data_1NJB # _model_server_result.job_id xLtwLge1GxmOzfu7bmnqeQ _model_server_result.datetime_utc '2025-04-10 15:32:32' _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 1njb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":317}' # _entry.id 1NJB # _exptl.entry_id 1NJB _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 1NJB _cell.length_a 78.7 _cell.length_b 78.7 _cell.length_c 242.1 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NJB _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 _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 -121.05 # _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 358 n n N1 C6 UMP sing 359 n n N1 C1' UMP sing 360 n n C2 N3 UMP sing 361 n n C2 O2 UMP doub 362 n n N3 C4 UMP sing 363 n n N3 HN3 UMP sing 364 n n C4 C5 UMP sing 365 n n C4 O4 UMP doub 366 n n C5 C6 UMP doub 367 n n C5 H5 UMP sing 368 n n C6 H6 UMP sing 369 n n C1' C2' UMP sing 370 n n C1' O4' UMP sing 371 n n C1' H1' UMP sing 372 n n C2' C3' UMP sing 373 n n C2' H2' UMP sing 374 n n C2' "H2''" UMP sing 375 n n C3' C4' UMP sing 376 n n C3' O3' UMP sing 377 n n C3' H3' UMP sing 378 n n C4' O4' UMP sing 379 n n C4' C5' UMP sing 380 n n C4' H4' UMP sing 381 n n O3' HO3' UMP sing 382 n n C5' O5' UMP sing 383 n n C5' H5' UMP sing 384 n n C5' "H5''" UMP sing 385 n n O5' P UMP sing 386 n n P OP1 UMP doub 387 n n P OP2 UMP sing 388 n n P OP3 UMP sing 389 n n OP2 HOP2 UMP sing 390 n n OP3 HOP3 UMP sing 391 n n # _atom_sites.entry_id 1NJB _atom_sites.fract_transf_matrix[1][1] 0.012706 _atom_sites.fract_transf_matrix[1][2] 0.007336 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014672 _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] 0.004131 _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 HOH A 1 319 319 HOH HOH . C 3 HOH A 2 320 320 HOH HOH . C 3 HOH A 3 322 322 HOH HOH . C 3 HOH A 4 323 323 HOH HOH . C 3 HOH A 5 325 325 HOH HOH . C 3 HOH A 6 326 326 HOH HOH . C 3 HOH A 7 327 327 HOH HOH . C 3 HOH A 8 333 333 HOH HOH . C 3 HOH A 9 336 336 HOH HOH . C 3 HOH A 10 337 337 HOH HOH . C 3 HOH A 11 338 338 HOH HOH . C 3 HOH A 12 354 354 HOH HOH . C 3 HOH A 13 357 357 HOH HOH . C 3 HOH A 14 358 358 HOH HOH . C 3 HOH A 15 359 359 HOH HOH . C 3 HOH A 16 360 360 HOH HOH . C 3 HOH A 17 362 362 HOH HOH . C 3 HOH A 18 363 363 HOH HOH . C 3 HOH A 19 367 367 HOH HOH . C 3 HOH A 20 368 368 HOH HOH . C 3 HOH A 21 372 372 HOH HOH . C 3 HOH A 22 377 377 HOH HOH . C 3 HOH A 23 379 379 HOH HOH . C 3 HOH A 24 380 380 HOH HOH . C 3 HOH A 25 382 382 HOH HOH . C 3 HOH A 26 383 383 HOH HOH . C 3 HOH A 27 388 388 HOH HOH . C 3 HOH A 28 389 389 HOH HOH . C 3 HOH A 29 390 390 HOH HOH . C 3 HOH A 30 391 391 HOH HOH . C 3 HOH A 31 392 392 HOH HOH . C 3 HOH A 32 394 394 HOH HOH . C 3 HOH A 33 395 395 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 14.835 48.667 -53.722 1 51.89 ? N1 UMP 317 A 1 HETATM 2 C C2 UMP . . . B 2 14.001 47.604 -53.293 1 57.17 ? C2 UMP 317 A 1 HETATM 3 N N3 UMP . . . B 2 13.135 47.837 -52.21 1 59.03 ? N3 UMP 317 A 1 HETATM 4 C C4 UMP . . . B 2 13.041 49.046 -51.529 1 59.76 ? C4 UMP 317 A 1 HETATM 5 C C5 UMP . . . B 2 13.955 50.078 -52.028 1 58.52 ? C5 UMP 317 A 1 HETATM 6 C C6 UMP . . . B 2 14.823 49.834 -53.113 1 55.84 ? C6 UMP 317 A 1 HETATM 7 O O2 UMP . . . B 2 13.993 46.48 -53.791 1 61.38 ? O2 UMP 317 A 1 HETATM 8 O O4 UMP . . . B 2 12.215 49.194 -50.628 1 59.75 ? O4 UMP 317 A 1 HETATM 9 C C1' UMP . . . B 2 15.701 48.597 -54.96 1 47.07 ? C1' UMP 317 A 1 HETATM 10 C C2' UMP . . . B 2 15.214 47.897 -56.23 1 43.33 ? C2' UMP 317 A 1 HETATM 11 C C3' UMP . . . B 2 16.368 48.135 -57.192 1 39.83 ? C3' UMP 317 A 1 HETATM 12 C C4' UMP . . . B 2 16.752 49.613 -57.054 1 38.94 ? C4' UMP 317 A 1 HETATM 13 O O3' UMP . . . B 2 17.461 47.373 -56.731 1 32.2 ? O3' UMP 317 A 1 HETATM 14 O O4' UMP . . . B 2 16.477 49.78 -55.579 1 42.39 ? O4' UMP 317 A 1 HETATM 15 C C5' UMP . . . B 2 15.789 50.496 -57.856 1 37.76 ? C5' UMP 317 A 1 HETATM 16 O O5' UMP . . . B 2 15.917 50.285 -59.318 1 33.25 ? O5' UMP 317 A 1 HETATM 17 P P UMP . . . B 2 15.982 51.565 -60.287 1 33.15 ? P UMP 317 A 1 HETATM 18 O OP1 UMP . . . B 2 16.22 51.125 -61.703 1 32.17 ? OP1 UMP 317 A 1 HETATM 19 O OP2 UMP . . . B 2 14.769 52.356 -60.065 1 41.48 ? OP2 UMP 317 A 1 HETATM 20 O OP3 UMP . . . B 2 17.026 52.401 -59.776 1 39.02 ? OP3 UMP 317 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 350 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #