data_3I0D # _model_server_result.job_id ILjHMfUmZfeM6GyuJyYTFA _model_server_result.datetime_utc '2024-12-23 06:33:12' _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 3i0d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1}' # _entry.id 3I0D # _exptl.entry_id 3I0D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _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 3I0D _cell.length_a 52.296 _cell.length_b 149.262 _cell.length_c 79.559 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3I0D _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _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 _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' 3_554 -x,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -39.7795 # _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 # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna 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 N1 C2 UDP sing 358 n n N1 C6 UDP sing 359 n n N1 C1' UDP sing 360 n n C2 N3 UDP sing 361 n n C2 O2 UDP doub 362 n n N3 C4 UDP sing 363 n n N3 HN3 UDP sing 364 n n C4 C5 UDP sing 365 n n C4 O4 UDP doub 366 n n C5 C6 UDP doub 367 n n C5 H5 UDP sing 368 n n C6 H6 UDP sing 369 n n C1' C2' UDP sing 370 n n C1' O4' UDP sing 371 n n C1' H1' UDP sing 372 n n C2' O2' UDP sing 373 n n C2' C3' UDP sing 374 n n C2' H2' UDP sing 375 n n O2' HO2' UDP sing 376 n n C3' C4' UDP sing 377 n n C3' O3' UDP sing 378 n n C3' H3' UDP sing 379 n n C4' O4' UDP sing 380 n n C4' C5' UDP sing 381 n n C4' H4' UDP sing 382 n n O3' HO3' UDP sing 383 n n C5' O5' UDP sing 384 n n C5' "H5'1" UDP sing 385 n n C5' "H5'2" UDP sing 386 n n O5' PA UDP sing 387 n n PA O1A UDP doub 388 n n PA O2A UDP sing 389 n n PA O3A UDP sing 390 n n O2A HOA2 UDP sing 391 n n O3A PB UDP sing 392 n n PB O1B UDP doub 393 n n PB O2B UDP sing 394 n n PB O3B UDP sing 395 n n O2B HOB2 UDP sing 396 n n O3B HOB3 UDP sing 397 n n # _atom_sites.entry_id 3I0D _atom_sites.fract_transf_matrix[1][1] 0.019122 _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] 0.0067 _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] 0.012569 _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 UDP A 1 1 1 UDP UDP . C 3 HOH A 1 2 2 HOH HOH . C 3 HOH A 2 3 3 HOH HOH . C 3 HOH A 3 4 4 HOH HOH . C 3 HOH A 4 5 5 HOH HOH . C 3 HOH A 5 6 6 HOH HOH . C 3 HOH A 6 7 7 HOH HOH . C 3 HOH A 7 8 8 HOH HOH . C 3 HOH A 8 9 9 HOH HOH . C 3 HOH A 9 10 10 HOH HOH . C 3 HOH A 10 11 11 HOH HOH . C 3 HOH A 11 12 12 HOH HOH . C 3 HOH A 12 13 13 HOH HOH . C 3 HOH A 13 14 14 HOH HOH . C 3 HOH A 14 15 15 HOH HOH . C 3 HOH A 15 16 16 HOH HOH . C 3 HOH A 16 17 17 HOH HOH . C 3 HOH A 17 18 18 HOH HOH . C 3 HOH A 18 19 19 HOH HOH . C 3 HOH A 19 20 20 HOH HOH . C 3 HOH A 20 21 21 HOH HOH . C 3 HOH A 21 22 22 HOH HOH . C 3 HOH A 22 23 23 HOH HOH . C 3 HOH A 23 24 24 HOH HOH . C 3 HOH A 24 25 25 HOH HOH . C 3 HOH A 25 26 26 HOH HOH . C 3 HOH A 26 27 27 HOH HOH . C 3 HOH A 27 28 28 HOH HOH . C 3 HOH A 28 29 29 HOH HOH . C 3 HOH A 29 30 30 HOH HOH . C 3 HOH A 30 31 31 HOH HOH . C 3 HOH A 31 32 32 HOH HOH . C 3 HOH A 32 33 33 HOH HOH . C 3 HOH A 33 34 34 HOH HOH . C 3 HOH A 34 35 35 HOH HOH . C 3 HOH A 35 36 36 HOH HOH . C 3 HOH A 36 37 37 HOH HOH . C 3 HOH A 37 38 38 HOH HOH . C 3 HOH A 38 39 39 HOH HOH . C 3 HOH A 39 40 40 HOH HOH . C 3 HOH A 40 41 41 HOH HOH . C 3 HOH A 41 42 42 HOH HOH . C 3 HOH A 42 43 43 HOH HOH . C 3 HOH A 43 44 44 HOH HOH . C 3 HOH A 44 45 45 HOH HOH . C 3 HOH A 45 46 46 HOH HOH . C 3 HOH A 46 47 47 HOH HOH . C 3 HOH A 47 48 48 HOH HOH . C 3 HOH A 48 49 49 HOH HOH . C 3 HOH A 49 50 50 HOH HOH . C 3 HOH A 50 51 51 HOH HOH . C 3 HOH A 51 52 52 HOH HOH . C 3 HOH A 52 53 53 HOH HOH . C 3 HOH A 53 54 54 HOH HOH . C 3 HOH A 54 55 55 HOH HOH . C 3 HOH A 55 56 56 HOH HOH . C 3 HOH A 56 57 57 HOH HOH . C 3 HOH A 57 58 58 HOH HOH . C 3 HOH A 58 59 59 HOH HOH . C 3 HOH A 59 60 60 HOH HOH . C 3 HOH A 60 61 61 HOH HOH . C 3 HOH A 61 62 62 HOH HOH . C 3 HOH A 62 63 63 HOH HOH . C 3 HOH A 63 64 64 HOH HOH . C 3 HOH A 64 65 65 HOH HOH . C 3 HOH A 65 66 66 HOH HOH . C 3 HOH A 66 67 67 HOH HOH . C 3 HOH A 67 68 68 HOH HOH . C 3 HOH A 68 356 210 HOH HOH . C 3 HOH A 69 357 1 HOH HOH . C 3 HOH A 70 358 69 HOH HOH . C 3 HOH A 71 359 70 HOH HOH . C 3 HOH A 72 360 71 HOH HOH . C 3 HOH A 73 361 72 HOH HOH . C 3 HOH A 74 362 73 HOH HOH . C 3 HOH A 75 363 74 HOH HOH . C 3 HOH A 76 364 75 HOH HOH . C 3 HOH A 77 365 76 HOH HOH . C 3 HOH A 78 366 77 HOH HOH . C 3 HOH A 79 367 78 HOH HOH . C 3 HOH A 80 368 79 HOH HOH . C 3 HOH A 81 369 80 HOH HOH . C 3 HOH A 82 370 81 HOH HOH . C 3 HOH A 83 371 82 HOH HOH . C 3 HOH A 84 372 83 HOH HOH . C 3 HOH A 85 373 84 HOH HOH . C 3 HOH A 86 374 85 HOH HOH . C 3 HOH A 87 375 86 HOH HOH . C 3 HOH A 88 376 87 HOH HOH . C 3 HOH A 89 377 88 HOH HOH . C 3 HOH A 90 378 89 HOH HOH . C 3 HOH A 91 379 90 HOH HOH . C 3 HOH A 92 380 91 HOH HOH . C 3 HOH A 93 381 92 HOH HOH . C 3 HOH A 94 382 93 HOH HOH . C 3 HOH A 95 383 94 HOH HOH . C 3 HOH A 96 384 95 HOH HOH . C 3 HOH A 97 385 96 HOH HOH . C 3 HOH A 98 386 97 HOH HOH . C 3 HOH A 99 387 98 HOH HOH . C 3 HOH A 100 388 99 HOH HOH . C 3 HOH A 101 389 100 HOH HOH . C 3 HOH A 102 390 101 HOH HOH . C 3 HOH A 103 391 102 HOH HOH . C 3 HOH A 104 392 103 HOH HOH . C 3 HOH A 105 393 104 HOH HOH . C 3 HOH A 106 394 105 HOH HOH . C 3 HOH A 107 395 106 HOH HOH . C 3 HOH A 108 396 107 HOH HOH . C 3 HOH A 109 397 108 HOH HOH . C 3 HOH A 110 398 109 HOH HOH . C 3 HOH A 111 399 110 HOH HOH . C 3 HOH A 112 400 111 HOH HOH . C 3 HOH A 113 401 112 HOH HOH . C 3 HOH A 114 402 113 HOH HOH . C 3 HOH A 115 403 114 HOH HOH . C 3 HOH A 116 404 115 HOH HOH . C 3 HOH A 117 405 116 HOH HOH . C 3 HOH A 118 406 117 HOH HOH . C 3 HOH A 119 407 118 HOH HOH . C 3 HOH A 120 408 119 HOH HOH . C 3 HOH A 121 409 120 HOH HOH . C 3 HOH A 122 410 121 HOH HOH . C 3 HOH A 123 411 122 HOH HOH . C 3 HOH A 124 412 123 HOH HOH . C 3 HOH A 125 413 124 HOH HOH . C 3 HOH A 126 414 125 HOH HOH . C 3 HOH A 127 415 126 HOH HOH . C 3 HOH A 128 416 127 HOH HOH . C 3 HOH A 129 417 128 HOH HOH . C 3 HOH A 130 418 129 HOH HOH . C 3 HOH A 131 419 130 HOH HOH . C 3 HOH A 132 420 131 HOH HOH . C 3 HOH A 133 421 132 HOH HOH . C 3 HOH A 134 422 133 HOH HOH . C 3 HOH A 135 423 134 HOH HOH . C 3 HOH A 136 424 135 HOH HOH . C 3 HOH A 137 425 136 HOH HOH . C 3 HOH A 138 426 137 HOH HOH . C 3 HOH A 139 427 138 HOH HOH . C 3 HOH A 140 428 139 HOH HOH . C 3 HOH A 141 429 140 HOH HOH . C 3 HOH A 142 430 141 HOH HOH . C 3 HOH A 143 431 142 HOH HOH . C 3 HOH A 144 432 143 HOH HOH . C 3 HOH A 145 433 144 HOH HOH . C 3 HOH A 146 434 145 HOH HOH . C 3 HOH A 147 435 146 HOH HOH . C 3 HOH A 148 436 147 HOH HOH . C 3 HOH A 149 437 148 HOH HOH . C 3 HOH A 150 438 149 HOH HOH . C 3 HOH A 151 439 150 HOH HOH . C 3 HOH A 152 440 151 HOH HOH . C 3 HOH A 153 441 152 HOH HOH . C 3 HOH A 154 442 153 HOH HOH . C 3 HOH A 155 443 154 HOH HOH . C 3 HOH A 156 444 155 HOH HOH . C 3 HOH A 157 445 156 HOH HOH . C 3 HOH A 158 446 157 HOH HOH . C 3 HOH A 159 447 158 HOH HOH . C 3 HOH A 160 448 159 HOH HOH . C 3 HOH A 161 449 160 HOH HOH . C 3 HOH A 162 450 161 HOH HOH . C 3 HOH A 163 451 162 HOH HOH . C 3 HOH A 164 452 163 HOH HOH . C 3 HOH A 165 453 164 HOH HOH . C 3 HOH A 166 454 165 HOH HOH . C 3 HOH A 167 455 166 HOH HOH . C 3 HOH A 168 456 167 HOH HOH . C 3 HOH A 169 457 168 HOH HOH . C 3 HOH A 170 458 169 HOH HOH . C 3 HOH A 171 459 170 HOH HOH . C 3 HOH A 172 460 171 HOH HOH . C 3 HOH A 173 461 172 HOH HOH . C 3 HOH A 174 462 173 HOH HOH . C 3 HOH A 175 463 174 HOH HOH . C 3 HOH A 176 464 175 HOH HOH . C 3 HOH A 177 465 176 HOH HOH . C 3 HOH A 178 466 177 HOH HOH . C 3 HOH A 179 467 178 HOH HOH . C 3 HOH A 180 468 179 HOH HOH . C 3 HOH A 181 469 180 HOH HOH . C 3 HOH A 182 470 181 HOH HOH . C 3 HOH A 183 471 182 HOH HOH . C 3 HOH A 184 472 183 HOH HOH . C 3 HOH A 185 473 184 HOH HOH . C 3 HOH A 186 474 185 HOH HOH . C 3 HOH A 187 475 186 HOH HOH . C 3 HOH A 188 476 187 HOH HOH . C 3 HOH A 189 477 188 HOH HOH . C 3 HOH A 190 478 189 HOH HOH . C 3 HOH A 191 479 190 HOH HOH . C 3 HOH A 192 480 191 HOH HOH . C 3 HOH A 193 481 192 HOH HOH . C 3 HOH A 194 482 193 HOH HOH . C 3 HOH A 195 483 194 HOH HOH . C 3 HOH A 196 484 195 HOH HOH . C 3 HOH A 197 485 196 HOH HOH . C 3 HOH A 198 486 197 HOH HOH . C 3 HOH A 199 487 198 HOH HOH . C 3 HOH A 200 488 199 HOH HOH . C 3 HOH A 201 489 200 HOH HOH . C 3 HOH A 202 490 201 HOH HOH . C 3 HOH A 203 491 202 HOH HOH . C 3 HOH A 204 492 203 HOH HOH . C 3 HOH A 205 493 204 HOH HOH . C 3 HOH A 206 494 205 HOH HOH . C 3 HOH A 207 495 206 HOH HOH . C 3 HOH A 208 496 207 HOH HOH . C 3 HOH A 209 497 208 HOH HOH . C 3 HOH A 210 498 209 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 UDP . . . B 2 -16.207 -23.018 7.676 1 37.69 ? N1 UDP 1 A 1 HETATM 2 C C2 UDP . . . B 2 -17.403 -23.728 7.963 1 38.76 ? C2 UDP 1 A 1 HETATM 3 N N3 UDP . . . B 2 -17.898 -23.688 9.292 1 39.76 ? N3 UDP 1 A 1 HETATM 4 C C4 UDP . . . B 2 -17.176 -22.985 10.308 1 43.23 ? C4 UDP 1 A 1 HETATM 5 C C5 UDP . . . B 2 -15.997 -22.291 9.993 1 41.66 ? C5 UDP 1 A 1 HETATM 6 C C6 UDP . . . B 2 -15.523 -22.301 8.683 1 41.56 ? C6 UDP 1 A 1 HETATM 7 O O2 UDP . . . B 2 -18.016 -24.324 7.054 1 25.02 ? O2 UDP 1 A 1 HETATM 8 O O4 UDP . . . B 2 -17.601 -22.983 11.469 1 41.47 ? O4 UDP 1 A 1 HETATM 9 C C1' UDP . . . B 2 -15.722 -23.053 6.273 1 36.73 ? C1' UDP 1 A 1 HETATM 10 C C2' UDP . . . B 2 -16.579 -22.153 5.391 1 30.09 ? C2' UDP 1 A 1 HETATM 11 O O2' UDP . . . B 2 -16.502 -22.602 4.056 1 29.37 ? O2' UDP 1 A 1 HETATM 12 C C3' UDP . . . B 2 -15.772 -20.913 5.422 1 30.95 ? C3' UDP 1 A 1 HETATM 13 C C4' UDP . . . B 2 -14.307 -21.367 5.473 1 36.5 ? C4' UDP 1 A 1 HETATM 14 O O4' UDP . . . B 2 -14.322 -22.597 6.214 1 34.38 ? O4' UDP 1 A 1 HETATM 15 O O3' UDP . . . B 2 -15.99 -20.169 4.184 1 33.23 ? O3' UDP 1 A 1 HETATM 16 C C5' UDP . . . B 2 -13.286 -20.36 6.174 1 34.43 ? C5' UDP 1 A 1 HETATM 17 O O5' UDP . . . B 2 -13.904 -19.515 7.232 1 42.13 ? O5' UDP 1 A 1 HETATM 18 P PA UDP . . . B 2 -14.372 -17.871 7.037 1 51.42 ? PA UDP 1 A 1 HETATM 19 O O1A UDP . . . B 2 -15.016 -18.09 8.529 1 49.71 ? O1A UDP 1 A 1 HETATM 20 O O2A UDP . . . B 2 -15.2 -18.18 5.777 1 45.9 ? O2A UDP 1 A 1 HETATM 21 O O3A UDP . . . B 2 -12.708 -17.825 6.971 1 54.27 ? O3A UDP 1 A 1 HETATM 22 P PB UDP . . . B 2 -11.913 -16.588 6.128 1 60.58 ? PB UDP 1 A 1 HETATM 23 O O1B UDP . . . B 2 -10.742 -17.353 7.11 1 62.67 ? O1B UDP 1 A 1 HETATM 24 O O2B UDP . . . B 2 -12.959 -15.561 6.596 1 55.21 ? O2B UDP 1 A 1 HETATM 25 O O3B UDP . . . B 2 -12.298 -17.553 4.852 1 63 ? O3B UDP 1 A 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 25 #