data_2TDM # _model_server_result.job_id MRnPtJ3H0QXH4vTztpqZWQ _model_server_result.datetime_utc '2024-11-26 23:21:24' _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 2tdm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":317}' # _entry.id 2TDM # _exptl.entry_id 2TDM _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 2TDM _cell.length_a 78.6 _cell.length_b 78.6 _cell.length_c 240.2 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2TDM _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 -120.1 # _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 2TDM _atom_sites.fract_transf_matrix[1][1] 0.012723 _atom_sites.fract_transf_matrix[1][2] 0.007345 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014691 _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] 0.004163 _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 1 318 318 HOH HOH . C 3 HOH A 2 319 319 HOH HOH . C 3 HOH A 3 320 320 HOH HOH . C 3 HOH A 4 321 321 HOH HOH . C 3 HOH A 5 322 322 HOH HOH . C 3 HOH A 6 323 323 HOH HOH . C 3 HOH A 7 324 324 HOH HOH . C 3 HOH A 8 325 325 HOH HOH . C 3 HOH A 9 326 326 HOH HOH . C 3 HOH A 10 327 327 HOH HOH . C 3 HOH A 11 328 328 HOH HOH . C 3 HOH A 12 329 329 HOH HOH . C 3 HOH A 13 330 330 HOH HOH . C 3 HOH A 14 331 331 HOH HOH . C 3 HOH A 15 332 332 HOH HOH . C 3 HOH A 16 333 333 HOH HOH . C 3 HOH A 17 334 334 HOH HOH . C 3 HOH A 18 335 335 HOH HOH . C 3 HOH A 19 336 336 HOH HOH . C 3 HOH A 20 337 337 HOH HOH . C 3 HOH A 21 338 338 HOH HOH . C 3 HOH A 22 339 339 HOH HOH . C 3 HOH A 23 340 340 HOH HOH . C 3 HOH A 24 341 341 HOH HOH . C 3 HOH A 25 342 342 HOH HOH . C 3 HOH A 26 343 343 HOH HOH . C 3 HOH A 27 344 344 HOH HOH . C 3 HOH A 28 345 345 HOH HOH . C 3 HOH A 29 346 346 HOH HOH . C 3 HOH A 30 347 347 HOH HOH . C 3 HOH A 31 348 348 HOH HOH . C 3 HOH A 32 349 349 HOH HOH . C 3 HOH A 33 350 350 HOH HOH . C 3 HOH A 34 351 351 HOH HOH . C 3 HOH A 35 352 352 HOH HOH . C 3 HOH A 36 353 353 HOH HOH . C 3 HOH A 37 354 354 HOH HOH . C 3 HOH A 38 355 355 HOH HOH . C 3 HOH A 39 356 356 HOH HOH . C 3 HOH A 40 357 357 HOH HOH . C 3 HOH A 41 358 358 HOH HOH . C 3 HOH A 42 359 359 HOH HOH . C 3 HOH A 43 360 360 HOH HOH . C 3 HOH A 44 361 361 HOH HOH . C 3 HOH A 45 362 362 HOH HOH . C 3 HOH A 46 363 363 HOH HOH . C 3 HOH A 47 364 364 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 14.491 48.51 -53.525 1 21.54 ? N1 UMP 317 A 1 HETATM 2 C C2 UMP . . . B 2 13.706 47.489 -53.067 1 23.93 ? C2 UMP 317 A 1 HETATM 3 N N3 UMP . . . B 2 12.789 47.81 -52.082 1 32.05 ? N3 UMP 317 A 1 HETATM 4 C C4 UMP . . . B 2 12.622 49.094 -51.524 1 33.3 ? C4 UMP 317 A 1 HETATM 5 C C5 UMP . . . B 2 13.5 50.102 -52.081 1 26.88 ? C5 UMP 317 A 1 HETATM 6 C C6 UMP . . . B 2 14.404 49.736 -53.084 1 21.73 ? C6 UMP 317 A 1 HETATM 7 O O2 UMP . . . B 2 13.799 46.348 -53.498 1 21.44 ? O2 UMP 317 A 1 HETATM 8 O O4 UMP . . . B 2 11.803 49.311 -50.627 1 33.01 ? O4 UMP 317 A 1 HETATM 9 C C1' UMP . . . B 2 15.559 48.25 -54.505 1 25.11 ? C1' UMP 317 A 1 HETATM 10 C C2' UMP . . . B 2 15.129 47.753 -55.883 1 25.87 ? C2' UMP 317 A 1 HETATM 11 C C3' UMP . . . B 2 16.367 47.995 -56.728 1 24.14 ? C3' UMP 317 A 1 HETATM 12 C C4' UMP . . . B 2 16.875 49.387 -56.34 1 29.82 ? C4' UMP 317 A 1 HETATM 13 O O3' UMP . . . B 2 17.303 47.012 -56.311 1 31.84 ? O3' UMP 317 A 1 HETATM 14 O O4' UMP . . . B 2 16.441 49.409 -54.901 1 29.07 ? O4' UMP 317 A 1 HETATM 15 C C5' UMP . . . B 2 16.109 50.481 -57.088 1 29.79 ? C5' UMP 317 A 1 HETATM 16 O O5' UMP . . . B 2 16.527 50.43 -58.471 1 23.49 ? O5' UMP 317 A 1 HETATM 17 P P UMP . . . B 2 15.803 51.285 -59.566 1 29.64 ? P UMP 317 A 1 HETATM 18 O OP1 UMP . . . B 2 16.65 51.221 -60.78 1 18.31 ? OP1 UMP 317 A 1 HETATM 19 O OP2 UMP . . . B 2 14.519 50.617 -59.836 1 26.69 ? OP2 UMP 317 A 1 HETATM 20 O OP3 UMP . . . B 2 15.54 52.695 -59.192 1 15.71 ? OP3 UMP 317 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 359 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 20 #