data_3C06 # _model_server_result.job_id atBXa6jS0df1ibKs00I6Iw _model_server_result.datetime_utc '2024-11-24 00:02:10' _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 3c06 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":317}' # _entry.id 3C06 # _exptl.entry_id 3C06 _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 3C06 _cell.length_a 76.573 _cell.length_b 76.573 _cell.length_c 212.931 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3C06 _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 _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' 10_554 -y,-x,-z-1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 0 0 -35.4885 # _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 388 n n N1 C6 UMP sing 389 n n N1 C1' UMP sing 390 n n C2 N3 UMP sing 391 n n C2 O2 UMP doub 392 n n N3 C4 UMP sing 393 n n N3 HN3 UMP sing 394 n n C4 C5 UMP sing 395 n n C4 O4 UMP doub 396 n n C5 C6 UMP doub 397 n n C5 H5 UMP sing 398 n n C6 H6 UMP sing 399 n n C1' C2' UMP sing 400 n n C1' O4' UMP sing 401 n n C1' H1' UMP sing 402 n n C2' C3' UMP sing 403 n n C2' H2' UMP sing 404 n n C2' "H2''" UMP sing 405 n n C3' C4' UMP sing 406 n n C3' O3' UMP sing 407 n n C3' H3' UMP sing 408 n n C4' O4' UMP sing 409 n n C4' C5' UMP sing 410 n n C4' H4' UMP sing 411 n n O3' HO3' UMP sing 412 n n C5' O5' UMP sing 413 n n C5' H5' UMP sing 414 n n C5' "H5''" UMP sing 415 n n O5' P UMP sing 416 n n P OP1 UMP doub 417 n n P OP2 UMP sing 418 n n P OP3 UMP sing 419 n n OP2 HOP2 UMP sing 420 n n OP3 HOP3 UMP sing 421 n n # _atom_sites.entry_id 3C06 _atom_sites.fract_transf_matrix[1][1] 0.013059 _atom_sites.fract_transf_matrix[1][2] 0.00754 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01508 _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] 0.004696 _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 14C A 1 318 1 14C C14 . 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 14 HOH HOH . D 4 HOH A 14 332 15 HOH HOH . D 4 HOH A 15 333 16 HOH HOH . D 4 HOH A 16 334 17 HOH HOH . D 4 HOH A 17 335 18 HOH HOH . D 4 HOH A 18 336 19 HOH HOH . D 4 HOH A 19 337 21 HOH HOH . D 4 HOH A 20 338 25 HOH HOH . D 4 HOH A 21 339 26 HOH HOH . D 4 HOH A 22 340 28 HOH HOH . D 4 HOH A 23 341 30 HOH HOH . D 4 HOH A 24 342 31 HOH HOH . D 4 HOH A 25 343 32 HOH HOH . D 4 HOH A 26 344 33 HOH HOH . D 4 HOH A 27 345 35 HOH HOH . D 4 HOH A 28 346 36 HOH HOH . D 4 HOH A 29 347 37 HOH HOH . D 4 HOH A 30 348 38 HOH HOH . D 4 HOH A 31 349 39 HOH HOH . D 4 HOH A 32 350 41 HOH HOH . D 4 HOH A 33 351 42 HOH HOH . D 4 HOH A 34 352 43 HOH HOH . D 4 HOH A 35 353 44 HOH HOH . D 4 HOH A 36 354 45 HOH HOH . D 4 HOH A 37 355 46 HOH HOH . D 4 HOH A 38 356 47 HOH HOH . D 4 HOH A 39 357 48 HOH HOH . D 4 HOH A 40 358 49 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 27.645 -33.814 -13.916 1 29.85 ? N1 UMP 317 A 1 HETATM 2 C C2 UMP . . . B 2 27.098 -32.765 -13.218 1 28.89 ? C2 UMP 317 A 1 HETATM 3 N N3 UMP . . . B 2 27.683 -32.253 -12.089 1 28.9 ? N3 UMP 317 A 1 HETATM 4 C C4 UMP . . . B 2 28.842 -32.807 -11.587 1 32.4 ? C4 UMP 317 A 1 HETATM 5 C C5 UMP . . . B 2 29.431 -33.89 -12.279 1 32.95 ? C5 UMP 317 A 1 HETATM 6 C C6 UMP . . . B 2 28.803 -34.386 -13.444 1 32.4 ? C6 UMP 317 A 1 HETATM 7 O O2 UMP . . . B 2 26.074 -32.228 -13.611 1 31.41 ? O2 UMP 317 A 1 HETATM 8 O O4 UMP . . . B 2 29.345 -32.312 -10.551 1 32.46 ? O4 UMP 317 A 1 HETATM 9 C C1' UMP . . . B 2 26.94 -34.337 -15.117 1 30.56 ? C1' UMP 317 A 1 HETATM 10 C C2' UMP . . . B 2 26.885 -33.467 -16.356 1 28.83 ? C2' UMP 317 A 1 HETATM 11 C C3' UMP . . . B 2 26.619 -34.502 -17.431 1 29.41 ? C3' UMP 317 A 1 HETATM 12 C C4' UMP . . . B 2 27.121 -35.825 -16.889 1 31.92 ? C4' UMP 317 A 1 HETATM 13 O O3' UMP . . . B 2 25.254 -34.713 -17.634 1 28.4 ? O3' UMP 317 A 1 HETATM 14 O O4' UMP . . . B 2 27.426 -35.604 -15.522 1 30.78 ? O4' UMP 317 A 1 HETATM 15 C C5' UMP . . . B 2 28.355 -36.306 -17.691 1 34.69 ? C5' UMP 317 A 1 HETATM 16 O O5' UMP . . . B 2 29.099 -35.197 -18.235 1 34.11 ? O5' UMP 317 A 1 HETATM 17 P P UMP . . . B 2 29.655 -35.092 -19.786 1 31.11 ? P UMP 317 A 1 HETATM 18 O OP1 UMP . . . B 2 31.144 -35.455 -19.767 1 28.28 ? OP1 UMP 317 A 1 HETATM 19 O OP2 UMP . . . B 2 28.962 -36 -20.779 1 29.4 ? OP2 UMP 317 A 1 HETATM 20 O OP3 UMP . . . B 2 29.46 -33.652 -20.185 1 32.21 ? OP3 UMP 317 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 257 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 20 #