data_3QEN # _model_server_result.job_id dRQ-Ix_fnF088E26PVE9QQ _model_server_result.datetime_utc '2025-03-04 07:31:54' _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 3qen # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 3QEN # _exptl.entry_id 3QEN _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 2 _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 3QEN _cell.length_a 69.14 _cell.length_b 69.14 _cell.length_c 118.9 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3QEN _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # _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,D,E,F,G,H _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 ? 2 C N N ? 2 E N 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 388 n n N1 C6 UDP sing 389 n n N1 C1' UDP sing 390 n n C2 N3 UDP sing 391 n n C2 O2 UDP doub 392 n n N3 C4 UDP sing 393 n n N3 HN3 UDP sing 394 n n C4 C5 UDP sing 395 n n C4 O4 UDP doub 396 n n C5 C6 UDP doub 397 n n C5 H5 UDP sing 398 n n C6 H6 UDP sing 399 n n C1' C2' UDP sing 400 n n C1' O4' UDP sing 401 n n C1' H1' UDP sing 402 n n C2' O2' UDP sing 403 n n C2' C3' UDP sing 404 n n C2' H2' UDP sing 405 n n O2' HO2' UDP sing 406 n n C3' C4' UDP sing 407 n n C3' O3' UDP sing 408 n n C3' H3' UDP sing 409 n n C4' O4' UDP sing 410 n n C4' C5' UDP sing 411 n n C4' H4' UDP sing 412 n n O3' HO3' UDP sing 413 n n C5' O5' UDP sing 414 n n C5' "H5'1" UDP sing 415 n n C5' "H5'2" UDP sing 416 n n O5' PA UDP sing 417 n n PA O1A UDP doub 418 n n PA O2A UDP sing 419 n n PA O3A UDP sing 420 n n O2A HOA2 UDP sing 421 n n O3A PB UDP sing 422 n n PB O1B UDP doub 423 n n PB O2B UDP sing 424 n n PB O3B UDP sing 425 n n O2B HOB2 UDP sing 426 n n O3B HOB3 UDP sing 427 n n # _atom_sites.entry_id 3QEN _atom_sites.fract_transf_matrix[1][1] 0.014463 _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] 0.014463 _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] 0.00841 _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 C 2 UDP A 1 401 401 UDP UDP . D 3 5BT A 1 402 402 5BT 5BT . E 2 UDP B 1 401 401 UDP UDP . F 3 5BT B 1 402 402 5BT 5BT . G 4 HOH A 1 261 3 HOH HOH . G 4 HOH A 2 262 5 HOH HOH . G 4 HOH A 3 263 7 HOH HOH . G 4 HOH A 4 264 8 HOH HOH . G 4 HOH A 5 265 9 HOH HOH . G 4 HOH A 6 266 10 HOH HOH . G 4 HOH A 7 267 11 HOH HOH . G 4 HOH A 8 268 13 HOH HOH . G 4 HOH A 9 269 14 HOH HOH . G 4 HOH A 10 270 17 HOH HOH . G 4 HOH A 11 271 19 HOH HOH . G 4 HOH A 12 272 23 HOH HOH . G 4 HOH A 13 273 24 HOH HOH . G 4 HOH A 14 274 26 HOH HOH . G 4 HOH A 15 275 28 HOH HOH . G 4 HOH A 16 276 33 HOH HOH . G 4 HOH A 17 277 34 HOH HOH . G 4 HOH A 18 278 39 HOH HOH . G 4 HOH A 19 279 42 HOH HOH . G 4 HOH A 20 280 43 HOH HOH . G 4 HOH A 21 281 44 HOH HOH . G 4 HOH A 22 282 48 HOH HOH . G 4 HOH A 23 283 49 HOH HOH . G 4 HOH A 24 284 50 HOH HOH . G 4 HOH A 25 285 52 HOH HOH . G 4 HOH A 26 286 53 HOH HOH . G 4 HOH A 27 287 57 HOH HOH . G 4 HOH A 28 288 63 HOH HOH . G 4 HOH A 29 289 67 HOH HOH . G 4 HOH A 30 290 72 HOH HOH . G 4 HOH A 31 291 73 HOH HOH . G 4 HOH A 32 292 77 HOH HOH . G 4 HOH A 33 293 78 HOH HOH . G 4 HOH A 34 294 84 HOH HOH . G 4 HOH A 35 295 89 HOH HOH . G 4 HOH A 36 296 90 HOH HOH . G 4 HOH A 37 297 91 HOH HOH . G 4 HOH A 38 298 95 HOH HOH . G 4 HOH A 39 299 96 HOH HOH . G 4 HOH A 40 300 97 HOH HOH . G 4 HOH A 41 301 102 HOH HOH . G 4 HOH A 42 302 103 HOH HOH . G 4 HOH A 43 303 107 HOH HOH . G 4 HOH A 44 304 109 HOH HOH . G 4 HOH A 45 305 111 HOH HOH . G 4 HOH A 46 306 112 HOH HOH . G 4 HOH A 47 307 115 HOH HOH . G 4 HOH A 48 308 118 HOH HOH . G 4 HOH A 49 309 119 HOH HOH . G 4 HOH A 50 310 121 HOH HOH . G 4 HOH A 51 311 122 HOH HOH . G 4 HOH A 52 312 123 HOH HOH . G 4 HOH A 53 313 126 HOH HOH . G 4 HOH A 54 314 129 HOH HOH . G 4 HOH A 55 315 130 HOH HOH . G 4 HOH A 56 316 135 HOH HOH . G 4 HOH A 57 317 143 HOH HOH . G 4 HOH A 58 318 145 HOH HOH . G 4 HOH A 59 319 146 HOH HOH . G 4 HOH A 60 320 148 HOH HOH . G 4 HOH A 61 321 153 HOH HOH . G 4 HOH A 62 322 154 HOH HOH . G 4 HOH A 63 323 155 HOH HOH . G 4 HOH A 64 324 160 HOH HOH . G 4 HOH A 65 325 161 HOH HOH . G 4 HOH A 66 326 162 HOH HOH . G 4 HOH A 67 327 163 HOH HOH . G 4 HOH A 68 328 164 HOH HOH . G 4 HOH A 69 329 165 HOH HOH . G 4 HOH A 70 330 64 HOH HOH . H 4 HOH B 1 261 1 HOH HOH . H 4 HOH B 2 262 2 HOH HOH . H 4 HOH B 3 263 4 HOH HOH . H 4 HOH B 4 264 6 HOH HOH . H 4 HOH B 5 265 12 HOH HOH . H 4 HOH B 6 266 15 HOH HOH . H 4 HOH B 7 267 18 HOH HOH . H 4 HOH B 8 268 20 HOH HOH . H 4 HOH B 9 269 21 HOH HOH . H 4 HOH B 10 270 25 HOH HOH . H 4 HOH B 11 271 27 HOH HOH . H 4 HOH B 12 272 29 HOH HOH . H 4 HOH B 13 273 31 HOH HOH . H 4 HOH B 14 274 32 HOH HOH . H 4 HOH B 15 275 35 HOH HOH . H 4 HOH B 16 276 36 HOH HOH . H 4 HOH B 17 277 37 HOH HOH . H 4 HOH B 18 278 45 HOH HOH . H 4 HOH B 19 279 46 HOH HOH . H 4 HOH B 20 280 47 HOH HOH . H 4 HOH B 21 281 51 HOH HOH . H 4 HOH B 22 282 55 HOH HOH . H 4 HOH B 23 283 58 HOH HOH . H 4 HOH B 24 284 59 HOH HOH . H 4 HOH B 25 285 60 HOH HOH . H 4 HOH B 26 286 61 HOH HOH . H 4 HOH B 27 287 62 HOH HOH . H 4 HOH B 28 289 65 HOH HOH . H 4 HOH B 29 290 66 HOH HOH . H 4 HOH B 30 291 68 HOH HOH . H 4 HOH B 31 292 70 HOH HOH . H 4 HOH B 32 293 71 HOH HOH . H 4 HOH B 33 294 74 HOH HOH . H 4 HOH B 34 295 75 HOH HOH . H 4 HOH B 35 296 76 HOH HOH . H 4 HOH B 36 297 79 HOH HOH . H 4 HOH B 37 298 86 HOH HOH . H 4 HOH B 38 299 87 HOH HOH . H 4 HOH B 39 300 88 HOH HOH . H 4 HOH B 40 301 92 HOH HOH . H 4 HOH B 41 302 93 HOH HOH . H 4 HOH B 42 303 94 HOH HOH . H 4 HOH B 43 304 98 HOH HOH . H 4 HOH B 44 305 99 HOH HOH . H 4 HOH B 45 306 100 HOH HOH . H 4 HOH B 46 307 101 HOH HOH . H 4 HOH B 47 308 104 HOH HOH . H 4 HOH B 48 309 108 HOH HOH . H 4 HOH B 49 310 116 HOH HOH . H 4 HOH B 50 311 125 HOH HOH . H 4 HOH B 51 312 128 HOH HOH . H 4 HOH B 52 313 131 HOH HOH . H 4 HOH B 53 314 132 HOH HOH . H 4 HOH B 54 315 133 HOH HOH . H 4 HOH B 55 316 134 HOH HOH . H 4 HOH B 56 317 136 HOH HOH . H 4 HOH B 57 318 137 HOH HOH . H 4 HOH B 58 319 138 HOH HOH . H 4 HOH B 59 320 141 HOH HOH . H 4 HOH B 60 321 142 HOH HOH . H 4 HOH B 61 322 144 HOH HOH . H 4 HOH B 62 323 147 HOH HOH . H 4 HOH B 63 324 149 HOH HOH . H 4 HOH B 64 325 152 HOH HOH . H 4 HOH B 65 326 156 HOH HOH . H 4 HOH B 66 327 157 HOH HOH . H 4 HOH B 67 328 159 HOH HOH . H 4 HOH B 68 329 166 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 . . . C 2 -29.318 24.674 -29.396 1 48.4 ? N1 UDP 401 A 1 HETATM 2 C C2 UDP . . . C 2 -30.481 24.655 -30.162 1 50.36 ? C2 UDP 401 A 1 HETATM 3 N N3 UDP . . . C 2 -30.568 23.792 -31.248 1 50.52 ? N3 UDP 401 A 1 HETATM 4 C C4 UDP . . . C 2 -29.505 22.964 -31.569 1 50.63 ? C4 UDP 401 A 1 HETATM 5 C C5 UDP . . . C 2 -28.337 23.01 -30.806 1 48.88 ? C5 UDP 401 A 1 HETATM 6 C C6 UDP . . . C 2 -28.319 23.758 -29.628 1 48.48 ? C6 UDP 401 A 1 HETATM 7 O O2 UDP . . . C 2 -31.435 25.4 -29.879 1 48.79 ? O2 UDP 401 A 1 HETATM 8 O O4 UDP . . . C 2 -29.588 22.205 -32.544 1 51.08 ? O4 UDP 401 A 1 HETATM 9 C C1' UDP . . . C 2 -29.237 25.631 -28.275 1 46.35 ? C1' UDP 401 A 1 HETATM 10 C C2' UDP . . . C 2 -29.167 25.053 -26.869 1 45.87 ? C2' UDP 401 A 1 HETATM 11 O O2' UDP . . . C 2 -30.444 24.849 -26.308 1 45.73 ? O2' UDP 401 A 1 HETATM 12 C C3' UDP . . . C 2 -28.36 26.133 -26.133 1 45.41 ? C3' UDP 401 A 1 HETATM 13 C C4' UDP . . . C 2 -27.491 26.755 -27.213 1 43.59 ? C4' UDP 401 A 1 HETATM 14 O O4' UDP . . . C 2 -28.07 26.417 -28.464 1 44.44 ? O4' UDP 401 A 1 HETATM 15 O O3' UDP . . . C 2 -29.155 27.161 -25.57 1 43.19 ? O3' UDP 401 A 1 HETATM 16 C C5' UDP . . . C 2 -26.062 26.232 -27.13 1 40.79 ? C5' UDP 401 A 1 HETATM 17 O O5' UDP . . . C 2 -26.072 24.806 -27.128 1 39.17 ? O5' UDP 401 A 1 HETATM 18 P PA UDP . . . C 2 -25.179 23.967 -26.078 1 37.44 ? PA UDP 401 A 1 HETATM 19 O O1A UDP . . . C 2 -25.583 24.296 -24.678 1 38.3 ? O1A UDP 401 A 1 HETATM 20 O O2A UDP . . . C 2 -25.364 22.547 -26.378 1 39.12 ? O2A UDP 401 A 1 HETATM 21 O O3A UDP . . . C 2 -23.693 24.54 -26.367 1 34.63 ? O3A UDP 401 A 1 HETATM 22 P PB UDP . . . C 2 -22.256 23.766 -26.397 1 33.36 ? PB UDP 401 A 1 HETATM 23 O O1B UDP . . . C 2 -22.333 22.683 -25.382 1 35.17 ? O1B UDP 401 A 1 HETATM 24 O O2B UDP . . . C 2 -21.308 24.773 -25.876 1 34.93 ? O2B UDP 401 A 1 HETATM 25 O O3B UDP . . . C 2 -21.765 23.302 -27.697 1 30.59 ? O3B UDP 401 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 241 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 25 #