data_5IOT # _model_server_result.job_id heufY7PtNb1WHcNq27nMow _model_server_result.datetime_utc '2024-11-13 14:23:04' _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 5iot # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":302}' # _entry.id 5IOT # _exptl.entry_id 5IOT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 4 _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 5IOT _cell.length_a 54.06 _cell.length_b 115.86 _cell.length_c 141.1 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5IOT _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 PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,H,I,J,K,L,M,N,O,P _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 H N N ? 3 J N N ? 3 L N N # _chem_comp.formula 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UMP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DUMP # 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 UMP sing 449 n n N1 C6 UMP sing 450 n n N1 C1' UMP sing 451 n n C2 N3 UMP sing 452 n n C2 O2 UMP doub 453 n n N3 C4 UMP sing 454 n n N3 HN3 UMP sing 455 n n C4 C5 UMP sing 456 n n C4 O4 UMP doub 457 n n C5 C6 UMP doub 458 n n C5 H5 UMP sing 459 n n C6 H6 UMP sing 460 n n C1' C2' UMP sing 461 n n C1' O4' UMP sing 462 n n C1' H1' UMP sing 463 n n C2' C3' UMP sing 464 n n C2' H2' UMP sing 465 n n C2' "H2''" UMP sing 466 n n C3' C4' UMP sing 467 n n C3' O3' UMP sing 468 n n C3' H3' UMP sing 469 n n C4' O4' UMP sing 470 n n C4' C5' UMP sing 471 n n C4' H4' UMP sing 472 n n O3' HO3' UMP sing 473 n n C5' O5' UMP sing 474 n n C5' H5' UMP sing 475 n n C5' "H5''" UMP sing 476 n n O5' P UMP sing 477 n n P OP1 UMP doub 478 n n P OP2 UMP sing 479 n n P OP3 UMP sing 480 n n OP2 HOP2 UMP sing 481 n n OP3 HOP3 UMP sing 482 n n # _atom_sites.entry_id 5IOT _atom_sites.fract_transf_matrix[1][1] 0.018498 _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] 0.008631 _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] 0.007087 _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 E 2 FAD A 1 301 318 FAD FAD . F 3 UMP A 1 302 3 UMP UMP . G 2 FAD B 1 301 317 FAD FAD . H 3 UMP B 1 302 4 UMP UMP . I 2 FAD C 1 301 316 FAD FAD . J 3 UMP C 1 302 1 UMP UMP . K 2 FAD D 1 301 315 FAD FAD . L 3 UMP D 1 302 2 UMP UMP . M 4 HOH A 1 401 162 HOH HOH . M 4 HOH A 2 402 92 HOH HOH . M 4 HOH A 3 403 126 HOH HOH . M 4 HOH A 4 404 37 HOH HOH . M 4 HOH A 5 405 3 HOH HOH . M 4 HOH A 6 406 77 HOH HOH . M 4 HOH A 7 407 22 HOH HOH . M 4 HOH A 8 408 85 HOH HOH . M 4 HOH A 9 409 106 HOH HOH . M 4 HOH A 10 410 153 HOH HOH . M 4 HOH A 11 411 201 HOH HOH . M 4 HOH A 12 412 243 HOH HOH . M 4 HOH A 13 413 205 HOH HOH . M 4 HOH A 14 414 117 HOH HOH . M 4 HOH A 15 415 276 HOH HOH . M 4 HOH A 16 416 95 HOH HOH . M 4 HOH A 17 417 8 HOH HOH . M 4 HOH A 18 418 168 HOH HOH . M 4 HOH A 19 419 112 HOH HOH . M 4 HOH A 20 420 138 HOH HOH . M 4 HOH A 21 421 12 HOH HOH . M 4 HOH A 22 422 195 HOH HOH . M 4 HOH A 23 423 67 HOH HOH . M 4 HOH A 24 424 63 HOH HOH . M 4 HOH A 25 425 135 HOH HOH . M 4 HOH A 26 426 246 HOH HOH . M 4 HOH A 27 427 206 HOH HOH . M 4 HOH A 28 428 98 HOH HOH . M 4 HOH A 29 429 137 HOH HOH . M 4 HOH A 30 430 157 HOH HOH . M 4 HOH A 31 431 44 HOH HOH . M 4 HOH A 32 432 149 HOH HOH . M 4 HOH A 33 433 214 HOH HOH . M 4 HOH A 34 434 10 HOH HOH . M 4 HOH A 35 435 179 HOH HOH . M 4 HOH A 36 436 59 HOH HOH . M 4 HOH A 37 437 265 HOH HOH . M 4 HOH A 38 438 21 HOH HOH . M 4 HOH A 39 439 183 HOH HOH . M 4 HOH A 40 440 26 HOH HOH . M 4 HOH A 41 441 258 HOH HOH . M 4 HOH A 42 442 115 HOH HOH . M 4 HOH A 43 443 224 HOH HOH . M 4 HOH A 44 444 278 HOH HOH . M 4 HOH A 45 445 259 HOH HOH . M 4 HOH A 46 446 48 HOH HOH . M 4 HOH A 47 447 268 HOH HOH . M 4 HOH A 48 448 147 HOH HOH . M 4 HOH A 49 449 272 HOH HOH . M 4 HOH A 50 450 133 HOH HOH . M 4 HOH A 51 451 282 HOH HOH . M 4 HOH A 52 452 213 HOH HOH . M 4 HOH A 53 453 152 HOH HOH . N 4 HOH B 1 401 46 HOH HOH . N 4 HOH B 2 402 83 HOH HOH . N 4 HOH B 3 403 74 HOH HOH . N 4 HOH B 4 404 53 HOH HOH . N 4 HOH B 5 405 196 HOH HOH . N 4 HOH B 6 406 171 HOH HOH . N 4 HOH B 7 407 29 HOH HOH . N 4 HOH B 8 408 33 HOH HOH . N 4 HOH B 9 409 121 HOH HOH . N 4 HOH B 10 410 248 HOH HOH . N 4 HOH B 11 411 102 HOH HOH . N 4 HOH B 12 412 7 HOH HOH . N 4 HOH B 13 413 194 HOH HOH . N 4 HOH B 14 414 220 HOH HOH . N 4 HOH B 15 415 199 HOH HOH . N 4 HOH B 16 416 81 HOH HOH . N 4 HOH B 17 417 165 HOH HOH . N 4 HOH B 18 418 184 HOH HOH . N 4 HOH B 19 419 154 HOH HOH . N 4 HOH B 20 420 4 HOH HOH . N 4 HOH B 21 421 32 HOH HOH . N 4 HOH B 22 422 229 HOH HOH . N 4 HOH B 23 423 71 HOH HOH . N 4 HOH B 24 424 34 HOH HOH . N 4 HOH B 25 425 200 HOH HOH . N 4 HOH B 26 426 6 HOH HOH . N 4 HOH B 27 427 191 HOH HOH . N 4 HOH B 28 428 42 HOH HOH . N 4 HOH B 29 429 113 HOH HOH . N 4 HOH B 30 430 62 HOH HOH . N 4 HOH B 31 431 31 HOH HOH . N 4 HOH B 32 432 148 HOH HOH . N 4 HOH B 33 433 87 HOH HOH . N 4 HOH B 34 434 127 HOH HOH . N 4 HOH B 35 435 120 HOH HOH . N 4 HOH B 36 436 116 HOH HOH . N 4 HOH B 37 437 19 HOH HOH . N 4 HOH B 38 438 11 HOH HOH . N 4 HOH B 39 439 244 HOH HOH . N 4 HOH B 40 440 150 HOH HOH . N 4 HOH B 41 441 234 HOH HOH . N 4 HOH B 42 442 55 HOH HOH . N 4 HOH B 43 443 161 HOH HOH . N 4 HOH B 44 444 139 HOH HOH . N 4 HOH B 45 445 13 HOH HOH . N 4 HOH B 46 446 94 HOH HOH . N 4 HOH B 47 447 144 HOH HOH . N 4 HOH B 48 448 132 HOH HOH . N 4 HOH B 49 449 128 HOH HOH . N 4 HOH B 50 450 274 HOH HOH . N 4 HOH B 51 451 118 HOH HOH . N 4 HOH B 52 452 252 HOH HOH . N 4 HOH B 53 453 114 HOH HOH . N 4 HOH B 54 454 209 HOH HOH . N 4 HOH B 55 455 273 HOH HOH . N 4 HOH B 56 456 69 HOH HOH . N 4 HOH B 57 457 18 HOH HOH . N 4 HOH B 58 458 124 HOH HOH . N 4 HOH B 59 459 1 HOH HOH . N 4 HOH B 60 460 173 HOH HOH . N 4 HOH B 61 461 182 HOH HOH . N 4 HOH B 62 462 266 HOH HOH . N 4 HOH B 63 463 65 HOH HOH . N 4 HOH B 64 464 245 HOH HOH . N 4 HOH B 65 465 219 HOH HOH . N 4 HOH B 66 466 283 HOH HOH . N 4 HOH B 67 467 263 HOH HOH . N 4 HOH B 68 468 166 HOH HOH . N 4 HOH B 69 469 262 HOH HOH . N 4 HOH B 70 470 235 HOH HOH . N 4 HOH B 71 471 27 HOH HOH . N 4 HOH B 72 472 228 HOH HOH . N 4 HOH B 73 473 236 HOH HOH . N 4 HOH B 74 474 281 HOH HOH . O 4 HOH C 1 401 24 HOH HOH . O 4 HOH C 2 402 91 HOH HOH . O 4 HOH C 3 403 73 HOH HOH . O 4 HOH C 4 404 58 HOH HOH . O 4 HOH C 5 405 129 HOH HOH . O 4 HOH C 6 406 212 HOH HOH . O 4 HOH C 7 407 57 HOH HOH . O 4 HOH C 8 408 39 HOH HOH . O 4 HOH C 9 409 163 HOH HOH . O 4 HOH C 10 410 36 HOH HOH . O 4 HOH C 11 411 134 HOH HOH . O 4 HOH C 12 412 204 HOH HOH . O 4 HOH C 13 413 158 HOH HOH . O 4 HOH C 14 414 249 HOH HOH . O 4 HOH C 15 415 99 HOH HOH . O 4 HOH C 16 416 86 HOH HOH . O 4 HOH C 17 417 142 HOH HOH . O 4 HOH C 18 418 167 HOH HOH . O 4 HOH C 19 419 164 HOH HOH . O 4 HOH C 20 420 47 HOH HOH . O 4 HOH C 21 421 131 HOH HOH . O 4 HOH C 22 422 111 HOH HOH . O 4 HOH C 23 423 177 HOH HOH . O 4 HOH C 24 424 217 HOH HOH . O 4 HOH C 25 425 45 HOH HOH . O 4 HOH C 26 426 242 HOH HOH . O 4 HOH C 27 427 151 HOH HOH . O 4 HOH C 28 428 20 HOH HOH . O 4 HOH C 29 429 193 HOH HOH . O 4 HOH C 30 430 225 HOH HOH . O 4 HOH C 31 431 80 HOH HOH . O 4 HOH C 32 432 2 HOH HOH . O 4 HOH C 33 433 9 HOH HOH . O 4 HOH C 34 434 141 HOH HOH . O 4 HOH C 35 435 23 HOH HOH . O 4 HOH C 36 436 75 HOH HOH . O 4 HOH C 37 437 76 HOH HOH . O 4 HOH C 38 438 78 HOH HOH . O 4 HOH C 39 439 190 HOH HOH . O 4 HOH C 40 440 172 HOH HOH . O 4 HOH C 41 441 90 HOH HOH . O 4 HOH C 42 442 180 HOH HOH . O 4 HOH C 43 443 257 HOH HOH . O 4 HOH C 44 444 30 HOH HOH . O 4 HOH C 45 445 255 HOH HOH . O 4 HOH C 46 446 211 HOH HOH . O 4 HOH C 47 447 192 HOH HOH . O 4 HOH C 48 448 108 HOH HOH . O 4 HOH C 49 449 107 HOH HOH . O 4 HOH C 50 450 160 HOH HOH . O 4 HOH C 51 451 155 HOH HOH . O 4 HOH C 52 452 156 HOH HOH . O 4 HOH C 53 453 54 HOH HOH . O 4 HOH C 54 454 109 HOH HOH . O 4 HOH C 55 455 61 HOH HOH . O 4 HOH C 56 456 207 HOH HOH . O 4 HOH C 57 457 136 HOH HOH . O 4 HOH C 58 458 233 HOH HOH . O 4 HOH C 59 459 170 HOH HOH . O 4 HOH C 60 460 70 HOH HOH . O 4 HOH C 61 461 100 HOH HOH . O 4 HOH C 62 462 254 HOH HOH . O 4 HOH C 63 463 79 HOH HOH . O 4 HOH C 64 464 5 HOH HOH . O 4 HOH C 65 465 105 HOH HOH . O 4 HOH C 66 466 277 HOH HOH . O 4 HOH C 67 467 66 HOH HOH . O 4 HOH C 68 468 89 HOH HOH . O 4 HOH C 69 469 240 HOH HOH . O 4 HOH C 70 470 267 HOH HOH . O 4 HOH C 71 471 104 HOH HOH . O 4 HOH C 72 472 260 HOH HOH . O 4 HOH C 73 473 261 HOH HOH . O 4 HOH C 74 474 269 HOH HOH . O 4 HOH C 75 475 271 HOH HOH . O 4 HOH C 76 476 284 HOH HOH . P 4 HOH D 1 401 97 HOH HOH . P 4 HOH D 2 402 176 HOH HOH . P 4 HOH D 3 403 188 HOH HOH . P 4 HOH D 4 404 101 HOH HOH . P 4 HOH D 5 405 40 HOH HOH . P 4 HOH D 6 406 88 HOH HOH . P 4 HOH D 7 407 130 HOH HOH . P 4 HOH D 8 408 35 HOH HOH . P 4 HOH D 9 409 72 HOH HOH . P 4 HOH D 10 410 145 HOH HOH . P 4 HOH D 11 411 96 HOH HOH . P 4 HOH D 12 412 28 HOH HOH . P 4 HOH D 13 413 68 HOH HOH . P 4 HOH D 14 414 140 HOH HOH . P 4 HOH D 15 415 186 HOH HOH . P 4 HOH D 16 416 198 HOH HOH . P 4 HOH D 17 417 122 HOH HOH . P 4 HOH D 18 418 181 HOH HOH . P 4 HOH D 19 419 222 HOH HOH . P 4 HOH D 20 420 14 HOH HOH . P 4 HOH D 21 421 256 HOH HOH . P 4 HOH D 22 422 16 HOH HOH . P 4 HOH D 23 423 275 HOH HOH . P 4 HOH D 24 424 146 HOH HOH . P 4 HOH D 25 425 125 HOH HOH . P 4 HOH D 26 426 93 HOH HOH . P 4 HOH D 27 427 169 HOH HOH . P 4 HOH D 28 428 51 HOH HOH . P 4 HOH D 29 429 226 HOH HOH . P 4 HOH D 30 430 25 HOH HOH . P 4 HOH D 31 431 119 HOH HOH . P 4 HOH D 32 432 103 HOH HOH . P 4 HOH D 33 433 216 HOH HOH . P 4 HOH D 34 434 17 HOH HOH . P 4 HOH D 35 435 218 HOH HOH . P 4 HOH D 36 436 123 HOH HOH . P 4 HOH D 37 437 50 HOH HOH . P 4 HOH D 38 438 202 HOH HOH . P 4 HOH D 39 439 49 HOH HOH . P 4 HOH D 40 440 43 HOH HOH . P 4 HOH D 41 441 232 HOH HOH . P 4 HOH D 42 442 64 HOH HOH . P 4 HOH D 43 443 56 HOH HOH . P 4 HOH D 44 444 15 HOH HOH . P 4 HOH D 45 445 60 HOH HOH . P 4 HOH D 46 446 197 HOH HOH . P 4 HOH D 47 447 208 HOH HOH . P 4 HOH D 48 448 223 HOH HOH . P 4 HOH D 49 449 143 HOH HOH . P 4 HOH D 50 450 84 HOH HOH . P 4 HOH D 51 451 270 HOH HOH . P 4 HOH D 52 452 241 HOH HOH . P 4 HOH D 53 453 38 HOH HOH . P 4 HOH D 54 454 237 HOH HOH . P 4 HOH D 55 455 210 HOH HOH . P 4 HOH D 56 456 264 HOH HOH . P 4 HOH D 57 457 230 HOH HOH . P 4 HOH D 58 458 159 HOH HOH . P 4 HOH D 59 459 280 HOH HOH . P 4 HOH D 60 460 279 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 UMP . . . L 3 0.843 18.765 -43.313 1 26.04 ? N1 UMP 302 D 1 HETATM 2 C C2 UMP . . . L 3 1.443 19.479 -42.288 1 24.6 ? C2 UMP 302 D 1 HETATM 3 N N3 UMP . . . L 3 2.702 19.924 -42.386 1 24.8 ? N3 UMP 302 D 1 HETATM 4 C C4 UMP . . . L 3 3.424 19.701 -43.488 1 27.79 ? C4 UMP 302 D 1 HETATM 5 C C5 UMP . . . L 3 2.871 18.97 -44.531 1 28.24 ? C5 UMP 302 D 1 HETATM 6 C C6 UMP . . . L 3 1.558 18.515 -44.422 1 28.36 ? C6 UMP 302 D 1 HETATM 7 O O2 UMP . . . L 3 0.74 19.707 -41.28 1 25.87 ? O2 UMP 302 D 1 HETATM 8 O O4 UMP . . . L 3 4.59 20.122 -43.577 1 28.09 ? O4 UMP 302 D 1 HETATM 9 C C1' UMP . . . L 3 -0.555 18.311 -43.128 1 24.95 ? C1' UMP 302 D 1 HETATM 10 C C2' UMP . . . L 3 -1.529 19.467 -43.242 1 25.3 ? C2' UMP 302 D 1 HETATM 11 C C3' UMP . . . L 3 -2.664 18.938 -44.094 1 26.72 ? C3' UMP 302 D 1 HETATM 12 C C4' UMP . . . L 3 -1.965 17.888 -44.916 1 26.48 ? C4' UMP 302 D 1 HETATM 13 O O3' UMP . . . L 3 -3.757 18.308 -43.371 1 26.95 ? O3' UMP 302 D 1 HETATM 14 O O4' UMP . . . L 3 -0.931 17.373 -44.109 1 24.09 ? O4' UMP 302 D 1 HETATM 15 C C5' UMP . . . L 3 -1.379 18.419 -46.238 1 26.58 ? C5' UMP 302 D 1 HETATM 16 O O5' UMP . . . L 3 -0.814 19.733 -46.154 1 25.75 ? O5' UMP 302 D 1 HETATM 17 P P UMP . . . L 3 0.192 20.27 -47.335 1 26.92 ? P UMP 302 D 1 HETATM 18 O OP1 UMP . . . L 3 -0.693 20.261 -48.577 1 24.69 ? OP1 UMP 302 D 1 HETATM 19 O OP2 UMP . . . L 3 1.315 19.297 -47.376 1 25.99 ? OP2 UMP 302 D 1 HETATM 20 O OP3 UMP . . . L 3 0.567 21.681 -46.858 1 23.14 ? OP3 UMP 302 D 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #