data_4XSD # _model_server_result.job_id kWHaREw2-BoM7z7X7JbugQ _model_server_result.datetime_utc '2024-11-13 14:13:04' _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 4xsd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1001}' # _entry.id 4XSD # _exptl.entry_id 4XSD _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 4 _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 4XSD _cell.length_a 150.17 _cell.length_b 150.17 _cell.length_c 89.16 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XSD _symmetry.cell_setting ? _symmetry.Int_Tables_number 145 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_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,E,F,I,J 1 1 C,D,G,H,K,L 2 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N 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 4XSD _atom_sites.fract_transf_matrix[1][1] 0.006659 _atom_sites.fract_transf_matrix[1][2] 0.003845 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007689 _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] 0.011216 _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 E 2 UMP A 1 1001 1001 UMP UMP . F 2 UMP B 1 1001 1001 UMP UMP . G 2 UMP C 1 1001 1001 UMP UMP . H 2 UMP D 1 1001 1001 UMP UMP . I 3 HOH A 1 1101 7 HOH HOH . I 3 HOH A 2 1102 8 HOH HOH . J 3 HOH B 1 1101 1 HOH HOH . J 3 HOH B 2 1102 2 HOH HOH . J 3 HOH B 3 1103 4 HOH HOH . J 3 HOH B 4 1104 3 HOH HOH . K 3 HOH C 1 1101 5 HOH HOH . K 3 HOH C 2 1102 6 HOH HOH . L 3 HOH D 1 1101 9 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 . . . E 2 2.054 72.558 -41.863 1 71.85 ? N1 UMP 1001 A 1 HETATM 2 C C2 UMP . . . E 2 0.676 72.859 -41.419 1 40.89 ? C2 UMP 1001 A 1 HETATM 3 N N3 UMP . . . E 2 -0.38 71.844 -41.61 1 43.59 ? N3 UMP 1001 A 1 HETATM 4 C C4 UMP . . . E 2 -0.078 70.584 -42.218 1 46.94 ? C4 UMP 1001 A 1 HETATM 5 C C5 UMP . . . E 2 1.282 70.3 -42.651 1 45.22 ? C5 UMP 1001 A 1 HETATM 6 C C6 UMP . . . E 2 2.33 71.306 -42.462 1 73.57 ? C6 UMP 1001 A 1 HETATM 7 O O2 UMP . . . E 2 0.387 73.903 -40.909 1 40.41 ? O2 UMP 1001 A 1 HETATM 8 O O4 UMP . . . E 2 -0.95 69.734 -42.382 1 41.63 ? O4 UMP 1001 A 1 HETATM 9 C C1' UMP . . . E 2 3.151 73.489 -41.713 1 67.58 ? C1' UMP 1001 A 1 HETATM 10 C C2' UMP . . . E 2 3.063 74.345 -40.397 1 36.35 ? C2' UMP 1001 A 1 HETATM 11 C C3' UMP . . . E 2 4.491 74.638 -40.072 1 62.95 ? C3' UMP 1001 A 1 HETATM 12 C C4' UMP . . . E 2 5.222 73.671 -40.641 1 69.18 ? C4' UMP 1001 A 1 HETATM 13 O O3' UMP . . . E 2 4.854 75.95 -40.703 1 56.46 ? O3' UMP 1001 A 1 HETATM 14 O O4' UMP . . . E 2 4.222 72.816 -41.564 1 82.62 ? O4' UMP 1001 A 1 HETATM 15 C C5' UMP . . . E 2 5.892 72.741 -39.634 1 57.41 ? C5' UMP 1001 A 1 HETATM 16 O O5' UMP . . . E 2 7.289 72.955 -39.697 1 37.52 ? O5' UMP 1001 A 1 HETATM 17 P P UMP . . . E 2 8.077 72.888 -38.344 1 42.76 ? P UMP 1001 A 1 HETATM 18 O OP1 UMP . . . E 2 9.53 73.234 -38.57 1 58.18 ? OP1 UMP 1001 A 1 HETATM 19 O OP2 UMP . . . E 2 7.472 73.911 -37.372 1 50.55 -1 OP2 UMP 1001 A 1 HETATM 20 O OP3 UMP . . . E 2 7.956 71.481 -37.769 1 56.09 1 OP3 UMP 1001 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #