data_3ELH # _model_server_result.job_id EXNOtjnZWg3jXyfF19z8rg _model_server_result.datetime_utc '2024-11-24 02:26:28' _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 3elh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":162}' # _entry.id 3ELH # _exptl.entry_id 3ELH _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 6 _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 3ELH _cell.length_a 80.717 _cell.length_b 153.576 _cell.length_c 185.795 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ELH _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? hexameric 6 author_defined_assembly 1 ? hexameric 6 author_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,E,G,H,K,L,O,P,S,U,W 1 1,2 B,D,F,I,J,M,N,Q,R,T,V,X 2 1,3 # 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' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 3 'crystal symmetry operation' 3_755 -x+2,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 161.434 0 92.8975 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 G N N ? 2 I N N ? 2 K N N ? 2 M N N ? 2 O N N ? 2 Q N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 G O3B DUD . A DUD 160 1_555 H MG MG . A MG 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc2 I O3B DUD . B DUD 161 1_555 J MG MG . B MG 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? metalc ? metalc3 K O3B DUD . C DUD 162 1_555 L MG MG . C MG 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc4 M O1A DUD . D DUD 163 1_555 N MG MG . D MG 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc5 O O1A DUD . E DUD 164 1_555 P MG MG . E MG 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc6 O O3B DUD . E DUD 164 1_555 P MG MG . E MG 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? metalc ? metalc7 Q O3B DUD . F DUD 165 1_555 R MG MG . F MG 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.456 ? # _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 3ELH _atom_sites.fract_transf_matrix[1][1] 0.012389 _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] 0.006511 _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] 0.005382 _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 G 2 DUD A 1 160 160 DUD DUD . H 3 MG A 1 161 160 MG MG . I 2 DUD B 1 161 161 DUD DUD . J 3 MG B 1 162 161 MG MG . K 2 DUD C 1 162 162 DUD DUD . L 3 MG C 1 163 162 MG MG . M 2 DUD D 1 163 163 DUD DUD . N 3 MG D 1 164 163 MG MG . O 2 DUD E 1 164 164 DUD DUD . P 3 MG E 1 165 164 MG MG . Q 2 DUD F 1 165 165 DUD DUD . R 3 MG F 1 166 165 MG MG . S 4 HOH A 1 162 3 HOH HOH . S 4 HOH A 2 163 5 HOH HOH . S 4 HOH A 3 164 7 HOH HOH . S 4 HOH A 4 165 15 HOH HOH . S 4 HOH A 5 166 25 HOH HOH . S 4 HOH A 6 167 28 HOH HOH . S 4 HOH A 7 168 29 HOH HOH . S 4 HOH A 8 169 32 HOH HOH . S 4 HOH A 9 170 33 HOH HOH . S 4 HOH A 10 171 36 HOH HOH . S 4 HOH A 11 172 39 HOH HOH . S 4 HOH A 12 173 60 HOH HOH . S 4 HOH A 13 174 61 HOH HOH . S 4 HOH A 14 175 86 HOH HOH . S 4 HOH A 15 176 97 HOH HOH . S 4 HOH A 16 177 102 HOH HOH . S 4 HOH A 17 178 104 HOH HOH . S 4 HOH A 18 179 118 HOH HOH . S 4 HOH A 19 180 120 HOH HOH . S 4 HOH A 20 181 121 HOH HOH . S 4 HOH A 21 182 133 HOH HOH . S 4 HOH A 22 183 134 HOH HOH . S 4 HOH A 23 184 135 HOH HOH . S 4 HOH A 24 185 152 HOH HOH . S 4 HOH A 25 186 155 HOH HOH . T 4 HOH B 1 163 30 HOH HOH . T 4 HOH B 2 164 34 HOH HOH . T 4 HOH B 3 165 42 HOH HOH . T 4 HOH B 4 166 44 HOH HOH . T 4 HOH B 5 167 45 HOH HOH . T 4 HOH B 6 168 47 HOH HOH . T 4 HOH B 7 169 65 HOH HOH . T 4 HOH B 8 170 68 HOH HOH . T 4 HOH B 9 171 76 HOH HOH . T 4 HOH B 10 172 87 HOH HOH . T 4 HOH B 11 173 92 HOH HOH . T 4 HOH B 12 174 96 HOH HOH . T 4 HOH B 13 175 99 HOH HOH . T 4 HOH B 14 176 105 HOH HOH . T 4 HOH B 15 177 125 HOH HOH . T 4 HOH B 16 178 132 HOH HOH . T 4 HOH B 17 179 141 HOH HOH . T 4 HOH B 18 180 147 HOH HOH . T 4 HOH B 19 181 153 HOH HOH . U 4 HOH C 1 164 4 HOH HOH . U 4 HOH C 2 165 6 HOH HOH . U 4 HOH C 3 166 8 HOH HOH . U 4 HOH C 4 167 9 HOH HOH . U 4 HOH C 5 168 10 HOH HOH . U 4 HOH C 6 169 11 HOH HOH . U 4 HOH C 7 170 12 HOH HOH . U 4 HOH C 8 171 14 HOH HOH . U 4 HOH C 9 172 18 HOH HOH . U 4 HOH C 10 173 22 HOH HOH . U 4 HOH C 11 174 23 HOH HOH . U 4 HOH C 12 175 26 HOH HOH . U 4 HOH C 13 176 27 HOH HOH . U 4 HOH C 14 177 31 HOH HOH . U 4 HOH C 15 178 48 HOH HOH . U 4 HOH C 16 179 49 HOH HOH . U 4 HOH C 17 180 51 HOH HOH . U 4 HOH C 18 181 54 HOH HOH . U 4 HOH C 19 182 58 HOH HOH . U 4 HOH C 20 183 64 HOH HOH . U 4 HOH C 21 184 74 HOH HOH . U 4 HOH C 22 185 78 HOH HOH . U 4 HOH C 23 186 88 HOH HOH . U 4 HOH C 24 187 95 HOH HOH . U 4 HOH C 25 188 106 HOH HOH . U 4 HOH C 26 189 107 HOH HOH . U 4 HOH C 27 190 108 HOH HOH . U 4 HOH C 28 191 109 HOH HOH . U 4 HOH C 29 192 110 HOH HOH . U 4 HOH C 30 193 112 HOH HOH . U 4 HOH C 31 194 113 HOH HOH . U 4 HOH C 32 195 119 HOH HOH . U 4 HOH C 33 196 123 HOH HOH . U 4 HOH C 34 197 126 HOH HOH . U 4 HOH C 35 198 128 HOH HOH . U 4 HOH C 36 199 136 HOH HOH . U 4 HOH C 37 200 137 HOH HOH . U 4 HOH C 38 201 151 HOH HOH . V 4 HOH D 1 165 17 HOH HOH . V 4 HOH D 2 166 20 HOH HOH . V 4 HOH D 3 167 35 HOH HOH . V 4 HOH D 4 168 40 HOH HOH . V 4 HOH D 5 169 46 HOH HOH . V 4 HOH D 6 170 55 HOH HOH . V 4 HOH D 7 171 57 HOH HOH . V 4 HOH D 8 172 59 HOH HOH . V 4 HOH D 9 173 62 HOH HOH . V 4 HOH D 10 174 63 HOH HOH . V 4 HOH D 11 175 66 HOH HOH . V 4 HOH D 12 176 69 HOH HOH . V 4 HOH D 13 177 80 HOH HOH . V 4 HOH D 14 178 81 HOH HOH . V 4 HOH D 15 179 89 HOH HOH . V 4 HOH D 16 180 90 HOH HOH . V 4 HOH D 17 181 91 HOH HOH . V 4 HOH D 18 182 103 HOH HOH . V 4 HOH D 19 183 115 HOH HOH . V 4 HOH D 20 184 116 HOH HOH . V 4 HOH D 21 185 127 HOH HOH . V 4 HOH D 22 186 129 HOH HOH . V 4 HOH D 23 187 130 HOH HOH . V 4 HOH D 24 188 138 HOH HOH . V 4 HOH D 25 189 139 HOH HOH . V 4 HOH D 26 190 140 HOH HOH . V 4 HOH D 27 191 142 HOH HOH . V 4 HOH D 28 192 146 HOH HOH . W 4 HOH E 1 166 1 HOH HOH . W 4 HOH E 2 167 16 HOH HOH . W 4 HOH E 3 168 21 HOH HOH . W 4 HOH E 4 169 38 HOH HOH . W 4 HOH E 5 170 41 HOH HOH . W 4 HOH E 6 171 50 HOH HOH . W 4 HOH E 7 172 52 HOH HOH . W 4 HOH E 8 173 53 HOH HOH . W 4 HOH E 9 174 56 HOH HOH . W 4 HOH E 10 175 73 HOH HOH . W 4 HOH E 11 176 75 HOH HOH . W 4 HOH E 12 177 77 HOH HOH . W 4 HOH E 13 178 79 HOH HOH . W 4 HOH E 14 179 82 HOH HOH . W 4 HOH E 15 180 84 HOH HOH . W 4 HOH E 16 181 85 HOH HOH . W 4 HOH E 17 182 93 HOH HOH . W 4 HOH E 18 183 100 HOH HOH . W 4 HOH E 19 184 101 HOH HOH . W 4 HOH E 20 185 111 HOH HOH . W 4 HOH E 21 186 131 HOH HOH . W 4 HOH E 22 187 149 HOH HOH . X 4 HOH F 1 167 2 HOH HOH . X 4 HOH F 2 168 13 HOH HOH . X 4 HOH F 3 169 19 HOH HOH . X 4 HOH F 4 170 24 HOH HOH . X 4 HOH F 5 171 37 HOH HOH . X 4 HOH F 6 172 43 HOH HOH . X 4 HOH F 7 173 67 HOH HOH . X 4 HOH F 8 174 70 HOH HOH . X 4 HOH F 9 175 71 HOH HOH . X 4 HOH F 10 176 72 HOH HOH . X 4 HOH F 11 177 83 HOH HOH . X 4 HOH F 12 178 94 HOH HOH . X 4 HOH F 13 179 98 HOH HOH . X 4 HOH F 14 180 114 HOH HOH . X 4 HOH F 15 181 117 HOH HOH . X 4 HOH F 16 182 122 HOH HOH . X 4 HOH F 17 183 124 HOH HOH . X 4 HOH F 18 184 150 HOH HOH . X 4 HOH F 19 185 154 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 . . . K 2 8.487 27.328 -12.73 1 47.97 ? N1 DUD 162 C 1 HETATM 2 C C2 DUD . . . K 2 9.765 27.382 -13.321 1 45.75 ? C2 DUD 162 C 1 HETATM 3 N N3 DUD . . . K 2 10.684 28.233 -12.852 1 50.18 ? N3 DUD 162 C 1 HETATM 4 C C4 DUD . . . K 2 10.417 29.034 -11.81 1 53.75 ? C4 DUD 162 C 1 HETATM 5 C C5 DUD . . . K 2 9.167 28.994 -11.195 1 47.81 ? C5 DUD 162 C 1 HETATM 6 C C6 DUD . . . K 2 8.208 28.109 -11.678 1 48.77 ? C6 DUD 162 C 1 HETATM 7 O O2 DUD . . . K 2 10.027 26.64 -14.294 1 42.83 ? O2 DUD 162 C 1 HETATM 8 O O4 DUD . . . K 2 11.296 29.825 -11.389 1 53.51 ? O4 DUD 162 C 1 HETATM 9 C C1' DUD . . . K 2 7.474 26.388 -13.224 1 47.39 ? C1' DUD 162 C 1 HETATM 10 C C2' DUD . . . K 2 7.291 25.235 -12.245 1 44.82 ? C2' DUD 162 C 1 HETATM 11 C C3' DUD . . . K 2 5.948 25.507 -11.595 1 43.86 ? C3' DUD 162 C 1 HETATM 12 C C4' DUD . . . K 2 5.221 26.365 -12.625 1 48.46 ? C4' DUD 162 C 1 HETATM 13 O O4' DUD . . . K 2 6.244 27.105 -13.3 1 45.87 ? O4' DUD 162 C 1 HETATM 14 O O3' DUD . . . K 2 5.24 24.297 -11.296 1 42.02 ? O3' DUD 162 C 1 HETATM 15 C C5' DUD . . . K 2 4.23 27.331 -11.97 1 48.45 ? C5' DUD 162 C 1 HETATM 16 O O5' DUD . . . K 2 4.974 28.059 -11 1 46.65 ? O5' DUD 162 C 1 HETATM 17 P PA DUD . . . K 2 4.434 28.272 -9.507 1 47.69 ? PA DUD 162 C 1 HETATM 18 O O1A DUD . . . K 2 2.972 28.654 -9.543 1 45.52 ? O1A DUD 162 C 1 HETATM 19 O O2A DUD . . . K 2 5.457 29.141 -8.806 1 44.27 ? O2A DUD 162 C 1 HETATM 20 O O3A DUD . . . K 2 4.605 26.807 -8.822 1 47.27 ? O3A DUD 162 C 1 HETATM 21 P PB DUD . . . K 2 3.373 25.849 -8.389 1 41.75 ? PB DUD 162 C 1 HETATM 22 O O1B DUD . . . K 2 3.93 25.194 -7.152 1 49.04 ? O1B DUD 162 C 1 HETATM 23 O O2B DUD . . . K 2 3.137 24.914 -9.563 1 43.18 ? O2B DUD 162 C 1 HETATM 24 O O3B DUD . . . K 2 2.238 26.795 -8.085 1 51.92 ? O3B DUD 162 C 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 42 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 1015 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 24 #