data_1BPJ # _model_server_result.job_id szAfGyw2mqZLN3Z1iG7HdQ _model_server_result.datetime_utc '2025-02-05 03:51:04' _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 1bpj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":318}' # _entry.id 1BPJ # _exptl.entry_id 1BPJ _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 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 1BPJ _cell.length_a 78.8 _cell.length_b 78.8 _cell.length_c 243.8 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1BPJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 PISA,PQS dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D 1 1,2 A,B,C,D 2 1,3 # 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' 9_654 -x+1,-x+y,-z-1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 78.8 0 -81.266667 3 'crystal symmetry operation' 11_554 -x+y,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -121.9 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A OG SER 183 A SER 183 1_555 B K K . A K 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.865 ? metalc ? metalc2 A OG SER 183 A SER 183 11_554 B K K . A K 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.857 ? metalc ? metalc3 A O TRP 185 A TRP 185 1_555 B K K . A K 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc4 A O TRP 185 A TRP 185 11_554 B K K . A K 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? # _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 1BPJ _atom_sites.fract_transf_matrix[1][1] 0.01269 _atom_sites.fract_transf_matrix[1][2] 0.007327 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014653 _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] 0.004102 _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 K A 1 317 35 K POT . C 3 UMP A 1 318 317 UMP DUM . D 4 HOH A 1 319 1 HOH HOH . D 4 HOH A 2 320 2 HOH HOH . D 4 HOH A 3 321 3 HOH HOH . D 4 HOH A 4 322 4 HOH HOH . D 4 HOH A 5 323 5 HOH HOH . D 4 HOH A 6 324 6 HOH HOH . D 4 HOH A 7 325 7 HOH HOH . D 4 HOH A 8 326 8 HOH HOH . D 4 HOH A 9 327 9 HOH HOH . D 4 HOH A 10 328 10 HOH HOH . D 4 HOH A 11 329 11 HOH HOH . D 4 HOH A 12 330 12 HOH HOH . D 4 HOH A 13 331 13 HOH HOH . D 4 HOH A 14 332 14 HOH HOH . D 4 HOH A 15 333 15 HOH HOH . D 4 HOH A 16 334 16 HOH HOH . D 4 HOH A 17 335 17 HOH HOH . D 4 HOH A 18 336 18 HOH HOH . D 4 HOH A 19 337 19 HOH HOH . D 4 HOH A 20 338 20 HOH HOH . D 4 HOH A 21 339 21 HOH HOH . D 4 HOH A 22 340 22 HOH HOH . D 4 HOH A 23 341 23 HOH HOH . D 4 HOH A 24 342 24 HOH HOH . D 4 HOH A 25 343 25 HOH HOH . D 4 HOH A 26 344 26 HOH HOH . D 4 HOH A 27 345 27 HOH HOH . D 4 HOH A 28 346 28 HOH HOH . D 4 HOH A 29 347 29 HOH HOH . D 4 HOH A 30 348 30 HOH HOH . D 4 HOH A 31 349 31 HOH HOH . D 4 HOH A 32 350 32 HOH HOH . D 4 HOH A 33 351 33 HOH HOH . D 4 HOH A 34 352 34 HOH HOH . D 4 HOH A 35 353 36 HOH HOH . D 4 HOH A 36 354 37 HOH HOH . D 4 HOH A 37 355 38 HOH HOH . D 4 HOH A 38 356 39 HOH HOH . D 4 HOH A 39 357 40 HOH HOH . D 4 HOH A 40 358 41 HOH HOH . D 4 HOH A 41 359 42 HOH HOH . D 4 HOH A 42 360 43 HOH HOH . D 4 HOH A 43 361 44 HOH HOH . D 4 HOH A 44 362 45 HOH HOH . D 4 HOH A 45 363 46 HOH HOH . D 4 HOH A 46 364 47 HOH HOH . D 4 HOH A 47 365 48 HOH HOH . D 4 HOH A 48 366 49 HOH HOH . D 4 HOH A 49 367 50 HOH HOH . D 4 HOH A 50 368 51 HOH HOH . D 4 HOH A 51 369 52 HOH HOH . D 4 HOH A 52 370 53 HOH HOH . D 4 HOH A 53 371 54 HOH HOH . D 4 HOH A 54 372 55 HOH HOH . D 4 HOH A 55 373 56 HOH HOH . D 4 HOH A 56 374 57 HOH HOH . D 4 HOH A 57 375 58 HOH HOH . D 4 HOH A 58 376 59 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 . . . C 3 14.727 48.839 -53.909 0.9 60.71 ? N1 UMP 318 A 1 HETATM 2 C C2 UMP . . . C 3 13.691 47.898 -53.702 0.9 59.06 ? C2 UMP 318 A 1 HETATM 3 N N3 UMP . . . C 3 13.044 48.009 -52.47 0.9 59.8 ? N3 UMP 318 A 1 HETATM 4 C C4 UMP . . . C 3 13.349 48.956 -51.478 0.9 61.34 ? C4 UMP 318 A 1 HETATM 5 C C5 UMP . . . C 3 14.428 49.855 -51.805 0.9 61.24 ? C5 UMP 318 A 1 HETATM 6 C C6 UMP . . . C 3 15.07 49.744 -53.029 0.9 59.49 ? C6 UMP 318 A 1 HETATM 7 O O2 UMP . . . C 3 13.349 47.018 -54.491 0.9 53.98 ? O2 UMP 318 A 1 HETATM 8 O O4 UMP . . . C 3 12.739 49.042 -50.411 0.9 58.82 ? O4 UMP 318 A 1 HETATM 9 C C1' UMP . . . C 3 15.635 48.893 -55.07 0.9 61.6 ? C1' UMP 318 A 1 HETATM 10 C C2' UMP . . . C 3 15.08 48.756 -56.488 0.9 59.74 ? C2' UMP 318 A 1 HETATM 11 C C3' UMP . . . C 3 16.358 48.942 -57.287 0.9 60.79 ? C3' UMP 318 A 1 HETATM 12 C C4' UMP . . . C 3 17.059 50.167 -56.695 0.9 64.02 ? C4' UMP 318 A 1 HETATM 13 O O3' UMP . . . C 3 17.182 47.803 -56.997 0.9 59.73 ? O3' UMP 318 A 1 HETATM 14 O O4' UMP . . . C 3 16.511 50.098 -55.299 0.9 60.63 ? O4' UMP 318 A 1 HETATM 15 C C5' UMP . . . C 3 16.57 51.456 -57.356 0.9 67.81 ? C5' UMP 318 A 1 HETATM 16 O O5' UMP . . . C 3 16.987 51.514 -58.765 0.9 75.05 ? O5' UMP 318 A 1 HETATM 17 P P UMP . . . C 3 16.032 50.929 -59.955 1 79.78 ? P UMP 318 A 1 HETATM 18 O OP1 UMP . . . C 3 16.089 51.845 -61.116 1 79.88 ? OP1 UMP 318 A 1 HETATM 19 O OP2 UMP . . . C 3 16.462 49.566 -60.412 1 75.75 ? OP2 UMP 318 A 1 HETATM 20 O OP3 UMP . . . C 3 14.631 50.889 -59.477 1 81.03 ? OP3 UMP 318 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #