data_1P61 # _model_server_result.job_id EqIM2BiK-abLM0iMtD4G2Q _model_server_result.datetime_utc '2024-10-16 10:32:24' _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 1p61 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 1P61 # _exptl.entry_id 1P61 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 227.217 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYCYTIDINE" _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 90 _cell.entry_id 1P61 _cell.length_a 80.001 _cell.length_b 80.001 _cell.length_c 93.946 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1P61 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA,PQS _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 8_665 -y+1,-x+1,-z+1/2 0 -1 0 -1 0 0 0 0 -1 80.001 80.001 46.973 # _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 'C9 H13 N3 O4' _chem_comp.formula_weight 227.217 _chem_comp.id DCZ _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYCYTIDINE" _chem_comp.type 'dna oh 5 prime terminus' _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 DCZ sing 127 n n N1 C6 DCZ sing 128 n n N1 C1' DCZ sing 129 n n C2 N3 DCZ sing 130 n n C2 O2 DCZ doub 131 n n N3 C4 DCZ doub 132 n n C4 C5 DCZ sing 133 n n C4 N4 DCZ sing 134 n n C5 C6 DCZ doub 135 n n C5 H5 DCZ sing 136 n n C6 H6 DCZ sing 137 n n N4 HN41 DCZ sing 138 n n N4 HN42 DCZ sing 139 n n C1' C2' DCZ sing 140 n n C1' O4' DCZ sing 141 n n C1' H1' DCZ sing 142 n n C2' C3' DCZ sing 143 n n C2' "H2'1" DCZ sing 144 n n C2' "H2'2" DCZ sing 145 n n C3' C4' DCZ sing 146 n n C3' O3' DCZ sing 147 n n C3' H3' DCZ sing 148 n n C4' O4' DCZ sing 149 n n C4' C5' DCZ sing 150 n n C4' H4' DCZ sing 151 n n O3' HO3' DCZ sing 152 n n C5' O5' DCZ sing 153 n n C5' "H5'1" DCZ sing 154 n n C5' "H5'2" DCZ sing 155 n n O5' HO51 DCZ sing 156 n n # _atom_sites.entry_id 1P61 _atom_sites.fract_transf_matrix[1][1] 0.0125 _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] 0.0125 _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] 0.010644 _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 ADP B 1 301 301 ADP ADP . C 3 DCZ B 1 302 302 DCZ DCY . D 4 HOH B 1 303 1 HOH HOH . D 4 HOH B 2 304 2 HOH HOH . D 4 HOH B 3 305 3 HOH HOH . D 4 HOH B 4 306 4 HOH HOH . D 4 HOH B 5 307 5 HOH HOH . D 4 HOH B 6 308 6 HOH HOH . D 4 HOH B 7 309 7 HOH HOH . D 4 HOH B 8 310 8 HOH HOH . D 4 HOH B 9 311 9 HOH HOH . D 4 HOH B 10 312 11 HOH HOH . D 4 HOH B 11 313 12 HOH HOH . D 4 HOH B 12 314 13 HOH HOH . D 4 HOH B 13 315 14 HOH HOH . D 4 HOH B 14 316 15 HOH HOH . D 4 HOH B 15 317 16 HOH HOH . D 4 HOH B 16 318 17 HOH HOH . D 4 HOH B 17 319 18 HOH HOH . D 4 HOH B 18 320 19 HOH HOH . D 4 HOH B 19 321 20 HOH HOH . D 4 HOH B 20 322 21 HOH HOH . D 4 HOH B 21 323 23 HOH HOH . D 4 HOH B 22 324 25 HOH HOH . D 4 HOH B 23 325 26 HOH HOH . D 4 HOH B 24 326 27 HOH HOH . D 4 HOH B 25 327 28 HOH HOH . D 4 HOH B 26 328 31 HOH HOH . D 4 HOH B 27 329 32 HOH HOH . D 4 HOH B 28 330 33 HOH HOH . D 4 HOH B 29 331 35 HOH HOH . D 4 HOH B 30 332 37 HOH HOH . D 4 HOH B 31 333 38 HOH HOH . D 4 HOH B 32 334 39 HOH HOH . D 4 HOH B 33 335 40 HOH HOH . D 4 HOH B 34 336 41 HOH HOH . D 4 HOH B 35 337 42 HOH HOH . D 4 HOH B 36 338 43 HOH HOH . D 4 HOH B 37 339 45 HOH HOH . D 4 HOH B 38 340 47 HOH HOH . D 4 HOH B 39 341 49 HOH HOH . D 4 HOH B 40 342 50 HOH HOH . D 4 HOH B 41 343 51 HOH HOH . D 4 HOH B 42 344 52 HOH HOH . D 4 HOH B 43 345 53 HOH HOH . D 4 HOH B 44 346 55 HOH HOH . D 4 HOH B 45 347 56 HOH HOH . D 4 HOH B 46 348 57 HOH HOH . D 4 HOH B 47 349 58 HOH HOH . D 4 HOH B 48 350 59 HOH HOH . D 4 HOH B 49 351 60 HOH HOH . D 4 HOH B 50 352 61 HOH HOH . D 4 HOH B 51 353 62 HOH HOH . D 4 HOH B 52 354 63 HOH HOH . D 4 HOH B 53 355 64 HOH HOH . D 4 HOH B 54 356 65 HOH HOH . D 4 HOH B 55 357 66 HOH HOH . D 4 HOH B 56 358 67 HOH HOH . D 4 HOH B 57 359 68 HOH HOH . D 4 HOH B 58 360 70 HOH HOH . D 4 HOH B 59 361 71 HOH HOH . D 4 HOH B 60 362 72 HOH HOH . D 4 HOH B 61 363 73 HOH HOH . D 4 HOH B 62 364 75 HOH HOH . D 4 HOH B 63 365 78 HOH HOH . D 4 HOH B 64 366 81 HOH HOH . D 4 HOH B 65 367 82 HOH HOH . D 4 HOH B 66 368 83 HOH HOH . D 4 HOH B 67 369 84 HOH HOH . D 4 HOH B 68 370 87 HOH HOH . D 4 HOH B 69 371 88 HOH HOH . D 4 HOH B 70 372 89 HOH HOH . D 4 HOH B 71 373 92 HOH HOH . D 4 HOH B 72 374 95 HOH HOH . D 4 HOH B 73 375 96 HOH HOH . D 4 HOH B 74 376 97 HOH HOH . D 4 HOH B 75 377 98 HOH HOH . D 4 HOH B 76 378 99 HOH HOH . D 4 HOH B 77 379 100 HOH HOH . D 4 HOH B 78 380 102 HOH HOH . D 4 HOH B 79 381 103 HOH HOH . D 4 HOH B 80 382 104 HOH HOH . D 4 HOH B 81 383 105 HOH HOH . D 4 HOH B 82 384 106 HOH HOH . D 4 HOH B 83 385 108 HOH HOH . D 4 HOH B 84 386 109 HOH HOH . D 4 HOH B 85 387 110 HOH HOH . D 4 HOH B 86 388 117 HOH HOH . D 4 HOH B 87 389 120 HOH HOH . D 4 HOH B 88 390 121 HOH HOH . D 4 HOH B 89 391 123 HOH HOH . D 4 HOH B 90 392 124 HOH HOH . D 4 HOH B 91 393 126 HOH HOH . D 4 HOH B 92 394 130 HOH HOH . D 4 HOH B 93 395 131 HOH HOH . D 4 HOH B 94 396 133 HOH HOH . D 4 HOH B 95 397 134 HOH HOH . D 4 HOH B 96 398 135 HOH HOH . D 4 HOH B 97 399 136 HOH HOH . D 4 HOH B 98 400 137 HOH HOH . D 4 HOH B 99 401 141 HOH HOH . D 4 HOH B 100 402 145 HOH HOH . D 4 HOH B 101 403 148 HOH HOH . D 4 HOH B 102 404 150 HOH HOH . D 4 HOH B 103 405 151 HOH HOH . D 4 HOH B 104 406 152 HOH HOH . D 4 HOH B 105 407 153 HOH HOH . D 4 HOH B 106 408 154 HOH HOH . D 4 HOH B 107 409 156 HOH HOH . D 4 HOH B 108 410 157 HOH HOH . D 4 HOH B 109 411 164 HOH HOH . D 4 HOH B 110 412 167 HOH HOH . D 4 HOH B 111 413 170 HOH HOH . D 4 HOH B 112 414 171 HOH HOH . D 4 HOH B 113 415 177 HOH HOH . D 4 HOH B 114 416 178 HOH HOH . D 4 HOH B 115 417 180 HOH HOH . D 4 HOH B 116 418 181 HOH HOH . D 4 HOH B 117 419 182 HOH HOH . D 4 HOH B 118 420 183 HOH HOH . D 4 HOH B 119 421 184 HOH HOH . D 4 HOH B 120 422 185 HOH HOH . D 4 HOH B 121 423 186 HOH HOH . D 4 HOH B 122 424 187 HOH HOH . D 4 HOH B 123 425 188 HOH HOH . D 4 HOH B 124 426 190 HOH HOH . D 4 HOH B 125 427 191 HOH HOH . D 4 HOH B 126 428 193 HOH HOH . D 4 HOH B 127 429 195 HOH HOH . D 4 HOH B 128 430 196 HOH HOH . D 4 HOH B 129 431 198 HOH HOH . D 4 HOH B 130 432 199 HOH HOH . D 4 HOH B 131 433 200 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 DCZ . . . C 3 67.179 33.834 19.099 1 33.97 ? N1 DCZ 302 B 1 HETATM 2 C C2 DCZ . . . C 3 66.701 32.676 18.636 1 30.68 ? C2 DCZ 302 B 1 HETATM 3 N N3 DCZ . . . C 3 65.465 32.626 18.156 1 31.36 ? N3 DCZ 302 B 1 HETATM 4 C C4 DCZ . . . C 3 64.741 33.747 18.21 1 31.11 ? C4 DCZ 302 B 1 HETATM 5 C C5 DCZ . . . C 3 65.217 34.854 18.639 1 28.22 ? C5 DCZ 302 B 1 HETATM 6 C C6 DCZ . . . C 3 66.417 34.878 19.09 1 31.8 ? C6 DCZ 302 B 1 HETATM 7 O O2 DCZ . . . C 3 67.373 31.566 18.592 1 32.12 ? O2 DCZ 302 B 1 HETATM 8 N N4 DCZ . . . C 3 63.528 33.64 17.734 1 30.87 ? N4 DCZ 302 B 1 HETATM 9 C C1' DCZ . . . C 3 68.538 33.891 19.672 1 33.4 ? C1' DCZ 302 B 1 HETATM 10 C C2' DCZ . . . C 3 69.604 34.676 18.939 1 32.52 ? C2' DCZ 302 B 1 HETATM 11 C C3' DCZ . . . C 3 70.502 35.159 20.058 1 34.57 ? C3' DCZ 302 B 1 HETATM 12 C C4' DCZ . . . C 3 69.551 35.364 21.248 1 36.11 ? C4' DCZ 302 B 1 HETATM 13 O O4' DCZ . . . C 3 68.405 34.542 20.95 1 33.41 ? O4' DCZ 302 B 1 HETATM 14 O O3' DCZ . . . C 3 71.406 34.09 20.43 1 32.9 ? O3' DCZ 302 B 1 HETATM 15 C C5' DCZ . . . C 3 69.121 36.802 21.442 1 37.38 ? C5' DCZ 302 B 1 HETATM 16 O O5' DCZ . . . C 3 68.778 37.454 20.189 1 38.69 ? O5' DCZ 302 B 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 16 #