data_5EDD # _model_server_result.job_id ApDd2dgjb0Qa51TvbBIkww _model_server_result.datetime_utc '2025-08-03 00:26:29' _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 5edd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 5EDD # _exptl.entry_id 5EDD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 467.157 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE" _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 5EDD _cell.length_a 55.052 _cell.length_b 55.052 _cell.length_c 83.827 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EDD _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details 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 1,2,3 # 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_545 -y,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 27.526 -47.676431 0 3 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 55.052 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 # 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 C O1A DUP . A DUP 202 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc2 C O1B DUP . A DUP 202 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc3 C O2G DUP . A DUP 202 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc4 D MG MG . A MG 203 1_555 E O HOH . A HOH 313 2_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc5 D MG MG . A MG 203 1_555 E O HOH . A HOH 322 2_545 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc6 D MG MG . A MG 203 1_555 E O HOH . A HOH 377 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? # _chem_comp.formula 'C9 H16 N3 O13 P3' _chem_comp.formula_weight 467.157 _chem_comp.id DUP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE" _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 O4 C4 DUP doub 70 n n C4 C5 DUP sing 71 n y C4 N3 DUP sing 72 n y C5 C6 DUP doub 73 n y C5 H5 DUP sing 74 n n C6 N1 DUP sing 75 n y C6 H6 DUP sing 76 n n N3 C2 DUP sing 77 n y N3 HN3 DUP sing 78 n n C2 O2 DUP doub 79 n n C2 N1 DUP sing 80 n y N1 C1' DUP sing 81 n n C1' C2' DUP sing 82 n n C1' O4' DUP sing 83 n n C1' H1' DUP sing 84 n n C2' C3' DUP sing 85 n n C2' "H2'1" DUP sing 86 n n C2' "H2'2" DUP sing 87 n n C3' O3' DUP sing 88 n n C3' C4' DUP sing 89 n n C3' H1 DUP sing 90 n n O3' H3' DUP sing 91 n n O4' C4' DUP sing 92 n n C4' C5' DUP sing 93 n n C4' H4' DUP sing 94 n n C5' O5' DUP sing 95 n n C5' "H5'1" DUP sing 96 n n C5' "H5'2" DUP sing 97 n n O5' PA DUP sing 98 n n PA O1A DUP doub 99 n n PA O2A DUP sing 100 n n PA N3A DUP sing 101 n n O2A H2A DUP sing 102 n n N3A PB DUP sing 103 n n N3A H3A DUP sing 104 n n PB O1B DUP doub 105 n n PB O2B DUP sing 106 n n PB O3B DUP sing 107 n n O2B H2B DUP sing 108 n n O3B PG DUP sing 109 n n PG O2G DUP doub 110 n n PG O1G DUP sing 111 n n PG O3G DUP sing 112 n n O1G H1G DUP sing 113 n n O3G H3G DUP sing 114 n n # _atom_sites.entry_id 5EDD _atom_sites.fract_transf_matrix[1][1] 0.018165 _atom_sites.fract_transf_matrix[1][2] 0.010487 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020975 _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] 0.011929 _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 TRS A 1 201 202 TRS TRS . C 3 DUP A 1 202 777 DUP DUP . D 4 MG A 1 203 1 MG MG . E 5 HOH A 1 301 148 HOH HOH . E 5 HOH A 2 302 74 HOH HOH . E 5 HOH A 3 303 126 HOH HOH . E 5 HOH A 4 304 72 HOH HOH . E 5 HOH A 5 305 7 HOH HOH . E 5 HOH A 6 306 18 HOH HOH . E 5 HOH A 7 307 174 HOH HOH . E 5 HOH A 8 308 15 HOH HOH . E 5 HOH A 9 309 49 HOH HOH . E 5 HOH A 10 310 37 HOH HOH . E 5 HOH A 11 311 105 HOH HOH . E 5 HOH A 12 312 39 HOH HOH . E 5 HOH A 13 313 35 HOH HOH . E 5 HOH A 14 314 11 HOH HOH . E 5 HOH A 15 315 69 HOH HOH . E 5 HOH A 16 316 5 HOH HOH . E 5 HOH A 17 317 153 HOH HOH . E 5 HOH A 18 318 29 HOH HOH . E 5 HOH A 19 319 25 HOH HOH . E 5 HOH A 20 320 88 HOH HOH . E 5 HOH A 21 321 127 HOH HOH . E 5 HOH A 22 322 122 HOH HOH . E 5 HOH A 23 323 67 HOH HOH . E 5 HOH A 24 324 21 HOH HOH . E 5 HOH A 25 325 138 HOH HOH . E 5 HOH A 26 326 1 HOH HOH . E 5 HOH A 27 327 86 HOH HOH . E 5 HOH A 28 328 16 HOH HOH . E 5 HOH A 29 329 42 HOH HOH . E 5 HOH A 30 330 8 HOH HOH . E 5 HOH A 31 331 20 HOH HOH . E 5 HOH A 32 332 57 HOH HOH . E 5 HOH A 33 333 41 HOH HOH . E 5 HOH A 34 334 73 HOH HOH . E 5 HOH A 35 335 44 HOH HOH . E 5 HOH A 36 336 80 HOH HOH . E 5 HOH A 37 337 51 HOH HOH . E 5 HOH A 38 338 90 HOH HOH . E 5 HOH A 39 339 120 HOH HOH . E 5 HOH A 40 340 3 HOH HOH . E 5 HOH A 41 341 27 HOH HOH . E 5 HOH A 42 342 47 HOH HOH . E 5 HOH A 43 343 10 HOH HOH . E 5 HOH A 44 344 40 HOH HOH . E 5 HOH A 45 345 144 HOH HOH . E 5 HOH A 46 346 22 HOH HOH . E 5 HOH A 47 347 38 HOH HOH . E 5 HOH A 48 348 26 HOH HOH . E 5 HOH A 49 349 64 HOH HOH . E 5 HOH A 50 350 23 HOH HOH . E 5 HOH A 51 351 139 HOH HOH . E 5 HOH A 52 352 14 HOH HOH . E 5 HOH A 53 353 6 HOH HOH . E 5 HOH A 54 354 59 HOH HOH . E 5 HOH A 55 355 155 HOH HOH . E 5 HOH A 56 356 9 HOH HOH . E 5 HOH A 57 357 4 HOH HOH . E 5 HOH A 58 358 87 HOH HOH . E 5 HOH A 59 359 60 HOH HOH . E 5 HOH A 60 360 78 HOH HOH . E 5 HOH A 61 361 58 HOH HOH . E 5 HOH A 62 362 2 HOH HOH . E 5 HOH A 63 363 34 HOH HOH . E 5 HOH A 64 364 13 HOH HOH . E 5 HOH A 65 365 82 HOH HOH . E 5 HOH A 66 366 77 HOH HOH . E 5 HOH A 67 367 81 HOH HOH . E 5 HOH A 68 368 19 HOH HOH . E 5 HOH A 69 369 31 HOH HOH . E 5 HOH A 70 370 171 HOH HOH . E 5 HOH A 71 371 83 HOH HOH . E 5 HOH A 72 372 30 HOH HOH . E 5 HOH A 73 373 46 HOH HOH . E 5 HOH A 74 374 17 HOH HOH . E 5 HOH A 75 375 61 HOH HOH . E 5 HOH A 76 376 48 HOH HOH . E 5 HOH A 77 377 36 HOH HOH . E 5 HOH A 78 378 68 HOH HOH . E 5 HOH A 79 379 130 HOH HOH . E 5 HOH A 80 380 63 HOH HOH . E 5 HOH A 81 381 76 HOH HOH . E 5 HOH A 82 382 52 HOH HOH . E 5 HOH A 83 383 143 HOH HOH . E 5 HOH A 84 384 79 HOH HOH . E 5 HOH A 85 385 136 HOH HOH . E 5 HOH A 86 386 32 HOH HOH . E 5 HOH A 87 387 54 HOH HOH . E 5 HOH A 88 388 50 HOH HOH . E 5 HOH A 89 389 96 HOH HOH . E 5 HOH A 90 390 112 HOH HOH . E 5 HOH A 91 391 28 HOH HOH . E 5 HOH A 92 392 140 HOH HOH . E 5 HOH A 93 393 124 HOH HOH . E 5 HOH A 94 394 173 HOH HOH . E 5 HOH A 95 395 121 HOH HOH . E 5 HOH A 96 396 33 HOH HOH . E 5 HOH A 97 397 172 HOH HOH . E 5 HOH A 98 398 160 HOH HOH . E 5 HOH A 99 399 141 HOH HOH . E 5 HOH A 100 400 45 HOH HOH . E 5 HOH A 101 401 85 HOH HOH . E 5 HOH A 102 402 157 HOH HOH . E 5 HOH A 103 403 70 HOH HOH . E 5 HOH A 104 404 94 HOH HOH . E 5 HOH A 105 405 169 HOH HOH . E 5 HOH A 106 406 101 HOH HOH . E 5 HOH A 107 407 56 HOH HOH . E 5 HOH A 108 408 55 HOH HOH . E 5 HOH A 109 409 24 HOH HOH . E 5 HOH A 110 410 154 HOH HOH . E 5 HOH A 111 411 95 HOH HOH . E 5 HOH A 112 412 149 HOH HOH . E 5 HOH A 113 413 84 HOH HOH . E 5 HOH A 114 414 132 HOH HOH . E 5 HOH A 115 415 108 HOH HOH . E 5 HOH A 116 416 12 HOH HOH . E 5 HOH A 117 417 175 HOH HOH . E 5 HOH A 118 418 151 HOH HOH . E 5 HOH A 119 419 125 HOH HOH . E 5 HOH A 120 420 53 HOH HOH . E 5 HOH A 121 421 167 HOH HOH . E 5 HOH A 122 422 129 HOH HOH . E 5 HOH A 123 423 62 HOH HOH . E 5 HOH A 124 424 170 HOH HOH . E 5 HOH A 125 425 116 HOH HOH . E 5 HOH A 126 426 177 HOH HOH . E 5 HOH A 127 427 168 HOH HOH . E 5 HOH A 128 428 107 HOH HOH . E 5 HOH A 129 429 71 HOH HOH . E 5 HOH A 130 430 146 HOH HOH . E 5 HOH A 131 431 43 HOH HOH . E 5 HOH A 132 432 135 HOH HOH . E 5 HOH A 133 433 128 HOH HOH . E 5 HOH A 134 434 119 HOH HOH . E 5 HOH A 135 435 163 HOH HOH . E 5 HOH A 136 436 65 HOH HOH . E 5 HOH A 137 437 162 HOH HOH . E 5 HOH A 138 438 176 HOH HOH . E 5 HOH A 139 439 100 HOH HOH . E 5 HOH A 140 440 75 HOH HOH . E 5 HOH A 141 441 145 HOH HOH . E 5 HOH A 142 442 178 HOH HOH . E 5 HOH A 143 443 166 HOH HOH . E 5 HOH A 144 444 115 HOH HOH . E 5 HOH A 145 445 66 HOH HOH . E 5 HOH A 146 446 106 HOH HOH . E 5 HOH A 147 447 111 HOH HOH . E 5 HOH A 148 448 117 HOH HOH . E 5 HOH A 149 449 123 HOH HOH . E 5 HOH A 150 450 93 HOH HOH . E 5 HOH A 151 451 147 HOH HOH . E 5 HOH A 152 452 97 HOH HOH . E 5 HOH A 153 453 91 HOH HOH . E 5 HOH A 154 454 133 HOH HOH . E 5 HOH A 155 455 159 HOH HOH . E 5 HOH A 156 456 134 HOH HOH . E 5 HOH A 157 457 92 HOH HOH . E 5 HOH A 158 458 158 HOH HOH . E 5 HOH A 159 459 114 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 O O4 DUP . . . C 3 21.564 -7.077 1.006 1 16.3 ? O4 DUP 202 A 1 HETATM 2 C C4 DUP . . . C 3 20.376 -6.692 0.509 1 16.29 ? C4 DUP 202 A 1 HETATM 3 C C5 DUP . . . C 3 19.511 -7.638 -0.009 1 18.08 ? C5 DUP 202 A 1 HETATM 4 C C6 DUP . . . C 3 18.31 -7.242 -0.556 1 16.24 ? C6 DUP 202 A 1 HETATM 5 N N3 DUP . . . C 3 20.041 -5.392 0.456 1 15.54 ? N3 DUP 202 A 1 HETATM 6 C C2 DUP . . . C 3 18.887 -5.024 -0.133 1 16.23 ? C2 DUP 202 A 1 HETATM 7 O O2 DUP . . . C 3 18.584 -3.702 -0.194 1 15.8 ? O2 DUP 202 A 1 HETATM 8 N N1 DUP . . . C 3 18.02 -5.943 -0.613 1 17.02 ? N1 DUP 202 A 1 HETATM 9 C C1' DUP . . . C 3 16.752 -5.494 -1.219 1 16.68 ? C1' DUP 202 A 1 HETATM 10 C C2' DUP . . . C 3 16.883 -5.593 -2.745 1 16.6 ? C2' DUP 202 A 1 HETATM 11 C C3' DUP . . . C 3 16.144 -6.868 -3.11 1 15.27 ? C3' DUP 202 A 1 HETATM 12 O O3' DUP . . . C 3 15.684 -6.893 -4.467 1 15.69 ? O3' DUP 202 A 1 HETATM 13 O O4' DUP . . . C 3 15.661 -6.338 -0.875 1 17.76 ? O4' DUP 202 A 1 HETATM 14 C C4' DUP . . . C 3 15.051 -6.874 -2.045 1 17.09 ? C4' DUP 202 A 1 HETATM 15 C C5' DUP . . . C 3 14.495 -8.239 -1.683 1 17.86 ? C5' DUP 202 A 1 HETATM 16 O O5' DUP . . . C 3 15.592 -9.056 -1.188 1 19.4 ? O5' DUP 202 A 1 HETATM 17 P PA DUP . . . C 3 15.23 -10.539 -0.66 1 22.41 ? PA DUP 202 A 1 HETATM 18 O O1A DUP . . . C 3 14.382 -11.144 -1.728 1 23.01 ? O1A DUP 202 A 1 HETATM 19 O O2A DUP . . . C 3 16.569 -11.197 -0.303 1 21.33 ? O2A DUP 202 A 1 HETATM 20 N N3A DUP . . . C 3 14.317 -10.243 0.695 1 21.04 ? N3A DUP 202 A 1 HETATM 21 P PB DUP . . . C 3 12.813 -10.834 1.11 1 21.94 ? PB DUP 202 A 1 HETATM 22 O O1B DUP . . . C 3 12.639 -12.17 0.372 1 21.69 ? O1B DUP 202 A 1 HETATM 23 O O2B DUP . . . C 3 12.786 -10.839 2.648 1 16.01 ? O2B DUP 202 A 1 HETATM 24 O O3B DUP . . . C 3 11.683 -9.777 0.604 1 23.86 ? O3B DUP 202 A 1 HETATM 25 P PG DUP . . . C 3 10.774 -9.8 -0.767 1 26.73 ? PG DUP 202 A 1 HETATM 26 O O2G DUP . . . C 3 11.512 -10.58 -1.844 1 24.31 ? O2G DUP 202 A 1 HETATM 27 O O1G DUP . . . C 3 9.527 -10.48 -0.254 1 24.65 ? O1G DUP 202 A 1 HETATM 28 O O3G DUP . . . C 3 10.758 -8.29 -1.062 1 26.38 ? O3G DUP 202 A 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 28 #