data_3QEJ # _model_server_result.job_id YW8vv1zIA7PuzjQwWD2pvg _model_server_result.datetime_utc '2024-11-20 12:36:47' _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 3qej # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 3QEJ # _exptl.entry_id 3QEJ _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 3QEJ _cell.length_a 68.43 _cell.length_b 68.43 _cell.length_c 120.37 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3QEJ _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 _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 D 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 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 3QEJ _atom_sites.fract_transf_matrix[1][1] 0.014613 _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] 0.014613 _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] 0.008308 _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 2 UDP B 1 402 402 UDP UDP . E 3 HOH A 1 261 3 HOH HOH . E 3 HOH A 2 262 5 HOH HOH . E 3 HOH A 3 263 7 HOH HOH . E 3 HOH A 4 264 8 HOH HOH . E 3 HOH A 5 265 9 HOH HOH . E 3 HOH A 6 266 11 HOH HOH . E 3 HOH A 7 267 13 HOH HOH . E 3 HOH A 8 268 14 HOH HOH . E 3 HOH A 9 269 16 HOH HOH . E 3 HOH A 10 270 17 HOH HOH . E 3 HOH A 11 271 18 HOH HOH . E 3 HOH A 12 272 19 HOH HOH . E 3 HOH A 13 273 22 HOH HOH . E 3 HOH A 14 274 23 HOH HOH . E 3 HOH A 15 275 28 HOH HOH . E 3 HOH A 16 276 29 HOH HOH . E 3 HOH A 17 277 30 HOH HOH . E 3 HOH A 18 278 33 HOH HOH . E 3 HOH A 19 279 34 HOH HOH . E 3 HOH A 20 280 36 HOH HOH . E 3 HOH A 21 281 43 HOH HOH . E 3 HOH A 22 282 45 HOH HOH . E 3 HOH A 23 283 49 HOH HOH . E 3 HOH A 24 284 50 HOH HOH . E 3 HOH A 25 285 55 HOH HOH . E 3 HOH A 26 286 56 HOH HOH . E 3 HOH A 27 287 57 HOH HOH . E 3 HOH A 28 288 59 HOH HOH . E 3 HOH A 29 289 60 HOH HOH . E 3 HOH A 30 290 63 HOH HOH . E 3 HOH A 31 291 64 HOH HOH . E 3 HOH A 32 292 67 HOH HOH . E 3 HOH A 33 293 68 HOH HOH . E 3 HOH A 34 294 69 HOH HOH . E 3 HOH A 35 295 71 HOH HOH . E 3 HOH A 36 296 72 HOH HOH . E 3 HOH A 37 297 73 HOH HOH . E 3 HOH A 38 298 74 HOH HOH . E 3 HOH A 39 299 76 HOH HOH . E 3 HOH A 40 300 79 HOH HOH . E 3 HOH A 41 301 82 HOH HOH . E 3 HOH A 42 302 84 HOH HOH . E 3 HOH A 43 303 88 HOH HOH . E 3 HOH A 44 304 89 HOH HOH . F 3 HOH B 1 261 1 HOH HOH . F 3 HOH B 2 262 2 HOH HOH . F 3 HOH B 3 263 4 HOH HOH . F 3 HOH B 4 264 6 HOH HOH . F 3 HOH B 5 265 10 HOH HOH . F 3 HOH B 6 266 12 HOH HOH . F 3 HOH B 7 267 15 HOH HOH . F 3 HOH B 8 268 20 HOH HOH . F 3 HOH B 9 269 21 HOH HOH . F 3 HOH B 10 270 24 HOH HOH . F 3 HOH B 11 271 25 HOH HOH . F 3 HOH B 12 272 26 HOH HOH . F 3 HOH B 13 273 27 HOH HOH . F 3 HOH B 14 274 31 HOH HOH . F 3 HOH B 15 275 32 HOH HOH . F 3 HOH B 16 276 35 HOH HOH . F 3 HOH B 17 277 37 HOH HOH . F 3 HOH B 18 278 38 HOH HOH . F 3 HOH B 19 279 39 HOH HOH . F 3 HOH B 20 280 40 HOH HOH . F 3 HOH B 21 281 41 HOH HOH . F 3 HOH B 22 282 42 HOH HOH . F 3 HOH B 23 283 44 HOH HOH . F 3 HOH B 24 284 46 HOH HOH . F 3 HOH B 25 285 47 HOH HOH . F 3 HOH B 26 286 48 HOH HOH . F 3 HOH B 27 287 51 HOH HOH . F 3 HOH B 28 288 52 HOH HOH . F 3 HOH B 29 289 53 HOH HOH . F 3 HOH B 30 290 54 HOH HOH . F 3 HOH B 31 291 58 HOH HOH . F 3 HOH B 32 292 61 HOH HOH . F 3 HOH B 33 293 62 HOH HOH . F 3 HOH B 34 294 65 HOH HOH . F 3 HOH B 35 295 66 HOH HOH . F 3 HOH B 36 296 70 HOH HOH . F 3 HOH B 37 297 75 HOH HOH . F 3 HOH B 38 298 77 HOH HOH . F 3 HOH B 39 299 78 HOH HOH . F 3 HOH B 40 300 80 HOH HOH . F 3 HOH B 41 301 81 HOH HOH . F 3 HOH B 42 302 83 HOH HOH . F 3 HOH B 43 303 85 HOH HOH . F 3 HOH B 44 304 86 HOH HOH . F 3 HOH B 45 305 90 HOH HOH . F 3 HOH B 46 306 87 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 . . . D 2 28.546 25.271 2.945 1 73.26 ? N1 UDP 402 B 1 HETATM 2 C C2 UDP . . . D 2 29.757 25.075 3.599 1 73.53 ? C2 UDP 402 B 1 HETATM 3 N N3 UDP . . . D 2 29.835 24.159 4.629 1 73.48 ? N3 UDP 402 B 1 HETATM 4 C C4 UDP . . . D 2 28.711 23.435 4.997 1 72.61 ? C4 UDP 402 B 1 HETATM 5 C C5 UDP . . . D 2 27.497 23.635 4.334 1 73.13 ? C5 UDP 402 B 1 HETATM 6 C C6 UDP . . . D 2 27.398 24.691 3.437 1 73.5 ? C6 UDP 402 B 1 HETATM 7 O O2 UDP . . . D 2 30.762 25.708 3.28 1 74.45 ? O2 UDP 402 B 1 HETATM 8 O O4 UDP . . . D 2 28.787 22.628 5.917 1 69.8 ? O4 UDP 402 B 1 HETATM 9 C C1' UDP . . . D 2 28.461 26.231 1.835 1 71.39 ? C1' UDP 402 B 1 HETATM 10 C C2' UDP . . . D 2 28.22 25.443 0.563 1 70.5 ? C2' UDP 402 B 1 HETATM 11 O O2' UDP . . . D 2 29.407 24.909 0.022 1 71.81 ? O2' UDP 402 B 1 HETATM 12 C C3' UDP . . . D 2 27.492 26.442 -0.325 1 70.7 ? C3' UDP 402 B 1 HETATM 13 C C4' UDP . . . D 2 26.761 27.33 0.683 1 70.94 ? C4' UDP 402 B 1 HETATM 14 O O4' UDP . . . D 2 27.352 27.106 1.957 1 71.08 ? O4' UDP 402 B 1 HETATM 15 O O3' UDP . . . D 2 28.375 27.228 -1.105 1 68.21 ? O3' UDP 402 B 1 HETATM 16 C C5' UDP . . . D 2 25.264 27.022 0.734 1 71.32 ? C5' UDP 402 B 1 HETATM 17 O O5' UDP . . . D 2 25.035 25.662 1.043 1 71.24 ? O5' UDP 402 B 1 HETATM 18 P PA UDP . . . D 2 24.216 24.695 0.055 1 71.3 ? PA UDP 402 B 1 HETATM 19 O O1A UDP . . . D 2 24.344 25.123 -1.36 1 70.74 ? O1A UDP 402 B 1 HETATM 20 O O2A UDP . . . D 2 24.638 23.286 0.212 1 70.67 ? O2A UDP 402 B 1 HETATM 21 O O3A UDP . . . D 2 22.761 25.02 0.673 1 69.87 ? O3A UDP 402 B 1 HETATM 22 P PB UDP . . . D 2 21.388 24.283 0.295 1 67.41 ? PB UDP 402 B 1 HETATM 23 O O1B UDP . . . D 2 21.721 23.176 -0.598 1 69.33 ? O1B UDP 402 B 1 HETATM 24 O O2B UDP . . . D 2 20.477 25.222 -0.4 1 67.71 ? O2B UDP 402 B 1 HETATM 25 O O3B UDP . . . D 2 20.729 23.783 1.522 1 68.55 ? O3B UDP 402 B 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 25 #