data_8I0I # _model_server_result.job_id vkd2F9fIAq5KWYCx-ASGPQ _model_server_result.datetime_utc '2024-10-11 06:17:43' _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 8i0i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":602}' # _entry.id 8I0I # _exptl.entry_id 8I0I _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 468.142 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "DEOXYURIDINE-5'-TRIPHOSPHATE" _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 90 _cell.entry_id 8I0I _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8I0I _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,I,J,K,L,M,N,O,P _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 ? _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 ? 3 F N N ? 3 I N N ? 3 L N N ? 3 O 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 F O2A DUT . A DUT 602 1_555 J MG MG . C MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc2 F O2G DUT . A DUT 602 1_555 J MG MG . C MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? metalc ? metalc3 G MG MG . A MG 603 1_555 I O2A DUT . C DUT 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc4 G MG MG . A MG 603 1_555 I O2G DUT . C DUT 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.804 ? metalc ? metalc5 L O1A DUT . D DUT 602 1_555 P MG MG . E MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc6 L O2G DUT . D DUT 602 1_555 P MG MG . E MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.758 ? metalc ? metalc7 M MG MG . D MG 603 1_555 O O2G DUT . E DUT 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.762 ? metalc ? metalc8 M MG MG . D MG 603 1_555 O O1A DUT . E DUT 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? # _chem_comp.formula 'C9 H15 N2 O14 P3' _chem_comp.formula_weight 468.142 _chem_comp.id DUT _chem_comp.mon_nstd_flag . _chem_comp.name "DEOXYURIDINE-5'-TRIPHOSPHATE" _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 DUT sing 131 n n N1 C6 DUT sing 132 n n N1 C1' DUT sing 133 n n C2 N3 DUT sing 134 n n C2 O2 DUT doub 135 n n N3 C4 DUT sing 136 n n N3 HN3 DUT sing 137 n n C4 C5 DUT sing 138 n n C4 O4 DUT doub 139 n n C5 C6 DUT doub 140 n n C5 H5 DUT sing 141 n n C6 H6 DUT sing 142 n n C1' C2' DUT sing 143 n n C1' O4' DUT sing 144 n n C1' H1' DUT sing 145 n n C2' C3' DUT sing 146 n n C2' "H2'1" DUT sing 147 n n C2' "H2'2" DUT sing 148 n n C3' C4' DUT sing 149 n n C3' O3' DUT sing 150 n n C3' H3' DUT sing 151 n n C4' O4' DUT sing 152 n n C4' C5' DUT sing 153 n n C4' H4' DUT sing 154 n n O3' HO3' DUT sing 155 n n C5' O5' DUT sing 156 n n C5' "H5'1" DUT sing 157 n n C5' "H5'2" DUT sing 158 n n O5' PA DUT sing 159 n n PA O1A DUT doub 160 n n PA O2A DUT sing 161 n n PA O3A DUT sing 162 n n O2A HOA2 DUT sing 163 n n O3A PB DUT sing 164 n n PB O1B DUT doub 165 n n PB O2B DUT sing 166 n n PB O3B DUT sing 167 n n O2B HOB2 DUT sing 168 n n O3B PG DUT sing 169 n n PG O1G DUT doub 170 n n PG O2G DUT sing 171 n n PG O3G DUT sing 172 n n O2G HOG2 DUT sing 173 n n O3G HOG3 DUT sing 174 n n # _atom_sites.entry_id 8I0I _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 DTP A 1 601 601 DTP DTP . F 3 DUT A 1 602 602 DUT DUT . G 4 MG A 1 603 1 MG MG . H 2 DTP C 1 601 601 DTP DTP . I 3 DUT C 1 602 602 DUT DUT . J 4 MG C 1 603 1 MG MG . K 2 DTP D 1 601 601 DTP DTP . L 3 DUT D 1 602 602 DUT DUT . M 4 MG D 1 603 1 MG MG . N 2 DTP E 1 601 601 DTP DTP . O 3 DUT E 1 602 602 DUT DUT . P 4 MG E 1 603 1 MG MG . # 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 DUT . . . O 3 149.435 134.368 117.428 1 44.14 ? N1 DUT 602 E 1 HETATM 2 C C2 DUT . . . O 3 150.243 135.617 117.51 1 44.14 ? C2 DUT 602 E 1 HETATM 3 N N3 DUT . . . O 3 149.791 136.846 116.777 1 44.14 ? N3 DUT 602 E 1 HETATM 4 C C4 DUT . . . O 3 148.568 136.812 115.991 1 44.14 ? C4 DUT 602 E 1 HETATM 5 C C5 DUT . . . O 3 147.773 135.558 115.919 1 44.14 ? C5 DUT 602 E 1 HETATM 6 C C6 DUT . . . O 3 148.221 134.347 116.643 1 44.14 ? C6 DUT 602 E 1 HETATM 7 O O2 DUT . . . O 3 151.237 135.635 118.151 1 44.14 ? O2 DUT 602 E 1 HETATM 8 O O4 DUT . . . O 3 148.198 137.782 115.412 1 44.14 ? O4 DUT 602 E 1 HETATM 9 C C1' DUT . . . O 3 149.865 133.202 118.128 1 44.14 ? C1' DUT 602 E 1 HETATM 10 C C2' DUT . . . O 3 149.284 133.163 119.317 1 44.14 ? C2' DUT 602 E 1 HETATM 11 C C3' DUT . . . O 3 148.216 132.077 119.206 1 44.14 ? C3' DUT 602 E 1 HETATM 12 C C4' DUT . . . O 3 148.846 131.08 118.163 1 44.14 ? C4' DUT 602 E 1 HETATM 13 O O4' DUT . . . O 3 149.423 131.849 117.311 1 44.14 ? O4' DUT 602 E 1 HETATM 14 O O3' DUT . . . O 3 148.035 131.471 120.382 1 44.14 ? O3' DUT 602 E 1 HETATM 15 C C5' DUT . . . O 3 147.738 130.285 117.464 1 44.14 ? C5' DUT 602 E 1 HETATM 16 O O5' DUT . . . O 3 146.99 131.129 116.641 1 44.14 ? O5' DUT 602 E 1 HETATM 17 P PA DUT . . . O 3 145.907 130.384 115.666 1 44.14 ? PA DUT 602 E 1 HETATM 18 O O1A DUT . . . O 3 146.565 129.993 114.369 1 44.14 ? O1A DUT 602 E 1 HETATM 19 O O2A DUT . . . O 3 144.739 131.292 115.394 1 44.14 ? O2A DUT 602 E 1 HETATM 20 O O3A DUT . . . O 3 145.372 129.019 116.443 1 44.14 ? O3A DUT 602 E 1 HETATM 21 P PB DUT . . . O 3 144.484 127.849 115.678 1 44.14 ? PB DUT 602 E 1 HETATM 22 O O1B DUT . . . O 3 145.317 127.194 114.603 1 44.14 ? O1B DUT 602 E 1 HETATM 23 O O2B DUT . . . O 3 144.017 126.818 116.669 1 44.14 ? O2B DUT 602 E 1 HETATM 24 O O3B DUT . . . O 3 143.18 128.586 114.963 1 44.14 ? O3B DUT 602 E 1 HETATM 25 P PG DUT . . . O 3 143.073 128.77 113.313 1 44.14 ? PG DUT 602 E 1 HETATM 26 O O1G DUT . . . O 3 142.771 127.426 112.699 1 44.14 ? O1G DUT 602 E 1 HETATM 27 O O2G DUT . . . O 3 144.389 129.285 112.781 1 44.14 ? O2G DUT 602 E 1 HETATM 28 O O3G DUT . . . O 3 141.975 129.747 112.986 1 44.14 ? O3G DUT 602 E 1 # _model_server_stats.io_time_ms 107 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #