data_8CGA # _model_server_result.job_id Osk8IlaXL563ujWrizIAWg _model_server_result.datetime_utc '2024-11-14 13:36:40' _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 8cga # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":200}' # _entry.id 8CGA # _exptl.entry_id 8CGA _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 8CGA _cell.length_a 55.249 _cell.length_b 55.249 _cell.length_c 83.751 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8CGA _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall 'P 6c' _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,G _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 27.6245 -47.847038 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 55.249 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 O1A DUP . A DUP 200 1_555 C MG MG . A MG 201 2_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc2 B O1B DUP . A DUP 200 1_555 C MG MG . A MG 201 2_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc3 B O2G DUP . A DUP 200 1_555 C MG MG . A MG 201 2_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc4 C MG MG . A MG 201 1_555 G O HOH . A HOH 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc5 C MG MG . A MG 201 1_555 G O HOH . A HOH 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc6 C MG MG . A MG 201 1_555 G O HOH . A HOH 371 3_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? # _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 8CGA _atom_sites.fract_transf_matrix[1][1] 0.0181 _atom_sites.fract_transf_matrix[1][2] 0.01045 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.0209 _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] 0.01194 _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 1 200 200 DUP DUP . C 3 MG A 1 201 201 MG MG . D 4 SO4 A 1 202 202 SO4 SO4 . E 5 GOL A 1 203 203 GOL GOL . F 6 TRS A 1 204 204 TRS TRS . G 7 HOH A 1 301 45 HOH HOH . G 7 HOH A 2 302 57 HOH HOH . G 7 HOH A 3 303 26 HOH HOH . G 7 HOH A 4 304 16 HOH HOH . G 7 HOH A 5 305 23 HOH HOH . G 7 HOH A 6 306 53 HOH HOH . G 7 HOH A 7 307 75 HOH HOH . G 7 HOH A 8 308 49 HOH HOH . G 7 HOH A 9 309 36 HOH HOH . G 7 HOH A 10 310 21 HOH HOH . G 7 HOH A 11 311 58 HOH HOH . G 7 HOH A 12 312 6 HOH HOH . G 7 HOH A 13 313 7 HOH HOH . G 7 HOH A 14 314 12 HOH HOH . G 7 HOH A 15 315 66 HOH HOH . G 7 HOH A 16 316 46 HOH HOH . G 7 HOH A 17 317 74 HOH HOH . G 7 HOH A 18 318 14 HOH HOH . G 7 HOH A 19 319 73 HOH HOH . G 7 HOH A 20 320 22 HOH HOH . G 7 HOH A 21 321 55 HOH HOH . G 7 HOH A 22 322 11 HOH HOH . G 7 HOH A 23 323 62 HOH HOH . G 7 HOH A 24 324 80 HOH HOH . G 7 HOH A 25 325 41 HOH HOH . G 7 HOH A 26 326 39 HOH HOH . G 7 HOH A 27 327 33 HOH HOH . G 7 HOH A 28 328 67 HOH HOH . G 7 HOH A 29 329 1 HOH HOH . G 7 HOH A 30 330 10 HOH HOH . G 7 HOH A 31 331 15 HOH HOH . G 7 HOH A 32 332 28 HOH HOH . G 7 HOH A 33 333 97 HOH HOH . G 7 HOH A 34 334 17 HOH HOH . G 7 HOH A 35 335 65 HOH HOH . G 7 HOH A 36 336 13 HOH HOH . G 7 HOH A 37 337 85 HOH HOH . G 7 HOH A 38 338 99 HOH HOH . G 7 HOH A 39 339 31 HOH HOH . G 7 HOH A 40 340 63 HOH HOH . G 7 HOH A 41 341 24 HOH HOH . G 7 HOH A 42 342 18 HOH HOH . G 7 HOH A 43 343 68 HOH HOH . G 7 HOH A 44 344 19 HOH HOH . G 7 HOH A 45 345 5 HOH HOH . G 7 HOH A 46 346 20 HOH HOH . G 7 HOH A 47 347 37 HOH HOH . G 7 HOH A 48 348 2 HOH HOH . G 7 HOH A 49 349 25 HOH HOH . G 7 HOH A 50 350 50 HOH HOH . G 7 HOH A 51 351 8 HOH HOH . G 7 HOH A 52 352 4 HOH HOH . G 7 HOH A 53 353 3 HOH HOH . G 7 HOH A 54 354 48 HOH HOH . G 7 HOH A 55 355 30 HOH HOH . G 7 HOH A 56 356 64 HOH HOH . G 7 HOH A 57 357 51 HOH HOH . G 7 HOH A 58 358 35 HOH HOH . G 7 HOH A 59 359 86 HOH HOH . G 7 HOH A 60 360 54 HOH HOH . G 7 HOH A 61 361 79 HOH HOH . G 7 HOH A 62 362 94 HOH HOH . G 7 HOH A 63 363 71 HOH HOH . G 7 HOH A 64 364 32 HOH HOH . G 7 HOH A 65 365 29 HOH HOH . G 7 HOH A 66 366 91 HOH HOH . G 7 HOH A 67 367 27 HOH HOH . G 7 HOH A 68 368 34 HOH HOH . G 7 HOH A 69 369 38 HOH HOH . G 7 HOH A 70 370 98 HOH HOH . G 7 HOH A 71 371 9 HOH HOH . G 7 HOH A 72 372 52 HOH HOH . G 7 HOH A 73 373 70 HOH HOH . G 7 HOH A 74 374 40 HOH HOH . G 7 HOH A 75 375 56 HOH HOH . G 7 HOH A 76 376 69 HOH HOH . G 7 HOH A 77 377 90 HOH HOH . G 7 HOH A 78 378 78 HOH HOH . G 7 HOH A 79 379 76 HOH HOH . G 7 HOH A 80 380 81 HOH HOH . G 7 HOH A 81 381 60 HOH HOH . G 7 HOH A 82 382 61 HOH HOH . G 7 HOH A 83 383 95 HOH HOH . G 7 HOH A 84 384 43 HOH HOH . G 7 HOH A 85 385 44 HOH HOH . G 7 HOH A 86 386 100 HOH HOH . G 7 HOH A 87 387 42 HOH HOH . G 7 HOH A 88 388 92 HOH HOH . G 7 HOH A 89 389 47 HOH HOH . G 7 HOH A 90 390 84 HOH HOH . G 7 HOH A 91 391 89 HOH HOH . G 7 HOH A 92 392 93 HOH HOH . G 7 HOH A 93 393 96 HOH HOH . G 7 HOH A 94 394 101 HOH HOH . G 7 HOH A 95 395 87 HOH HOH . G 7 HOH A 96 396 88 HOH HOH . G 7 HOH A 97 397 82 HOH HOH . G 7 HOH A 98 398 72 HOH HOH . G 7 HOH A 99 399 83 HOH HOH . G 7 HOH A 100 400 59 HOH HOH . G 7 HOH A 101 401 77 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 21.489 -7.147 -0.256 1 9.75 ? O4 DUP 200 A 1 HETATM 2 C C4 DUP . . . B 2 20.42 -6.823 -0.763 1 7.53 ? C4 DUP 200 A 1 HETATM 3 C C5 DUP . . . B 2 19.459 -7.731 -1.314 1 8.03 ? C5 DUP 200 A 1 HETATM 4 C C6 DUP . . . B 2 18.333 -7.261 -1.859 1 8.09 ? C6 DUP 200 A 1 HETATM 5 N N3 DUP . . . B 2 20.071 -5.491 -0.841 1 8.13 ? N3 DUP 200 A 1 HETATM 6 C C2 DUP . . . B 2 18.929 -4.975 -1.397 1 8.34 ? C2 DUP 200 A 1 HETATM 7 O O2 DUP . . . B 2 18.722 -3.767 -1.432 1 8.72 ? O2 DUP 200 A 1 HETATM 8 N N1 DUP . . . B 2 18.053 -5.917 -1.91 1 7.43 ? N1 DUP 200 A 1 HETATM 9 C C1' DUP . . . B 2 16.819 -5.446 -2.572 1 8.52 ? C1' DUP 200 A 1 HETATM 10 C C2' DUP . . . B 2 16.879 -5.557 -4.1 1 9.22 ? C2' DUP 200 A 1 HETATM 11 C C3' DUP . . . B 2 16.213 -6.894 -4.382 1 8.16 ? C3' DUP 200 A 1 HETATM 12 O O3' DUP . . . B 2 15.669 -6.924 -5.698 1 8.48 ? O3' DUP 200 A 1 HETATM 13 O O4' DUP . . . B 2 15.761 -6.303 -2.158 1 8.54 ? O4' DUP 200 A 1 HETATM 14 C C4' DUP . . . B 2 15.134 -6.901 -3.311 1 8.41 ? C4' DUP 200 A 1 HETATM 15 C C5' DUP . . . B 2 14.582 -8.251 -2.942 1 8.75 ? C5' DUP 200 A 1 HETATM 16 O O5' DUP . . . B 2 15.661 -9.137 -2.551 1 7.68 ? O5' DUP 200 A 1 HETATM 17 P PA DUP . . . B 2 15.295 -10.583 -1.994 1 7.8 ? PA DUP 200 A 1 HETATM 18 O O1A DUP . . . B 2 14.459 -11.284 -3.027 1 8.24 ? O1A DUP 200 A 1 HETATM 19 O O2A DUP . . . B 2 16.574 -11.226 -1.577 1 8.57 ? O2A DUP 200 A 1 HETATM 20 N N3A DUP . . . B 2 14.33 -10.269 -0.697 1 8.53 ? N3A DUP 200 A 1 HETATM 21 P PB DUP . . . B 2 12.873 -10.873 -0.277 1 8.79 ? PB DUP 200 A 1 HETATM 22 O O1B DUP . . . B 2 12.589 -12.133 -1.036 1 9.23 ? O1B DUP 200 A 1 HETATM 23 O O2B DUP . . . B 2 12.766 -10.916 1.211 1 10.13 ? O2B DUP 200 A 1 HETATM 24 O O3B DUP . . . B 2 11.825 -9.787 -0.791 1 11.34 ? O3B DUP 200 A 1 HETATM 25 P PG DUP . . . B 2 10.858 -9.818 -2.055 1 13.11 ? PG DUP 200 A 1 HETATM 26 O O2G DUP . . . B 2 11.59 -10.537 -3.151 1 10.48 ? O2G DUP 200 A 1 HETATM 27 O O1G DUP . . . B 2 9.636 -10.556 -1.573 1 19.33 ? O1G DUP 200 A 1 HETATM 28 O O3G DUP . . . B 2 10.59 -8.378 -2.375 1 17.91 ? O3G DUP 200 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #