data_3CA9 # _model_server_result.job_id hbWNZNBSSkM4e3XaUdxUUA _model_server_result.datetime_utc '2024-12-04 04:54:53' _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 3ca9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":778}' # _entry.id 3CA9 # _exptl.entry_id 3CA9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 388.162 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "DEOXYURIDINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 90 _cell.entry_id 3CA9 _cell.length_a 105.647 _cell.length_b 105.647 _cell.length_c 105.647 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CA9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 3' # 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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 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,C,D,G 1 1,2,3 B,E,F,H 2 1,4,5 # 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' 7_555 -z+1/2,-x,y+1/2 0 0 -1 -1 0 0 0 1 0 52.8235 0 52.8235 3 'crystal symmetry operation' 10_545 -y,z-1/2,-x+1/2 0 -1 0 0 0 1 -1 0 0 0 -52.8235 52.8235 4 'crystal symmetry operation' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 5 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F N N # _chem_comp.formula 'C9 H14 N2 O11 P2' _chem_comp.formula_weight 388.162 _chem_comp.id DUD _chem_comp.mon_nstd_flag . _chem_comp.name "DEOXYURIDINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 DUD sing 70 n n N1 C6 DUD sing 71 n n N1 C1' DUD sing 72 n n C2 N3 DUD sing 73 n n C2 O2 DUD doub 74 n n N3 C4 DUD sing 75 n n N3 HN3 DUD sing 76 n n C4 C5 DUD sing 77 n n C4 O4 DUD doub 78 n n C5 C6 DUD doub 79 n n C5 H5 DUD sing 80 n n C6 H6 DUD sing 81 n n C1' C2' DUD sing 82 n n C1' O4' DUD sing 83 n n C1' H1' DUD sing 84 n n C2' C3' DUD sing 85 n n C2' "H2'1" DUD sing 86 n n C2' "H2'2" DUD sing 87 n n C3' C4' DUD sing 88 n n C3' O3' DUD sing 89 n n C3' H3' DUD sing 90 n n C4' O4' DUD sing 91 n n C4' C5' DUD sing 92 n n C4' H4' DUD sing 93 n n O3' HO3' DUD sing 94 n n C5' O5' DUD sing 95 n n C5' "H5'1" DUD sing 96 n n C5' "H5'2" DUD sing 97 n n O5' PA DUD sing 98 n n PA O1A DUD doub 99 n n PA O2A DUD sing 100 n n PA O3A DUD sing 101 n n O2A HOA2 DUD sing 102 n n O3A PB DUD sing 103 n n PB O1B DUD doub 104 n n PB O2B DUD sing 105 n n PB O3B DUD sing 106 n n O2B HOB2 DUD sing 107 n n O3B HOB3 DUD sing 108 n n # _atom_sites.entry_id 3CA9 _atom_sites.fract_transf_matrix[1][1] 0.009465 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009465 _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] 0.009465 _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 C 2 MG A 1 998 998 MG MG . D 3 DUD A 1 777 777 DUD DUD . E 2 MG B 1 999 999 MG MG . F 3 DUD B 1 778 778 DUD DUD . G 4 HOH A 1 999 1 HOH HOH . G 4 HOH A 2 1000 2 HOH HOH . G 4 HOH A 3 1001 4 HOH HOH . G 4 HOH A 4 1002 6 HOH HOH . G 4 HOH A 5 1003 7 HOH HOH . G 4 HOH A 6 1004 9 HOH HOH . G 4 HOH A 7 1005 11 HOH HOH . G 4 HOH A 8 1006 12 HOH HOH . G 4 HOH A 9 1007 14 HOH HOH . G 4 HOH A 10 1008 17 HOH HOH . G 4 HOH A 11 1009 18 HOH HOH . G 4 HOH A 12 1010 19 HOH HOH . H 4 HOH B 1 1000 3 HOH HOH . H 4 HOH B 2 1001 5 HOH HOH . H 4 HOH B 3 1002 8 HOH HOH . H 4 HOH B 4 1003 10 HOH HOH . H 4 HOH B 5 1004 13 HOH HOH . H 4 HOH B 6 1005 15 HOH HOH . H 4 HOH B 7 1006 16 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 DUD . . . F 3 16.166 24.576 36.067 1 23.02 ? N1 DUD 778 B 1 HETATM 2 C C2 DUD . . . F 3 16.337 23.236 36.242 1 21.2 ? C2 DUD 778 B 1 HETATM 3 N N3 DUD . . . F 3 16.707 22.454 35.189 1 22.19 ? N3 DUD 778 B 1 HETATM 4 C C4 DUD . . . F 3 16.915 22.988 33.94 1 21.84 ? C4 DUD 778 B 1 HETATM 5 C C5 DUD . . . F 3 16.741 24.379 33.729 1 22.56 ? C5 DUD 778 B 1 HETATM 6 C C6 DUD . . . F 3 16.37 25.148 34.792 1 23.33 ? C6 DUD 778 B 1 HETATM 7 O O2 DUD . . . F 3 16.168 22.726 37.317 1 19.76 ? O2 DUD 778 B 1 HETATM 8 O O4 DUD . . . F 3 17.249 22.276 33.016 1 22 ? O4 DUD 778 B 1 HETATM 9 C C1' DUD . . . F 3 15.769 25.45 37.195 1 23.24 ? C1' DUD 778 B 1 HETATM 10 C C2' DUD . . . F 3 16.904 26.459 37.516 1 24.56 ? C2' DUD 778 B 1 HETATM 11 C C3' DUD . . . F 3 16.232 27.836 37.56 1 25.43 ? C3' DUD 778 B 1 HETATM 12 C C4' DUD . . . F 3 14.751 27.562 37.307 1 27.06 ? C4' DUD 778 B 1 HETATM 13 O O4' DUD . . . F 3 14.605 26.215 36.819 1 24.32 ? O4' DUD 778 B 1 HETATM 14 O O3' DUD . . . F 3 16.417 28.444 38.821 1 28.92 ? O3' DUD 778 B 1 HETATM 15 C C5' DUD . . . F 3 14.232 28.541 36.297 1 31.81 ? C5' DUD 778 B 1 HETATM 16 O O5' DUD . . . F 3 12.873 28.255 35.992 1 38.03 ? O5' DUD 778 B 1 HETATM 17 P PA DUD . . . F 3 12.227 29.667 35.608 1 41.84 ? PA DUD 778 B 1 HETATM 18 O O1A DUD . . . F 3 13.222 30.597 34.995 1 41.59 ? O1A DUD 778 B 1 HETATM 19 O O2A DUD . . . F 3 11.68 30.309 36.978 1 44.75 ? O2A DUD 778 B 1 HETATM 20 O O3A DUD . . . F 3 10.986 29.42 34.621 1 45.19 ? O3A DUD 778 B 1 HETATM 21 P PB DUD . . . F 3 11.427 29.898 33.133 1 50.33 ? PB DUD 778 B 1 HETATM 22 O O1B DUD . . . F 3 12.612 29.107 32.682 1 49.53 ? O1B DUD 778 B 1 HETATM 23 O O2B DUD . . . F 3 10.193 29.652 32.119 1 50.23 ? O2B DUD 778 B 1 HETATM 24 O O3B DUD . . . F 3 11.817 31.473 33.122 1 50.29 ? O3B DUD 778 B 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 231 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 24 #