data_2D3Y # _model_server_result.job_id b3t8GzAvbvswnrtQCbxeQA _model_server_result.datetime_utc '2024-11-17 01:50:29' _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 2d3y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":221}' # _entry.id 2D3Y # _exptl.entry_id 2D3Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE-5'-MONOPHOSPHATE" _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 2D3Y _cell.length_a 48.18 _cell.length_b 62.35 _cell.length_c 63.04 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2D3Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _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 A SG CYS 13 A CYS 13 1_555 D FE1 SF4 . A SF4 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc2 A SG CYS 16 A CYS 16 1_555 D FE3 SF4 . A SF4 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc3 A SG CYS 115 A CYS 115 1_555 D FE2 SF4 . A SF4 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc4 A SG CYS 130 A CYS 130 1_555 D FE4 SF4 . A SF4 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? # _chem_comp.formula 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id DU _chem_comp.mon_nstd_flag y _chem_comp.name "2'-DEOXYURIDINE-5'-MONOPHOSPHATE" _chem_comp.type 'dna linking' _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 OP3 P DU sing 89 n n OP3 HOP3 DU sing 90 n n P OP1 DU doub 91 n n P OP2 DU sing 92 n n P O5' DU sing 93 n n OP2 HOP2 DU sing 94 n n O5' C5' DU sing 95 n n C5' C4' DU sing 96 n n C5' H5' DU sing 97 n n C5' "H5''" DU sing 98 n n C4' O4' DU sing 99 n n C4' C3' DU sing 100 n n C4' H4' DU sing 101 n n O4' C1' DU sing 102 n n C3' O3' DU sing 103 n n C3' C2' DU sing 104 n n C3' H3' DU sing 105 n n O3' HO3' DU sing 106 n n C2' C1' DU sing 107 n n C2' H2' DU sing 108 n n C2' "H2''" DU sing 109 n n C1' N1 DU sing 110 n n C1' H1' DU sing 111 n n N1 C2 DU sing 112 n n N1 C6 DU sing 113 n n C2 O2 DU doub 114 n n C2 N3 DU sing 115 n n N3 C4 DU sing 116 n n N3 H3 DU sing 117 n n C4 O4 DU doub 118 n n C4 C5 DU sing 119 n n C5 C6 DU doub 120 n n C5 H5 DU sing 121 n n C6 H6 DU sing 122 n n # _atom_sites.entry_id 2D3Y _atom_sites.fract_transf_matrix[1][1] 0.020755 _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] 0.016038 _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] 0.015863 _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 ACT A 1 222 222 ACT ACT . C 2 ACT A 1 223 223 ACT ACT . D 3 SF4 A 1 220 220 SF4 FS4 . E 4 DU A 1 221 221 DU UMP . F 5 HOH A 1 224 1 HOH TIP . F 5 HOH A 2 225 2 HOH TIP . F 5 HOH A 3 226 121 HOH TIP . F 5 HOH A 4 227 167 HOH TIP . F 5 HOH A 5 228 108 HOH TIP . F 5 HOH A 6 229 168 HOH TIP . F 5 HOH A 7 230 3 HOH TIP . F 5 HOH A 8 231 4 HOH TIP . F 5 HOH A 9 232 5 HOH TIP . F 5 HOH A 10 233 109 HOH TIP . F 5 HOH A 11 234 6 HOH TIP . F 5 HOH A 12 235 110 HOH TIP . F 5 HOH A 13 236 7 HOH TIP . F 5 HOH A 14 237 8 HOH TIP . F 5 HOH A 15 238 9 HOH TIP . F 5 HOH A 16 239 171 HOH TIP . F 5 HOH A 17 240 10 HOH TIP . F 5 HOH A 18 241 118 HOH TIP . F 5 HOH A 19 242 11 HOH TIP . F 5 HOH A 20 243 119 HOH TIP . F 5 HOH A 21 244 120 HOH TIP . F 5 HOH A 22 245 12 HOH TIP . F 5 HOH A 23 246 14 HOH TIP . F 5 HOH A 24 247 15 HOH TIP . F 5 HOH A 25 248 17 HOH TIP . F 5 HOH A 26 249 18 HOH TIP . F 5 HOH A 27 250 19 HOH TIP . F 5 HOH A 28 251 20 HOH TIP . F 5 HOH A 29 252 111 HOH TIP . F 5 HOH A 30 253 112 HOH TIP . F 5 HOH A 31 254 122 HOH TIP . F 5 HOH A 32 255 21 HOH TIP . F 5 HOH A 33 256 123 HOH TIP . F 5 HOH A 34 257 124 HOH TIP . F 5 HOH A 35 258 22 HOH TIP . F 5 HOH A 36 259 24 HOH TIP . F 5 HOH A 37 260 25 HOH TIP . F 5 HOH A 38 261 125 HOH TIP . F 5 HOH A 39 262 26 HOH TIP . F 5 HOH A 40 263 126 HOH TIP . F 5 HOH A 41 264 127 HOH TIP . F 5 HOH A 42 265 27 HOH TIP . F 5 HOH A 43 266 28 HOH TIP . F 5 HOH A 44 267 29 HOH TIP . F 5 HOH A 45 268 128 HOH TIP . F 5 HOH A 46 269 30 HOH TIP . F 5 HOH A 47 270 31 HOH TIP . F 5 HOH A 48 271 32 HOH TIP . F 5 HOH A 49 272 113 HOH TIP . F 5 HOH A 50 273 172 HOH TIP . F 5 HOH A 51 274 173 HOH TIP . F 5 HOH A 52 275 129 HOH TIP . F 5 HOH A 53 276 114 HOH TIP . F 5 HOH A 54 277 130 HOH TIP . F 5 HOH A 55 278 33 HOH TIP . F 5 HOH A 56 279 131 HOH TIP . F 5 HOH A 57 280 34 HOH TIP . F 5 HOH A 58 281 115 HOH TIP . F 5 HOH A 59 282 35 HOH TIP . F 5 HOH A 60 283 132 HOH TIP . F 5 HOH A 61 284 36 HOH TIP . F 5 HOH A 62 285 133 HOH TIP . F 5 HOH A 63 286 134 HOH TIP . F 5 HOH A 64 287 37 HOH TIP . F 5 HOH A 65 288 135 HOH TIP . F 5 HOH A 66 289 38 HOH TIP . F 5 HOH A 67 290 136 HOH TIP . F 5 HOH A 68 291 39 HOH TIP . F 5 HOH A 69 292 175 HOH TIP . F 5 HOH A 70 293 137 HOH TIP . F 5 HOH A 71 294 116 HOH TIP . F 5 HOH A 72 295 40 HOH TIP . F 5 HOH A 73 296 41 HOH TIP . F 5 HOH A 74 297 138 HOH TIP . F 5 HOH A 75 298 42 HOH TIP . F 5 HOH A 76 299 43 HOH TIP . F 5 HOH A 77 300 139 HOH TIP . F 5 HOH A 78 301 44 HOH TIP . F 5 HOH A 79 302 140 HOH TIP . F 5 HOH A 80 303 45 HOH TIP . F 5 HOH A 81 304 117 HOH TIP . F 5 HOH A 82 305 46 HOH TIP . F 5 HOH A 83 306 47 HOH TIP . F 5 HOH A 84 307 48 HOH TIP . F 5 HOH A 85 308 176 HOH TIP . F 5 HOH A 86 309 49 HOH TIP . F 5 HOH A 87 310 177 HOH TIP . F 5 HOH A 88 311 50 HOH TIP . F 5 HOH A 89 312 51 HOH TIP . F 5 HOH A 90 313 141 HOH TIP . F 5 HOH A 91 314 142 HOH TIP . F 5 HOH A 92 315 52 HOH TIP . F 5 HOH A 93 316 53 HOH TIP . F 5 HOH A 94 317 143 HOH TIP . F 5 HOH A 95 318 178 HOH TIP . F 5 HOH A 96 319 54 HOH TIP . F 5 HOH A 97 320 144 HOH TIP . F 5 HOH A 98 321 55 HOH TIP . F 5 HOH A 99 322 56 HOH TIP . F 5 HOH A 100 323 57 HOH TIP . F 5 HOH A 101 324 58 HOH TIP . F 5 HOH A 102 325 59 HOH TIP . F 5 HOH A 103 326 61 HOH TIP . F 5 HOH A 104 327 145 HOH TIP . F 5 HOH A 105 328 62 HOH TIP . F 5 HOH A 106 329 63 HOH TIP . F 5 HOH A 107 330 64 HOH TIP . F 5 HOH A 108 331 65 HOH TIP . F 5 HOH A 109 332 146 HOH TIP . F 5 HOH A 110 333 66 HOH TIP . F 5 HOH A 111 334 67 HOH TIP . F 5 HOH A 112 335 68 HOH TIP . F 5 HOH A 113 336 179 HOH TIP . F 5 HOH A 114 337 69 HOH TIP . F 5 HOH A 115 338 147 HOH TIP . F 5 HOH A 116 339 70 HOH TIP . F 5 HOH A 117 340 71 HOH TIP . F 5 HOH A 118 341 72 HOH TIP . F 5 HOH A 119 342 73 HOH TIP . F 5 HOH A 120 343 148 HOH TIP . F 5 HOH A 121 344 74 HOH TIP . F 5 HOH A 122 345 149 HOH TIP . F 5 HOH A 123 346 76 HOH TIP . F 5 HOH A 124 347 77 HOH TIP . F 5 HOH A 125 348 78 HOH TIP . F 5 HOH A 126 349 79 HOH TIP . F 5 HOH A 127 350 80 HOH TIP . F 5 HOH A 128 351 150 HOH TIP . F 5 HOH A 129 352 81 HOH TIP . F 5 HOH A 130 353 82 HOH TIP . F 5 HOH A 131 354 83 HOH TIP . F 5 HOH A 132 355 84 HOH TIP . F 5 HOH A 133 356 85 HOH TIP . F 5 HOH A 134 357 86 HOH TIP . F 5 HOH A 135 358 87 HOH TIP . F 5 HOH A 136 359 88 HOH TIP . F 5 HOH A 137 360 152 HOH TIP . F 5 HOH A 138 361 89 HOH TIP . F 5 HOH A 139 362 90 HOH TIP . F 5 HOH A 140 363 151 HOH TIP . F 5 HOH A 141 364 91 HOH TIP . F 5 HOH A 142 365 153 HOH TIP . F 5 HOH A 143 366 154 HOH TIP . F 5 HOH A 144 367 92 HOH TIP . F 5 HOH A 145 368 93 HOH TIP . F 5 HOH A 146 369 94 HOH TIP . F 5 HOH A 147 370 155 HOH TIP . F 5 HOH A 148 371 95 HOH TIP . F 5 HOH A 149 372 156 HOH TIP . F 5 HOH A 150 373 96 HOH TIP . F 5 HOH A 151 374 97 HOH TIP . F 5 HOH A 152 375 157 HOH TIP . F 5 HOH A 153 376 158 HOH TIP . F 5 HOH A 154 377 159 HOH TIP . F 5 HOH A 155 378 162 HOH TIP . F 5 HOH A 156 379 98 HOH TIP . F 5 HOH A 157 380 99 HOH TIP . F 5 HOH A 158 381 100 HOH TIP . F 5 HOH A 159 382 101 HOH TIP . F 5 HOH A 160 383 102 HOH TIP . F 5 HOH A 161 384 103 HOH TIP . F 5 HOH A 162 385 104 HOH TIP . F 5 HOH A 163 386 105 HOH TIP . F 5 HOH A 164 387 106 HOH TIP . F 5 HOH A 165 388 160 HOH TIP . F 5 HOH A 166 389 161 HOH TIP . F 5 HOH A 167 390 163 HOH TIP . F 5 HOH A 168 391 164 HOH TIP . F 5 HOH A 169 392 165 HOH TIP . F 5 HOH A 170 393 166 HOH TIP . F 5 HOH A 171 394 169 HOH TIP . F 5 HOH A 172 395 170 HOH TIP . F 5 HOH A 173 396 174 HOH TIP . F 5 HOH A 174 397 107 HOH TIP . F 5 HOH A 175 398 180 HOH TIP . F 5 HOH A 176 399 181 HOH TIP . F 5 HOH A 177 400 182 HOH TIP . F 5 HOH A 178 401 183 HOH TIP . F 5 HOH A 179 402 184 HOH TIP . F 5 HOH A 180 403 185 HOH TIP . F 5 HOH A 181 404 186 HOH TIP . F 5 HOH A 182 405 187 HOH TIP . F 5 HOH A 183 406 188 HOH TIP . F 5 HOH A 184 407 189 HOH TIP . F 5 HOH A 185 408 190 HOH TIP . F 5 HOH A 186 409 191 HOH TIP . F 5 HOH A 187 410 192 HOH TIP . F 5 HOH A 188 411 193 HOH TIP . F 5 HOH A 189 412 194 HOH TIP . F 5 HOH A 190 413 195 HOH TIP . F 5 HOH A 191 414 196 HOH TIP . F 5 HOH A 192 415 197 HOH TIP . F 5 HOH A 193 416 198 HOH TIP . F 5 HOH A 194 417 199 HOH TIP . F 5 HOH A 195 418 200 HOH TIP . F 5 HOH A 196 419 201 HOH TIP . F 5 HOH A 197 420 202 HOH TIP . F 5 HOH A 198 421 203 HOH TIP . F 5 HOH A 199 422 204 HOH TIP . F 5 HOH A 200 423 205 HOH TIP . F 5 HOH A 201 424 206 HOH TIP . F 5 HOH A 202 425 207 HOH TIP . F 5 HOH A 203 426 208 HOH TIP . F 5 HOH A 204 427 209 HOH TIP . F 5 HOH A 205 428 210 HOH TIP . F 5 HOH A 206 429 211 HOH TIP . F 5 HOH A 207 430 212 HOH TIP . F 5 HOH A 208 431 213 HOH TIP . F 5 HOH A 209 432 214 HOH TIP . F 5 HOH A 210 433 215 HOH TIP . # 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 OP3 DU . . . E 4 8.801 33.375 20.924 1 41.81 ? OP3 DU 221 A 1 HETATM 2 P P DU . . . E 4 8.5 33.745 19.538 1 42.44 ? P DU 221 A 1 HETATM 3 O OP1 DU . . . E 4 9.599 34.554 18.942 1 41.69 ? OP1 DU 221 A 1 HETATM 4 O OP2 DU . . . E 4 7.248 34.485 19.491 1 41.55 ? OP2 DU 221 A 1 HETATM 5 O O5' DU . . . E 4 8.331 32.435 18.662 1 39.84 ? O5' DU 221 A 1 HETATM 6 C C5' DU . . . E 4 8.956 32.202 17.369 1 36.04 ? C5' DU 221 A 1 HETATM 7 C C4' DU . . . E 4 8.531 30.804 16.866 1 33.42 ? C4' DU 221 A 1 HETATM 8 O O4' DU . . . E 4 9.593 30.207 16.012 1 31.55 ? O4' DU 221 A 1 HETATM 9 C C3' DU . . . E 4 8.497 29.747 17.968 1 32.64 ? C3' DU 221 A 1 HETATM 10 O O3' DU . . . E 4 7.671 28.667 17.469 1 34.27 ? O3' DU 221 A 1 HETATM 11 C C2' DU . . . E 4 10.019 29.266 18.167 1 30.76 ? C2' DU 221 A 1 HETATM 12 C C1' DU . . . E 4 10.53 29.253 16.694 1 28.88 ? C1' DU 221 A 1 HETATM 13 N N1 DU . . . E 4 11.984 29.668 16.878 1 25.52 ? N1 DU 221 A 1 HETATM 14 C C2 DU . . . E 4 12.955 28.774 17.551 1 23.98 ? C2 DU 221 A 1 HETATM 15 O O2 DU . . . E 4 12.689 27.681 18.006 1 20.72 ? O2 DU 221 A 1 HETATM 16 N N3 DU . . . E 4 14.274 29.302 17.631 1 23.09 ? N3 DU 221 A 1 HETATM 17 C C4 DU . . . E 4 14.741 30.571 17.142 1 24.82 ? C4 DU 221 A 1 HETATM 18 O O4 DU . . . E 4 15.927 30.883 17.289 1 25 ? O4 DU 221 A 1 HETATM 19 C C5 DU . . . E 4 13.747 31.404 16.496 1 24.68 ? C5 DU 221 A 1 HETATM 20 C C6 DU . . . E 4 12.469 30.953 16.388 1 25.48 ? C6 DU 221 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 20 #