data_1LCE # _model_server_result.job_id 7_Obz9gjfCpebt7lENl8xQ _model_server_result.datetime_utc '2024-11-23 11:23:51' _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 1lce # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":317}' # _entry.id 1LCE # _exptl.entry_id 1LCE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _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 120 _cell.entry_id 1LCE _cell.length_a 78.9 _cell.length_b 78.9 _cell.length_c 229.7 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1LCE _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA,PQS _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 _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' 11_554 -x+y,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -114.85 # _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 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 415 n n N1 C6 UMP sing 416 n n N1 C1' UMP sing 417 n n C2 N3 UMP sing 418 n n C2 O2 UMP doub 419 n n N3 C4 UMP sing 420 n n N3 HN3 UMP sing 421 n n C4 C5 UMP sing 422 n n C4 O4 UMP doub 423 n n C5 C6 UMP doub 424 n n C5 H5 UMP sing 425 n n C6 H6 UMP sing 426 n n C1' C2' UMP sing 427 n n C1' O4' UMP sing 428 n n C1' H1' UMP sing 429 n n C2' C3' UMP sing 430 n n C2' H2' UMP sing 431 n n C2' "H2''" UMP sing 432 n n C3' C4' UMP sing 433 n n C3' O3' UMP sing 434 n n C3' H3' UMP sing 435 n n C4' O4' UMP sing 436 n n C4' C5' UMP sing 437 n n C4' H4' UMP sing 438 n n O3' HO3' UMP sing 439 n n C5' O5' UMP sing 440 n n C5' H5' UMP sing 441 n n C5' "H5''" UMP sing 442 n n O5' P UMP sing 443 n n P OP1 UMP doub 444 n n P OP2 UMP sing 445 n n P OP3 UMP sing 446 n n OP2 HOP2 UMP sing 447 n n OP3 HOP3 UMP sing 448 n n # _atom_sites.entry_id 1LCE _atom_sites.fract_transf_matrix[1][1] 0.012674 _atom_sites.fract_transf_matrix[1][2] 0.007317 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014635 _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] 0.004354 _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 UMP A 1 317 317 UMP UMP . C 3 TMF A 1 318 318 TMF TMF . D 4 HOH A 1 319 319 HOH HOH . D 4 HOH A 2 321 321 HOH HOH . D 4 HOH A 3 323 323 HOH HOH . D 4 HOH A 4 325 325 HOH HOH . D 4 HOH A 5 326 326 HOH HOH . D 4 HOH A 6 328 328 HOH HOH . D 4 HOH A 7 329 329 HOH HOH . D 4 HOH A 8 330 330 HOH HOH . D 4 HOH A 9 331 331 HOH HOH . D 4 HOH A 10 332 332 HOH HOH . D 4 HOH A 11 333 333 HOH HOH . D 4 HOH A 12 334 334 HOH HOH . D 4 HOH A 13 335 335 HOH HOH . D 4 HOH A 14 338 338 HOH HOH . D 4 HOH A 15 339 339 HOH HOH . D 4 HOH A 16 340 340 HOH HOH . D 4 HOH A 17 341 341 HOH HOH . D 4 HOH A 18 342 342 HOH HOH . D 4 HOH A 19 343 343 HOH HOH . D 4 HOH A 20 344 344 HOH HOH . D 4 HOH A 21 345 345 HOH HOH . D 4 HOH A 22 346 346 HOH HOH . D 4 HOH A 23 347 347 HOH HOH . D 4 HOH A 24 348 348 HOH HOH . D 4 HOH A 25 349 349 HOH HOH . D 4 HOH A 26 350 350 HOH HOH . D 4 HOH A 27 351 351 HOH HOH . D 4 HOH A 28 352 352 HOH HOH . D 4 HOH A 29 355 355 HOH HOH . D 4 HOH A 30 358 358 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 . . . B 2 15.07 46.62 -52.503 1 18.59 ? N1 UMP 317 A 1 HETATM 2 C C2 UMP . . . B 2 14.45 45.664 -51.634 1 18.59 ? C2 UMP 317 A 1 HETATM 3 N N3 UMP . . . B 2 14.505 45.974 -50.277 1 18.59 ? N3 UMP 317 A 1 HETATM 4 C C4 UMP . . . B 2 15.157 47.106 -49.719 1 18.59 ? C4 UMP 317 A 1 HETATM 5 C C5 UMP . . . B 2 15.73 48.016 -50.696 1 18.59 ? C5 UMP 317 A 1 HETATM 6 C C6 UMP . . . B 2 15.644 47.713 -52.048 1 18.59 ? C6 UMP 317 A 1 HETATM 7 O O2 UMP . . . B 2 13.975 44.571 -51.956 1 18.59 ? O2 UMP 317 A 1 HETATM 8 O O4 UMP . . . B 2 15.474 47.257 -48.531 1 18.59 ? O4 UMP 317 A 1 HETATM 9 C C1' UMP . . . B 2 15.364 46.544 -53.981 1 18.59 ? C1' UMP 317 A 1 HETATM 10 C C2' UMP . . . B 2 15.98 45.405 -54.824 1 18.59 ? C2' UMP 317 A 1 HETATM 11 C C3' UMP . . . B 2 17.1 46.1 -55.664 1 18.59 ? C3' UMP 317 A 1 HETATM 12 C C4' UMP . . . B 2 16.958 47.593 -55.357 1 18.59 ? C4' UMP 317 A 1 HETATM 13 O O3' UMP . . . B 2 18.447 45.666 -55.343 1 18.59 ? O3' UMP 317 A 1 HETATM 14 O O4' UMP . . . B 2 15.59 47.734 -54.855 1 18.59 ? O4' UMP 317 A 1 HETATM 15 C C5' UMP . . . B 2 17.11 48.513 -56.572 1 18.59 ? C5' UMP 317 A 1 HETATM 16 O O5' UMP . . . B 2 16.167 48.335 -57.672 1 18.59 ? O5' UMP 317 A 1 HETATM 17 P P UMP . . . B 2 15.78 49.588 -58.634 1 11.71 ? P UMP 317 A 1 HETATM 18 O OP1 UMP . . . B 2 14.306 49.584 -58.644 1 18.59 ? OP1 UMP 317 A 1 HETATM 19 O OP2 UMP . . . B 2 16.271 50.834 -58.038 1 18.59 ? OP2 UMP 317 A 1 HETATM 20 O OP3 UMP . . . B 2 16.303 49.379 -60.022 1 18.59 ? OP3 UMP 317 A 1 HETATM 21 H HN3 UMP . . . B 2 13.811 45.45 -49.829 1 15 ? HN3 UMP 317 A 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 21 #