data_1TVW # _model_server_result.job_id yTzeeV7Qdmz2BsOf1ye89w _model_server_result.datetime_utc '2024-11-27 16:02:15' _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 1tvw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":317}' # _entry.id 1TVW # _exptl.entry_id 1TVW _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 1TVW _cell.length_a 78.5 _cell.length_b 78.5 _cell.length_c 230.1 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1TVW _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 -115.05 # _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 418 n n N1 C6 UMP sing 419 n n N1 C1' UMP sing 420 n n C2 N3 UMP sing 421 n n C2 O2 UMP doub 422 n n N3 C4 UMP sing 423 n n N3 HN3 UMP sing 424 n n C4 C5 UMP sing 425 n n C4 O4 UMP doub 426 n n C5 C6 UMP doub 427 n n C5 H5 UMP sing 428 n n C6 H6 UMP sing 429 n n C1' C2' UMP sing 430 n n C1' O4' UMP sing 431 n n C1' H1' UMP sing 432 n n C2' C3' UMP sing 433 n n C2' H2' UMP sing 434 n n C2' "H2''" UMP sing 435 n n C3' C4' UMP sing 436 n n C3' O3' UMP sing 437 n n C3' H3' UMP sing 438 n n C4' O4' UMP sing 439 n n C4' C5' UMP sing 440 n n C4' H4' UMP sing 441 n n O3' HO3' UMP sing 442 n n C5' O5' UMP sing 443 n n C5' H5' UMP sing 444 n n C5' "H5''" UMP sing 445 n n O5' P UMP sing 446 n n P OP1 UMP doub 447 n n P OP2 UMP sing 448 n n P OP3 UMP sing 449 n n OP2 HOP2 UMP sing 450 n n OP3 HOP3 UMP sing 451 n n # _atom_sites.entry_id 1TVW _atom_sites.fract_transf_matrix[1][1] 0.012739 _atom_sites.fract_transf_matrix[1][2] 0.007355 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01471 _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] 0.004346 _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 CB3 A 1 318 318 CB3 CB3 . D 4 HOH A 1 319 319 HOH HOH . D 4 HOH A 2 320 320 HOH HOH . D 4 HOH A 3 321 321 HOH HOH . D 4 HOH A 4 323 323 HOH HOH . D 4 HOH A 5 324 324 HOH HOH . D 4 HOH A 6 325 325 HOH HOH . D 4 HOH A 7 326 326 HOH HOH . D 4 HOH A 8 327 327 HOH HOH . D 4 HOH A 9 328 328 HOH HOH . D 4 HOH A 10 329 329 HOH HOH . D 4 HOH A 11 330 330 HOH HOH . D 4 HOH A 12 331 331 HOH HOH . D 4 HOH A 13 332 332 HOH HOH . D 4 HOH A 14 333 333 HOH HOH . D 4 HOH A 15 334 334 HOH HOH . D 4 HOH A 16 335 335 HOH HOH . D 4 HOH A 17 336 336 HOH HOH . D 4 HOH A 18 337 337 HOH HOH . D 4 HOH A 19 338 338 HOH HOH . D 4 HOH A 20 339 339 HOH HOH . D 4 HOH A 21 340 340 HOH HOH . D 4 HOH A 22 341 341 HOH HOH . D 4 HOH A 23 342 342 HOH HOH . D 4 HOH A 24 343 343 HOH HOH . D 4 HOH A 25 344 344 HOH HOH . D 4 HOH A 26 345 345 HOH HOH . D 4 HOH A 27 346 346 HOH HOH . D 4 HOH A 28 347 347 HOH HOH . D 4 HOH A 29 348 348 HOH HOH . D 4 HOH A 30 349 349 HOH HOH . D 4 HOH A 31 350 350 HOH HOH . D 4 HOH A 32 351 351 HOH HOH . D 4 HOH A 33 352 352 HOH HOH . D 4 HOH A 34 353 353 HOH HOH . D 4 HOH A 35 354 354 HOH HOH . D 4 HOH A 36 355 355 HOH HOH . D 4 HOH A 37 356 356 HOH HOH . D 4 HOH A 38 357 357 HOH HOH . D 4 HOH A 39 358 358 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 15.357 46.81 -52.373 1 24.37 ? N1 UMP 317 A 1 HETATM 2 C C2 UMP . . . B 2 14.542 45.954 -51.649 1 25.32 ? C2 UMP 317 A 1 HETATM 3 N N3 UMP . . . B 2 13.888 46.524 -50.589 1 27.09 ? N3 UMP 317 A 1 HETATM 4 C C4 UMP . . . B 2 13.961 47.866 -50.221 1 26.84 ? C4 UMP 317 A 1 HETATM 5 C C5 UMP . . . B 2 14.85 48.685 -51.036 1 24.61 ? C5 UMP 317 A 1 HETATM 6 C C6 UMP . . . B 2 15.522 48.094 -52.103 1 24.69 ? C6 UMP 317 A 1 HETATM 7 O O2 UMP . . . B 2 14.371 44.759 -51.894 1 25.57 ? O2 UMP 317 A 1 HETATM 8 O O4 UMP . . . B 2 13.238 48.262 -49.299 1 28.67 ? O4 UMP 317 A 1 HETATM 9 C C1' UMP . . . B 2 16.036 46.31 -53.552 1 24.77 ? C1' UMP 317 A 1 HETATM 10 C C2' UMP . . . B 2 15.258 46.25 -54.861 1 26.21 ? C2' UMP 317 A 1 HETATM 11 C C3' UMP . . . B 2 16.37 46.036 -55.869 1 26.91 ? C3' UMP 317 A 1 HETATM 12 C C4' UMP . . . B 2 17.462 47.042 -55.49 1 21.56 ? C4' UMP 317 A 1 HETATM 13 O O3' UMP . . . B 2 16.752 44.64 -55.646 1 23.72 ? O3' UMP 317 A 1 HETATM 14 O O4' UMP . . . B 2 17.185 47.122 -54.033 1 22.64 ? O4' UMP 317 A 1 HETATM 15 C C5' UMP . . . B 2 17.163 48.455 -56.046 1 19.45 ? C5' UMP 317 A 1 HETATM 16 O O5' UMP . . . B 2 17.138 48.634 -57.498 1 17.88 ? O5' UMP 317 A 1 HETATM 17 P P UMP . . . B 2 15.764 49.11 -58.107 1 12.06 ? P UMP 317 A 1 HETATM 18 O OP1 UMP . . . B 2 15.898 49.303 -59.589 1 10.1 ? OP1 UMP 317 A 1 HETATM 19 O OP2 UMP . . . B 2 14.742 48.042 -57.898 1 14.67 ? OP2 UMP 317 A 1 HETATM 20 O OP3 UMP . . . B 2 15.278 50.335 -57.449 1 3.43 ? OP3 UMP 317 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 243 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 20 #