH A 110 410 60 HOH HOH . D 4 HOH A 111 411 91 HOH HOH . D 4 HOH A 112 412 153 HOH HOH . D 4 HOH A 113 413 141 HOH HOH . D 4 HOH A 114 414 136 HOH HOH . D 4 HOH A 115 415 61 HOH HOH . D 4 HOH A 116 416 167 HOH HOH . D 4 HOH A 117 417 154 HOH HOH . D 4 HOH A 118 418 54 HOH HOH . D 4 HOH A 119 419 145 HOH HOH . D 4 HOH A 120 420 47 HOH HOH . D 4 HOH A 121 421 108 HOH HOH . D 4 HOH A 122 422 137 HOH HOH . D 4 HOH A 123 423 133 HOH HOH . D 4 HOH A 124 424 152 HOH HOH . D 4 HOH A 125 425 52 HOH HOH . D 4 HOH A 126 426 59 HOH HOH . D 4 HOH A 127 427 106 HOH HOH . D 4 HOH A 128 428 97 HOH HOH . D 4 HOH A 129 429 127 HOH HOH . D 4 HOH A 130 430 156 HOH HOH . D 4 HOH A 131 431 123 HOH HOH . D 4 HOH A 132 432 170 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 N N1 5AD . . . C 3 -34.161 32.108 21.428 1 15.76 ? N1 5AD 202 A 1 HETATM 2 C C2 5AD . . . C 3 -34.843 33.301 21.387 1 16.98 ? C2 5AD 202 A 1 HETATM 3 N N3 5AD . . . C 3 -34.219 34.481 21.61 1 17.12 ? N3 5AD 202 A 1 HETATM 4 C C4 5AD . . . C 3 -32.924 34.385 22.025 1 16.78 ? C4 5AD 202 A 1 HETATM 5 N N9 5AD . . . C 3 -32.049 35.364 22.332 1 17.32 ? N9 5AD 202 A 1 HETATM 6 C C8 5AD . . . C 3 -30.859 34.795 22.572 1 18.6 ? C8 5AD 202 A 1 HETATM 7 N N7 5AD . . . C 3 -30.92 33.449 22.438 1 18.24 ? N7 5AD 202 A 1 HETATM 8 C C5 5AD . . . C 3 -32.237 33.208 22.068 1 14.85 ? C5 5AD 202 A 1 HETATM 9 C C6 5AD . . . C 3 -32.894 32.058 21.765 1 14.75 ? C6 5AD 202 A 1 HETATM 10 N N6 5AD . . . C 3 -32.391 30.698 21.756 1 16.6 ? N6 5AD 202 A 1 HETATM 11 C C1' 5AD . . . C 3 -32.444 36.746 22.328 1 18.85 ? C1' 5AD 202 A 1 HETATM 12 C C2' 5AD . . . C 3 -31.535 37.658 23.099 1 19.53 ? C2' 5AD 202 A 1 HETATM 13 C C3' 5AD . . . C 3 -30.649 38.236 22.131 1 20.41 ? C3' 5AD 202 A 1 HETATM 14 C C4' 5AD . . . C 3 -31.632 38.439 20.943 1 22.57 ? C4' 5AD 202 A 1 HETATM 15 C C5' 5AD . . . C 3 -30.937 38.66 19.606 1 22.16 ? C5' 5AD 202 A 1 HETATM 16 O O4' 5AD . . . C 3 -32.376 37.307 20.892 1 20.8 ? O4' 5AD 202 A 1 HETATM 17 O O2' 5AD . . . C 3 -32.439 38.685 23.677 1 23.29 ? O2' 5AD 202 A 1 HETATM 18 O O3' 5AD . . . C 3 -30.073 39.483 22.534 1 23.41 ? O3' 5AD 202 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 18 #