data_3FCV # _model_server_result.job_id LbMaNWA6bjaebKAMNhOUFg _model_server_result.datetime_utc '2025-04-28 12:04:46' _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 3fcv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 3FCV # _exptl.entry_id 3FCV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 388.162 _entity.id 2 _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 120 _cell.entry_id 3FCV _cell.length_a 70.407 _cell.length_b 70.407 _cell.length_c 104.846 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3FCV _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 70.407 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 35.2035 60.974251 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E 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 83 n n N1 C6 DUD sing 84 n n N1 C1' DUD sing 85 n n C2 N3 DUD sing 86 n n C2 O2 DUD doub 87 n n N3 C4 DUD sing 88 n n N3 HN3 DUD sing 89 n n C4 C5 DUD sing 90 n n C4 O4 DUD doub 91 n n C5 C6 DUD doub 92 n n C5 H5 DUD sing 93 n n C6 H6 DUD sing 94 n n C1' C2' DUD sing 95 n n C1' O4' DUD sing 96 n n C1' H1' DUD sing 97 n n C2' C3' DUD sing 98 n n C2' "H2'1" DUD sing 99 n n C2' "H2'2" DUD sing 100 n n C3' C4' DUD sing 101 n n C3' O3' DUD sing 102 n n C3' H3' DUD sing 103 n n C4' O4' DUD sing 104 n n C4' C5' DUD sing 105 n n C4' H4' DUD sing 106 n n O3' HO3' DUD sing 107 n n C5' O5' DUD sing 108 n n C5' "H5'1" DUD sing 109 n n C5' "H5'2" DUD sing 110 n n O5' PA DUD sing 111 n n PA O1A DUD doub 112 n n PA O2A DUD sing 113 n n PA O3A DUD sing 114 n n O2A HOA2 DUD sing 115 n n O3A PB DUD sing 116 n n PB O1B DUD doub 117 n n PB O2B DUD sing 118 n n PB O3B DUD sing 119 n n O2B HOB2 DUD sing 120 n n O3B HOB3 DUD sing 121 n n # _atom_sites.entry_id 3FCV _atom_sites.fract_transf_matrix[1][1] 0.014203 _atom_sites.fract_transf_matrix[1][2] 0.0082 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.0164 _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] 0.009538 _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 DUD A 1 201 201 DUD DUD . D 3 MG A 1 202 202 MG MG . E 2 DUD B 1 201 201 DUD DUD . F 3 MG B 1 202 202 MG MG . G 4 HOH A 1 142 1 HOH HOH . G 4 HOH A 2 143 3 HOH HOH . G 4 HOH A 3 144 5 HOH HOH . G 4 HOH A 4 145 7 HOH HOH . G 4 HOH A 5 146 8 HOH HOH . G 4 HOH A 6 147 9 HOH HOH . G 4 HOH A 7 148 10 HOH HOH . G 4 HOH A 8 149 11 HOH HOH . G 4 HOH A 9 150 12 HOH HOH . G 4 HOH A 10 151 15 HOH HOH . G 4 HOH A 11 152 17 HOH HOH . G 4 HOH A 12 153 19 HOH HOH . G 4 HOH A 13 154 20 HOH HOH . G 4 HOH A 14 155 21 HOH HOH . G 4 HOH A 15 156 22 HOH HOH . G 4 HOH A 16 157 27 HOH HOH . G 4 HOH A 17 158 28 HOH HOH . G 4 HOH A 18 159 30 HOH HOH . G 4 HOH A 19 160 31 HOH HOH . G 4 HOH A 20 161 32 HOH HOH . G 4 HOH A 21 162 33 HOH HOH . G 4 HOH A 22 163 34 HOH HOH . G 4 HOH A 23 164 37 HOH HOH . G 4 HOH A 24 165 38 HOH HOH . G 4 HOH A 25 166 39 HOH HOH . G 4 HOH A 26 167 43 HOH HOH . G 4 HOH A 27 168 46 HOH HOH . G 4 HOH A 28 169 50 HOH HOH . G 4 HOH A 29 170 51 HOH HOH . G 4 HOH A 30 171 52 HOH HOH . G 4 HOH A 31 172 53 HOH HOH . G 4 HOH A 32 173 56 HOH HOH . G 4 HOH A 33 174 59 HOH HOH . G 4 HOH A 34 175 60 HOH HOH . G 4 HOH A 35 176 63 HOH HOH . G 4 HOH A 36 177 64 HOH HOH . G 4 HOH A 37 178 67 HOH HOH . G 4 HOH A 38 179 70 HOH HOH . G 4 HOH A 39 180 73 HOH HOH . G 4 HOH A 40 181 74 HOH HOH . G 4 HOH A 41 182 76 HOH HOH . G 4 HOH A 42 183 78 HOH HOH . G 4 HOH A 43 184 79 HOH HOH . G 4 HOH A 44 185 80 HOH HOH . G 4 HOH A 45 186 81 HOH HOH . G 4 HOH A 46 187 82 HOH HOH . G 4 HOH A 47 188 83 HOH HOH . G 4 HOH A 48 189 86 HOH HOH . G 4 HOH A 49 190 89 HOH HOH . G 4 HOH A 50 191 93 HOH HOH . G 4 HOH A 51 192 96 HOH HOH . G 4 HOH A 52 193 98 HOH HOH . G 4 HOH A 53 194 100 HOH HOH . G 4 HOH A 54 195 101 HOH HOH . G 4 HOH A 55 196 102 HOH HOH . G 4 HOH A 56 197 104 HOH HOH . G 4 HOH A 57 198 105 HOH HOH . G 4 HOH A 58 199 106 HOH HOH . G 4 HOH A 59 200 107 HOH HOH . G 4 HOH A 60 203 108 HOH HOH . H 4 HOH B 1 142 2 HOH HOH . H 4 HOH B 2 143 4 HOH HOH . H 4 HOH B 3 144 6 HOH HOH . H 4 HOH B 4 145 13 HOH HOH . H 4 HOH B 5 146 14 HOH HOH . H 4 HOH B 6 147 16 HOH HOH . H 4 HOH B 7 148 18 HOH HOH . H 4 HOH B 8 149 23 HOH HOH . H 4 HOH B 9 150 24 HOH HOH . H 4 HOH B 10 151 25 HOH HOH . H 4 HOH B 11 152 26 HOH HOH . H 4 HOH B 12 153 29 HOH HOH . H 4 HOH B 13 154 35 HOH HOH . H 4 HOH B 14 155 36 HOH HOH . H 4 HOH B 15 156 40 HOH HOH . H 4 HOH B 16 157 41 HOH HOH . H 4 HOH B 17 158 42 HOH HOH . H 4 HOH B 18 159 44 HOH HOH . H 4 HOH B 19 160 45 HOH HOH . H 4 HOH B 20 161 47 HOH HOH . H 4 HOH B 21 162 48 HOH HOH . H 4 HOH B 22 163 49 HOH HOH . H 4 HOH B 23 164 54 HOH HOH . H 4 HOH B 24 165 55 HOH HOH . H 4 HOH B 25 166 57 HOH HOH . H 4 HOH B 26 167 58 HOH HOH . H 4 HOH B 27 168 61 HOH HOH . H 4 HOH B 28 169 62 HOH HOH . H 4 HOH B 29 170 65 HOH HOH . H 4 HOH B 30 171 66 HOH HOH . H 4 HOH B 31 172 68 HOH HOH . H 4 HOH B 32 173 69 HOH HOH . H 4 HOH B 33 174 71 HOH HOH . H 4 HOH B 34 175 72 HOH HOH . H 4 HOH B 35 176 75 HOH HOH . H 4 HOH B 36 177 77 HOH HOH . H 4 HOH B 37 178 84 HOH HOH . H 4 HOH B 38 179 85 HOH HOH . H 4 HOH B 39 180 87 HOH HOH . H 4 HOH B 40 181 88 HOH HOH . H 4 HOH B 41 182 90 HOH HOH . H 4 HOH B 42 183 91 HOH HOH . H 4 HOH B 43 184 92 HOH HOH . H 4 HOH B 44 185 94 HOH HOH . H 4 HOH B 45 186 95 HOH HOH . H 4 HOH B 46 187 97 HOH HOH . H 4 HOH B 47 188 99 HOH HOH . H 4 HOH B 48 189 103 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 . . . E 2 53.452 33.655 -7.8 1 20.4 ? N1 DUD 201 B 1 HETATM 2 C C2 DUD . . . E 2 53.162 35.038 -7.762 1 19.57 ? C2 DUD 201 B 1 HETATM 3 N N3 DUD . . . E 2 52.611 35.629 -8.83 1 19.04 ? N3 DUD 201 B 1 HETATM 4 C C4 DUD . . . E 2 52.325 34.924 -9.934 1 19.97 ? C4 DUD 201 B 1 HETATM 5 C C5 DUD . . . E 2 52.596 33.562 -9.988 1 19.11 ? C5 DUD 201 B 1 HETATM 6 C C6 DUD . . . E 2 53.16 32.935 -8.888 1 19.04 ? C6 DUD 201 B 1 HETATM 7 O O2 DUD . . . E 2 53.424 35.71 -6.739 1 19.32 ? O2 DUD 201 B 1 HETATM 8 O O4 DUD . . . E 2 51.812 35.49 -10.925 1 20.04 ? O4 DUD 201 B 1 HETATM 9 C C1' DUD . . . E 2 54.042 32.959 -6.657 1 19.68 ? C1' DUD 201 B 1 HETATM 10 C C2' DUD . . . E 2 53.015 32.072 -5.966 1 18.39 ? C2' DUD 201 B 1 HETATM 11 C C3' DUD . . . E 2 53.555 30.661 -6.114 1 18 ? C3' DUD 201 B 1 HETATM 12 C C4' DUD . . . E 2 55.001 30.835 -6.549 1 18.69 ? C4' DUD 201 B 1 HETATM 13 O O4' DUD . . . E 2 55.064 32.111 -7.181 1 19.96 ? O4' DUD 201 B 1 HETATM 14 O O3' DUD . . . E 2 53.479 29.963 -4.868 1 17.27 ? O3' DUD 201 B 1 HETATM 15 C C5' DUD . . . E 2 55.428 29.769 -7.544 1 17.51 ? C5' DUD 201 B 1 HETATM 16 O O5' DUD . . . E 2 54.475 29.827 -8.603 1 18.54 ? O5' DUD 201 B 1 HETATM 17 P PA DUD . . . E 2 53.952 28.496 -9.336 1 16.83 ? PA DUD 201 B 1 HETATM 18 O O1A DUD . . . E 2 54.93 27.383 -9.054 1 17.85 ? O1A DUD 201 B 1 HETATM 19 O O2A DUD . . . E 2 53.602 28.861 -10.758 1 18.87 ? O2A DUD 201 B 1 HETATM 20 O O3A DUD . . . E 2 52.585 28.244 -8.516 1 19.7 ? O3A DUD 201 B 1 HETATM 21 P PB DUD . . . E 2 52.334 26.896 -7.666 1 16.19 ? PB DUD 201 B 1 HETATM 22 O O1B DUD . . . E 2 53.122 25.822 -8.376 1 18.2 ? O1B DUD 201 B 1 HETATM 23 O O2B DUD . . . E 2 50.843 26.685 -7.719 1 15.86 ? O2B DUD 201 B 1 HETATM 24 O O3B DUD . . . E 2 52.845 27.265 -6.294 1 17.47 ? O3B DUD 201 B 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 868 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 24 #