data_3I0I # _model_server_result.job_id IqpC1ANbrvu3j00R5jRKsQ _model_server_result.datetime_utc '2025-01-10 19:52:00' _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 3i0i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1}' # _entry.id 3I0I # _exptl.entry_id 3I0I _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 3I0I _cell.length_a 52.065 _cell.length_b 150.173 _cell.length_c 79.77 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3I0I _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_555 -x,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 39.885 # _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 3I0I _atom_sites.fract_transf_matrix[1][1] 0.019207 _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] 0.006659 _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] 0.012536 _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 X 1 1 1 UDP UDP . C 3 HOH X 1 2 2 HOH HOH . C 3 HOH X 2 3 3 HOH HOH . C 3 HOH X 3 4 4 HOH HOH . C 3 HOH X 4 5 5 HOH HOH . C 3 HOH X 5 6 6 HOH HOH . C 3 HOH X 6 7 7 HOH HOH . C 3 HOH X 7 8 8 HOH HOH . C 3 HOH X 8 9 9 HOH HOH . C 3 HOH X 9 10 10 HOH HOH . C 3 HOH X 10 11 11 HOH HOH . C 3 HOH X 11 12 12 HOH HOH . C 3 HOH X 12 13 13 HOH HOH . C 3 HOH X 13 14 14 HOH HOH . C 3 HOH X 14 15 15 HOH HOH . C 3 HOH X 15 16 16 HOH HOH . C 3 HOH X 16 17 17 HOH HOH . C 3 HOH X 17 18 18 HOH HOH . C 3 HOH X 18 19 19 HOH HOH . C 3 HOH X 19 20 20 HOH HOH . C 3 HOH X 20 21 21 HOH HOH . C 3 HOH X 21 22 22 HOH HOH . C 3 HOH X 22 23 23 HOH HOH . C 3 HOH X 23 24 24 HOH HOH . C 3 HOH X 24 25 25 HOH HOH . C 3 HOH X 25 26 26 HOH HOH . C 3 HOH X 26 27 27 HOH HOH . C 3 HOH X 27 28 28 HOH HOH . C 3 HOH X 28 29 29 HOH HOH . C 3 HOH X 29 30 30 HOH HOH . C 3 HOH X 30 31 31 HOH HOH . C 3 HOH X 31 32 32 HOH HOH . C 3 HOH X 32 33 33 HOH HOH . C 3 HOH X 33 34 34 HOH HOH . C 3 HOH X 34 35 35 HOH HOH . C 3 HOH X 35 36 36 HOH HOH . C 3 HOH X 36 37 37 HOH HOH . C 3 HOH X 37 38 38 HOH HOH . C 3 HOH X 38 39 39 HOH HOH . C 3 HOH X 39 40 40 HOH HOH . C 3 HOH X 40 41 41 HOH HOH . C 3 HOH X 41 42 42 HOH HOH . C 3 HOH X 42 43 43 HOH HOH . C 3 HOH X 43 44 44 HOH HOH . C 3 HOH X 44 45 45 HOH HOH . C 3 HOH X 45 46 46 HOH HOH . C 3 HOH X 46 47 47 HOH HOH . C 3 HOH X 47 48 48 HOH HOH . C 3 HOH X 48 49 49 HOH HOH . C 3 HOH X 49 50 50 HOH HOH . C 3 HOH X 50 51 51 HOH HOH . C 3 HOH X 51 52 52 HOH HOH . C 3 HOH X 52 53 53 HOH HOH . C 3 HOH X 53 54 54 HOH HOH . C 3 HOH X 54 55 55 HOH HOH . C 3 HOH X 55 56 56 HOH HOH . C 3 HOH X 56 57 57 HOH HOH . C 3 HOH X 57 58 58 HOH HOH . C 3 HOH X 58 59 59 HOH HOH . C 3 HOH X 59 60 60 HOH HOH . C 3 HOH X 60 61 61 HOH HOH . C 3 HOH X 61 62 62 HOH HOH . C 3 HOH X 62 63 63 HOH HOH . C 3 HOH X 63 64 64 HOH HOH . C 3 HOH X 64 65 65 HOH HOH . C 3 HOH X 65 66 66 HOH HOH . C 3 HOH X 66 67 67 HOH HOH . C 3 HOH X 67 68 68 HOH HOH . C 3 HOH X 68 356 227 HOH HOH . C 3 HOH X 69 357 1 HOH HOH . C 3 HOH X 70 358 69 HOH HOH . C 3 HOH X 71 359 70 HOH HOH . C 3 HOH X 72 360 71 HOH HOH . C 3 HOH X 73 361 72 HOH HOH . C 3 HOH X 74 362 73 HOH HOH . C 3 HOH X 75 363 74 HOH HOH . C 3 HOH X 76 364 75 HOH HOH . C 3 HOH X 77 365 76 HOH HOH . C 3 HOH X 78 366 77 HOH HOH . C 3 HOH X 79 367 78 HOH HOH . C 3 HOH X 80 368 79 HOH HOH . C 3 HOH X 81 369 80 HOH HOH . C 3 HOH X 82 370 81 HOH HOH . C 3 HOH X 83 371 82 HOH HOH . C 3 HOH X 84 372 83 HOH HOH . C 3 HOH X 85 373 84 HOH HOH . C 3 HOH X 86 374 85 HOH HOH . C 3 HOH X 87 375 86 HOH HOH . C 3 HOH X 88 376 87 HOH HOH . C 3 HOH X 89 377 88 HOH HOH . C 3 HOH X 90 378 89 HOH HOH . C 3 HOH X 91 379 90 HOH HOH . C 3 HOH X 92 380 91 HOH HOH . C 3 HOH X 93 381 92 HOH HOH . C 3 HOH X 94 382 93 HOH HOH . C 3 HOH X 95 383 94 HOH HOH . C 3 HOH X 96 384 95 HOH HOH . C 3 HOH X 97 385 96 HOH HOH . C 3 HOH X 98 386 97 HOH HOH . C 3 HOH X 99 387 98 HOH HOH . C 3 HOH X 100 388 99 HOH HOH . C 3 HOH X 101 389 100 HOH HOH . C 3 HOH X 102 390 101 HOH HOH . C 3 HOH X 103 391 102 HOH HOH . C 3 HOH X 104 392 103 HOH HOH . C 3 HOH X 105 393 104 HOH HOH . C 3 HOH X 106 394 105 HOH HOH . C 3 HOH X 107 395 106 HOH HOH . C 3 HOH X 108 396 107 HOH HOH . C 3 HOH X 109 397 108 HOH HOH . C 3 HOH X 110 398 109 HOH HOH . C 3 HOH X 111 399 110 HOH HOH . C 3 HOH X 112 400 111 HOH HOH . C 3 HOH X 113 401 112 HOH HOH . C 3 HOH X 114 402 113 HOH HOH . C 3 HOH X 115 403 114 HOH HOH . C 3 HOH X 116 404 115 HOH HOH . C 3 HOH X 117 405 116 HOH HOH . C 3 HOH X 118 406 117 HOH HOH . C 3 HOH X 119 407 118 HOH HOH . C 3 HOH X 120 408 119 HOH HOH . C 3 HOH X 121 409 120 HOH HOH . C 3 HOH X 122 410 121 HOH HOH . C 3 HOH X 123 411 122 HOH HOH . C 3 HOH X 124 412 123 HOH HOH . C 3 HOH X 125 413 124 HOH HOH . C 3 HOH X 126 414 125 HOH HOH . C 3 HOH X 127 415 126 HOH HOH . C 3 HOH X 128 416 127 HOH HOH . C 3 HOH X 129 417 128 HOH HOH . C 3 HOH X 130 418 129 HOH HOH . C 3 HOH X 131 419 130 HOH HOH . C 3 HOH X 132 420 131 HOH HOH . C 3 HOH X 133 421 132 HOH HOH . C 3 HOH X 134 422 133 HOH HOH . C 3 HOH X 135 423 134 HOH HOH . C 3 HOH X 136 424 135 HOH HOH . C 3 HOH X 137 425 136 HOH HOH . C 3 HOH X 138 426 137 HOH HOH . C 3 HOH X 139 427 138 HOH HOH . C 3 HOH X 140 428 139 HOH HOH . C 3 HOH X 141 429 140 HOH HOH . C 3 HOH X 142 430 141 HOH HOH . C 3 HOH X 143 431 142 HOH HOH . C 3 HOH X 144 432 143 HOH HOH . C 3 HOH X 145 433 144 HOH HOH . C 3 HOH X 146 434 145 HOH HOH . C 3 HOH X 147 435 146 HOH HOH . C 3 HOH X 148 436 147 HOH HOH . C 3 HOH X 149 437 148 HOH HOH . C 3 HOH X 150 438 149 HOH HOH . C 3 HOH X 151 439 150 HOH HOH . C 3 HOH X 152 440 151 HOH HOH . C 3 HOH X 153 441 152 HOH HOH . C 3 HOH X 154 442 153 HOH HOH . C 3 HOH X 155 443 154 HOH HOH . C 3 HOH X 156 444 155 HOH HOH . C 3 HOH X 157 445 156 HOH HOH . C 3 HOH X 158 446 157 HOH HOH . C 3 HOH X 159 447 158 HOH HOH . C 3 HOH X 160 448 159 HOH HOH . C 3 HOH X 161 449 160 HOH HOH . C 3 HOH X 162 450 161 HOH HOH . C 3 HOH X 163 451 162 HOH HOH . C 3 HOH X 164 452 163 HOH HOH . C 3 HOH X 165 453 164 HOH HOH . C 3 HOH X 166 454 165 HOH HOH . C 3 HOH X 167 455 166 HOH HOH . C 3 HOH X 168 456 167 HOH HOH . C 3 HOH X 169 457 168 HOH HOH . C 3 HOH X 170 458 169 HOH HOH . C 3 HOH X 171 459 170 HOH HOH . C 3 HOH X 172 460 171 HOH HOH . C 3 HOH X 173 461 172 HOH HOH . C 3 HOH X 174 462 173 HOH HOH . C 3 HOH X 175 463 174 HOH HOH . C 3 HOH X 176 464 175 HOH HOH . C 3 HOH X 177 465 176 HOH HOH . C 3 HOH X 178 466 177 HOH HOH . C 3 HOH X 179 467 178 HOH HOH . C 3 HOH X 180 468 179 HOH HOH . C 3 HOH X 181 469 180 HOH HOH . C 3 HOH X 182 470 181 HOH HOH . C 3 HOH X 183 471 182 HOH HOH . C 3 HOH X 184 472 183 HOH HOH . C 3 HOH X 185 473 184 HOH HOH . C 3 HOH X 186 474 185 HOH HOH . C 3 HOH X 187 475 186 HOH HOH . C 3 HOH X 188 476 187 HOH HOH . C 3 HOH X 189 477 188 HOH HOH . C 3 HOH X 190 478 189 HOH HOH . C 3 HOH X 191 479 190 HOH HOH . C 3 HOH X 192 480 191 HOH HOH . C 3 HOH X 193 481 192 HOH HOH . C 3 HOH X 194 482 193 HOH HOH . C 3 HOH X 195 483 194 HOH HOH . C 3 HOH X 196 484 195 HOH HOH . C 3 HOH X 197 485 196 HOH HOH . C 3 HOH X 198 486 197 HOH HOH . C 3 HOH X 199 487 198 HOH HOH . C 3 HOH X 200 488 199 HOH HOH . C 3 HOH X 201 489 200 HOH HOH . C 3 HOH X 202 490 201 HOH HOH . C 3 HOH X 203 491 202 HOH HOH . C 3 HOH X 204 492 203 HOH HOH . C 3 HOH X 205 493 204 HOH HOH . C 3 HOH X 206 494 205 HOH HOH . C 3 HOH X 207 495 206 HOH HOH . C 3 HOH X 208 496 207 HOH HOH . C 3 HOH X 209 497 208 HOH HOH . C 3 HOH X 210 498 209 HOH HOH . C 3 HOH X 211 499 210 HOH HOH . C 3 HOH X 212 500 211 HOH HOH . C 3 HOH X 213 501 212 HOH HOH . C 3 HOH X 214 502 213 HOH HOH . C 3 HOH X 215 503 214 HOH HOH . C 3 HOH X 216 504 215 HOH HOH . C 3 HOH X 217 505 216 HOH HOH . C 3 HOH X 218 506 217 HOH HOH . C 3 HOH X 219 507 218 HOH HOH . C 3 HOH X 220 508 219 HOH HOH . C 3 HOH X 221 509 220 HOH HOH . C 3 HOH X 222 510 221 HOH HOH . C 3 HOH X 223 511 222 HOH HOH . C 3 HOH X 224 512 223 HOH HOH . C 3 HOH X 225 513 224 HOH HOH . C 3 HOH X 226 514 225 HOH HOH . C 3 HOH X 227 515 226 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 16.24 -23.123 -7.622 1 38.99 ? N1 UDP 1 X 1 HETATM 2 C C2 UDP . . . B 2 17.404 -23.865 -7.899 1 38.76 ? C2 UDP 1 X 1 HETATM 3 N N3 UDP . . . B 2 17.85 -23.953 -9.238 0.75 38.6 ? N3 UDP 1 X 1 HETATM 4 C C4 UDP . . . B 2 17.131 -23.323 -10.279 1 39.91 ? C4 UDP 1 X 1 HETATM 5 C C5 UDP . . . B 2 15.975 -22.601 -9.988 0.5 38.27 ? C5 UDP 1 X 1 HETATM 6 C C6 UDP . . . B 2 15.527 -22.504 -8.671 0.5 39.03 ? C6 UDP 1 X 1 HETATM 7 O O2 UDP . . . B 2 18.031 -24.406 -6.982 1 34.1 ? O2 UDP 1 X 1 HETATM 8 O O4 UDP . . . B 2 17.539 -23.409 -11.44 1 39.08 ? O4 UDP 1 X 1 HETATM 9 C C1' UDP . . . B 2 15.783 -23.06 -6.198 1 40.32 ? C1' UDP 1 X 1 HETATM 10 C C2' UDP . . . B 2 16.667 -22.096 -5.442 1 39.05 ? C2' UDP 1 X 1 HETATM 11 O O2' UDP . . . B 2 16.712 -22.461 -4.074 1 38.01 ? O2' UDP 1 X 1 HETATM 12 C C3' UDP . . . B 2 15.885 -20.815 -5.555 1 39.93 ? C3' UDP 1 X 1 HETATM 13 C C4' UDP . . . B 2 14.414 -21.234 -5.451 1 40.76 ? C4' UDP 1 X 1 HETATM 14 O O4' UDP . . . B 2 14.384 -22.613 -5.967 1 42.81 ? O4' UDP 1 X 1 HETATM 15 O O3' UDP . . . B 2 16.205 -20.042 -4.411 1 43.52 ? O3' UDP 1 X 1 HETATM 16 C C5' UDP . . . B 2 13.463 -20.259 -6.221 1 39.72 ? C5' UDP 1 X 1 HETATM 17 O O5' UDP . . . B 2 14.159 -19.615 -7.311 0.5 40.05 ? O5' UDP 1 X 1 HETATM 18 P PA UDP . . . B 2 13.995 -18.068 -7.734 0.5 41.39 ? PA UDP 1 X 1 HETATM 19 O O1A UDP . . . B 2 15.44 -17.354 -7.673 0.5 39.89 ? O1A UDP 1 X 1 HETATM 20 O O2A UDP . . . B 2 13.437 -17.946 -9.111 0.5 42.21 ? O2A UDP 1 X 1 HETATM 21 O O3A UDP . . . B 2 13.074 -17.352 -6.623 0.5 40.96 ? O3A UDP 1 X 1 HETATM 22 P PB UDP . . . B 2 12.942 -15.75 -6.507 0.5 40.68 ? PB UDP 1 X 1 HETATM 23 O O1B UDP . . . B 2 13.792 -15.079 -7.707 1 42.59 ? O1B UDP 1 X 1 HETATM 24 O O2B UDP . . . B 2 13.737 -15.308 -5.171 0.5 40.19 ? O2B UDP 1 X 1 HETATM 25 O O3B UDP . . . B 2 11.517 -15.311 -6.514 0.5 40.7 ? O3B UDP 1 X 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 354 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 25 #