data_5ECT # _model_server_result.job_id eHfXVzFXp6K1fDD7MeABAA _model_server_result.datetime_utc '2025-04-18 06:22:30' _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 5ect # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 5ECT # _exptl.entry_id 5ECT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 467.157 _entity.id 2 _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 5ECT _cell.length_a 54.78 _cell.length_b 54.78 _cell.length_c 84.079 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ECT _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 author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 -27.39 47.440872 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 -54.78 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 B O2A DUP . A DUP 201 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc2 B O2B DUP . A DUP 201 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc3 B O1G DUP . A DUP 201 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc4 D MG MG . A MG 203 1_555 F O HOH . A HOH 305 3_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc5 D MG MG . A MG 203 1_555 F O HOH . A HOH 372 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc6 D MG MG . A MG 203 1_555 F O HOH . A HOH 378 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? # _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 5ECT _atom_sites.fract_transf_matrix[1][1] 0.018255 _atom_sites.fract_transf_matrix[1][2] 0.010539 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021079 _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] 0.011894 _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 DUP A 1 201 777 DUP DUP . C 3 TRS A 1 202 201 TRS TRS . D 4 MG A 1 203 1 MG MG . E 5 GOL A 1 204 202 GOL GOL . F 6 HOH A 1 301 142 HOH HOH . F 6 HOH A 2 302 47 HOH HOH . F 6 HOH A 3 303 129 HOH HOH . F 6 HOH A 4 304 77 HOH HOH . F 6 HOH A 5 305 16 HOH HOH . F 6 HOH A 6 306 113 HOH HOH . F 6 HOH A 7 307 115 HOH HOH . F 6 HOH A 8 308 5 HOH HOH . F 6 HOH A 9 309 70 HOH HOH . F 6 HOH A 10 310 135 HOH HOH . F 6 HOH A 11 311 103 HOH HOH . F 6 HOH A 12 312 29 HOH HOH . F 6 HOH A 13 313 73 HOH HOH . F 6 HOH A 14 314 78 HOH HOH . F 6 HOH A 15 315 106 HOH HOH . F 6 HOH A 16 316 110 HOH HOH . F 6 HOH A 17 317 159 HOH HOH . F 6 HOH A 18 318 38 HOH HOH . F 6 HOH A 19 319 25 HOH HOH . F 6 HOH A 20 320 102 HOH HOH . F 6 HOH A 21 321 83 HOH HOH . F 6 HOH A 22 322 105 HOH HOH . F 6 HOH A 23 323 76 HOH HOH . F 6 HOH A 24 324 48 HOH HOH . F 6 HOH A 25 325 100 HOH HOH . F 6 HOH A 26 326 15 HOH HOH . F 6 HOH A 27 327 155 HOH HOH . F 6 HOH A 28 328 35 HOH HOH . F 6 HOH A 29 329 36 HOH HOH . F 6 HOH A 30 330 166 HOH HOH . F 6 HOH A 31 331 1 HOH HOH . F 6 HOH A 32 332 98 HOH HOH . F 6 HOH A 33 333 92 HOH HOH . F 6 HOH A 34 334 11 HOH HOH . F 6 HOH A 35 335 34 HOH HOH . F 6 HOH A 36 336 116 HOH HOH . F 6 HOH A 37 337 18 HOH HOH . F 6 HOH A 38 338 23 HOH HOH . F 6 HOH A 39 339 128 HOH HOH . F 6 HOH A 40 340 31 HOH HOH . F 6 HOH A 41 341 39 HOH HOH . F 6 HOH A 42 342 19 HOH HOH . F 6 HOH A 43 343 95 HOH HOH . F 6 HOH A 44 344 107 HOH HOH . F 6 HOH A 45 345 13 HOH HOH . F 6 HOH A 46 346 12 HOH HOH . F 6 HOH A 47 347 46 HOH HOH . F 6 HOH A 48 348 17 HOH HOH . F 6 HOH A 49 349 72 HOH HOH . F 6 HOH A 50 350 26 HOH HOH . F 6 HOH A 51 351 117 HOH HOH . F 6 HOH A 52 352 108 HOH HOH . F 6 HOH A 53 353 109 HOH HOH . F 6 HOH A 54 354 141 HOH HOH . F 6 HOH A 55 355 30 HOH HOH . F 6 HOH A 56 356 27 HOH HOH . F 6 HOH A 57 357 144 HOH HOH . F 6 HOH A 58 358 71 HOH HOH . F 6 HOH A 59 359 94 HOH HOH . F 6 HOH A 60 360 130 HOH HOH . F 6 HOH A 61 361 133 HOH HOH . F 6 HOH A 62 362 32 HOH HOH . F 6 HOH A 63 363 160 HOH HOH . F 6 HOH A 64 364 14 HOH HOH . F 6 HOH A 65 365 122 HOH HOH . F 6 HOH A 66 366 3 HOH HOH . F 6 HOH A 67 367 28 HOH HOH . F 6 HOH A 68 368 134 HOH HOH . F 6 HOH A 69 369 131 HOH HOH . F 6 HOH A 70 370 81 HOH HOH . F 6 HOH A 71 371 33 HOH HOH . F 6 HOH A 72 372 10 HOH HOH . F 6 HOH A 73 373 85 HOH HOH . F 6 HOH A 74 374 74 HOH HOH . F 6 HOH A 75 375 97 HOH HOH . F 6 HOH A 76 376 154 HOH HOH . F 6 HOH A 77 377 164 HOH HOH . F 6 HOH A 78 378 9 HOH HOH . F 6 HOH A 79 379 88 HOH HOH . F 6 HOH A 80 380 43 HOH HOH . F 6 HOH A 81 381 138 HOH HOH . F 6 HOH A 82 382 101 HOH HOH . F 6 HOH A 83 383 89 HOH HOH . F 6 HOH A 84 384 163 HOH HOH . F 6 HOH A 85 385 50 HOH HOH . F 6 HOH A 86 386 149 HOH HOH . F 6 HOH A 87 387 96 HOH HOH . F 6 HOH A 88 388 6 HOH HOH . F 6 HOH A 89 389 104 HOH HOH . F 6 HOH A 90 390 170 HOH HOH . F 6 HOH A 91 391 143 HOH HOH . F 6 HOH A 92 392 145 HOH HOH . F 6 HOH A 93 393 79 HOH HOH . F 6 HOH A 94 394 22 HOH HOH . F 6 HOH A 95 395 24 HOH HOH . F 6 HOH A 96 396 91 HOH HOH . F 6 HOH A 97 397 151 HOH HOH . F 6 HOH A 98 398 161 HOH HOH . F 6 HOH A 99 399 139 HOH HOH . F 6 HOH A 100 400 21 HOH HOH . F 6 HOH A 101 401 137 HOH HOH . F 6 HOH A 102 402 82 HOH HOH . F 6 HOH A 103 403 4 HOH HOH . F 6 HOH A 104 404 132 HOH HOH . F 6 HOH A 105 405 87 HOH HOH . F 6 HOH A 106 406 150 HOH HOH . F 6 HOH A 107 407 42 HOH HOH . F 6 HOH A 108 408 157 HOH HOH . F 6 HOH A 109 409 93 HOH HOH . F 6 HOH A 110 410 20 HOH HOH . F 6 HOH A 111 411 146 HOH HOH . F 6 HOH A 112 412 99 HOH HOH . F 6 HOH A 113 413 80 HOH HOH . F 6 HOH A 114 414 118 HOH HOH . F 6 HOH A 115 415 156 HOH HOH . F 6 HOH A 116 416 136 HOH HOH . F 6 HOH A 117 417 114 HOH HOH . F 6 HOH A 118 418 165 HOH HOH . F 6 HOH A 119 419 169 HOH HOH . F 6 HOH A 120 420 75 HOH HOH . F 6 HOH A 121 421 152 HOH HOH . F 6 HOH A 122 422 168 HOH HOH . F 6 HOH A 123 423 167 HOH HOH . F 6 HOH A 124 424 158 HOH HOH . F 6 HOH A 125 425 84 HOH HOH . F 6 HOH A 126 426 153 HOH HOH . F 6 HOH A 127 427 119 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 . . . B 2 -16.689 14.945 -0.047 1 13.58 ? O4 DUP 201 A 1 HETATM 2 C C4 DUP . . . B 2 -15.851 14.153 0.439 1 12.28 ? C4 DUP 201 A 1 HETATM 3 C C5 DUP . . . B 2 -16.235 12.895 0.938 1 14.08 ? C5 DUP 201 A 1 HETATM 4 C C6 DUP . . . B 2 -15.266 12.09 1.458 1 13.6 ? C6 DUP 201 A 1 HETATM 5 N N3 DUP . . . B 2 -14.548 14.561 0.492 1 13.12 ? N3 DUP 201 A 1 HETATM 6 C C2 DUP . . . B 2 -13.619 13.805 1.067 1 13.16 ? C2 DUP 201 A 1 HETATM 7 O O2 DUP . . . B 2 -12.438 14.244 1.078 1 13.77 ? O2 DUP 201 A 1 HETATM 8 N N1 DUP . . . B 2 -13.959 12.547 1.55 1 12.63 ? N1 DUP 201 A 1 HETATM 9 C C1' DUP . . . B 2 -12.94 11.678 2.191 1 13.07 ? C1' DUP 201 A 1 HETATM 10 C C2' DUP . . . B 2 -13.103 11.698 3.724 1 12.29 ? C2' DUP 201 A 1 HETATM 11 C C3' DUP . . . B 2 -13.863 10.443 4.017 1 12.58 ? C3' DUP 201 A 1 HETATM 12 O O3' DUP . . . B 2 -13.594 9.97 5.341 1 13.3 ? O3' DUP 201 A 1 HETATM 13 O O4' DUP . . . B 2 -13.12 10.336 1.787 1 13.58 ? O4' DUP 201 A 1 HETATM 14 C C4' DUP . . . B 2 -13.31 9.507 2.943 1 13.16 ? C4' DUP 201 A 1 HETATM 15 C C5' DUP . . . B 2 -14.176 8.358 2.567 1 14.08 ? C5' DUP 201 A 1 HETATM 16 O O5' DUP . . . B 2 -15.469 8.862 2.123 1 12.88 ? O5' DUP 201 A 1 HETATM 17 P PA DUP . . . B 2 -16.542 7.783 1.535 1 13.71 ? PA DUP 201 A 1 HETATM 18 O O1A DUP . . . B 2 -17.78 8.587 1.106 1 14.3 ? O1A DUP 201 A 1 HETATM 19 O O2A DUP . . . B 2 -16.78 6.712 2.569 1 13.35 ? O2A DUP 201 A 1 HETATM 20 N N3A DUP . . . B 2 -15.76 7.137 0.202 1 13.97 ? N3A DUP 201 A 1 HETATM 21 P PB DUP . . . B 2 -15.571 5.527 -0.182 1 14.39 ? PB DUP 201 A 1 HETATM 22 O O1B DUP . . . B 2 -15.568 5.431 -1.702 1 14.82 ? O1B DUP 201 A 1 HETATM 23 O O2B DUP . . . B 2 -16.575 4.676 0.554 1 14.28 ? O2B DUP 201 A 1 HETATM 24 O O3B DUP . . . B 2 -14.095 5.134 0.292 1 16.6 ? O3B DUP 201 A 1 HETATM 25 P PG DUP . . . B 2 -13.612 4.372 1.626 1 16.73 ? PG DUP 201 A 1 HETATM 26 O O2G DUP . . . B 2 -13.328 2.974 1.221 1 22.61 ? O2G DUP 201 A 1 HETATM 27 O O1G DUP . . . B 2 -14.676 4.572 2.692 1 15.37 ? O1G DUP 201 A 1 HETATM 28 O O3G DUP . . . B 2 -12.3 5.091 1.96 1 20.56 ? O3G DUP 201 A 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 36 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 909 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 28 #