data_8D3R # _model_server_result.job_id CyAEkBoWsF7gPDy7qxEN8A _model_server_result.datetime_utc '2024-10-19 03:51:26' _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 8d3r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1301}' # _entry.id 8D3R # _exptl.entry_id 8D3R _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 467.157 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 disulf ? disulf1 A SG CYS 418 A CYS 418 1_555 A SG CYS 1077 A CYS 1077 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc1 A OD1 ASP 1135 A ASP 1135 1_555 G CA CA . A CA 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.059 ? metalc ? metalc2 F O2A DCP . A DCP 1301 1_555 G CA CA . A CA 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? hydrog WATSON-CRICK hydrog1 D N1 DA 3 P DA 3 1_555 E N3 DT 26 T DT 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 D N6 DA 3 P DA 3 1_555 E O4 DT 26 T DT 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 D N1 DA 4 P DA 4 1_555 E N3 DT 25 T DT 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 D N6 DA 4 P DA 4 1_555 E O4 DT 25 T DT 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 D N1 DA 5 P DA 5 1_555 E N3 DT 24 T DT 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 D N6 DA 5 P DA 5 1_555 E O4 DT 24 T DT 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 D N1 DA 6 P DA 6 1_555 E N3 DT 23 T DT 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 D N6 DA 6 P DA 6 1_555 E O4 DT 23 T DT 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 D N3 DC 7 P DC 7 1_555 E N1 DG 22 T DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 D N4 DC 7 P DC 7 1_555 E O6 DG 22 T DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 D O2 DC 7 P DC 7 1_555 E N2 DG 22 T DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 D N1 DG 8 P DG 8 1_555 E N3 DC 21 T DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 D N2 DG 8 P DG 8 1_555 E O2 DC 21 T DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 D O6 DG 8 P DG 8 1_555 E N4 DC 21 T DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 D N1 DA 9 P DA 9 1_555 E N3 DT 20 T DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 D N6 DA 9 P DA 9 1_555 E O4 DT 20 T DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 D N3 DC 10 P DC 10 1_555 E N1 DG 19 T DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 D N4 DC 10 P DC 10 1_555 E O6 DG 19 T DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 D O2 DC 10 P DC 10 1_555 E N2 DG 19 T DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 D N1 DG 11 P DG 11 1_555 E N3 DC 18 T DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 D N2 DG 11 P DG 11 1_555 E O2 DC 18 T DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 D O6 DG 11 P DG 11 1_555 E N4 DC 18 T DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 D N1 DG 12 P DG 12 1_555 E N3 DC 17 T DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 D N2 DG 12 P DG 12 1_555 E O2 DC 17 T DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 D O6 DG 12 P DG 12 1_555 E N4 DC 17 T DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 D N3 DC 13 P DC 13 1_555 E N1 DG 16 T DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 D N4 DC 13 P DC 13 1_555 E O6 DG 16 T DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 D O2 DC 13 P DC 13 1_555 E N2 DG 16 T DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog29 D N4 DC 14 P DC 14 1_555 E O6 DG 15 T DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 D N1 DA 15 P DA 15 1_555 E N3 DT 14 T DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 D N6 DA 15 P DA 15 1_555 E O4 DT 14 T DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 D N1 DG 16 P DG 16 1_555 E N3 DC 13 T DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 D N2 DG 16 P DG 16 1_555 E O2 DC 13 T DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 D O6 DG 16 P DG 16 1_555 E N4 DC 13 T DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 D N3 DT 17 P DT 17 1_555 E N1 DA 12 T DA 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 D O4 DT 17 P DT 17 1_555 E N6 DA 12 T DA 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 D N1 DG 18 P DG 18 1_555 E N3 DC 11 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 D N2 DG 18 P DG 18 1_555 E O2 DC 11 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 D O6 DG 18 P DG 18 1_555 E N4 DC 11 T DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 D N3 DC 19 P DC 19 1_555 E N1 DG 10 T DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 D N4 DC 19 P DC 19 1_555 E O6 DG 10 T DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 D O2 DC 19 P DC 19 1_555 E N2 DG 10 T DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 D N3 DC 20 P DC 20 1_555 E N1 DG 9 T DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 D N4 DC 20 P DC 20 1_555 E O6 DG 9 T DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog45 D O2 DC 20 P DC 20 1_555 E N2 DG 9 T DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog46 D N1 DA 21 P DA 21 1_555 E N3 DT 8 T DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog47 D N6 DA 21 P DA 21 1_555 E O4 DT 8 T DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog48 D N6 DA 23 P DA 23 1_555 E O4 DT 6 T DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H16 N3 O13 P3' _chem_comp.formula_weight 467.157 _chem_comp.id DCP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 8D3R _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 F 5 DCP A 1 1301 4000 DCP DCP . G 6 CA A 1 1302 4002 CA CA . # 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 DCP . . . F 5 130.485 138.437 166.851 1 106.82 ? N1 DCP 1301 A 1 HETATM 2 C C2 DCP . . . F 5 130.701 139.638 167.611 1 107.58 ? C2 DCP 1301 A 1 HETATM 3 N N3 DCP . . . F 5 129.892 140.764 167.351 1 105.61 ? N3 DCP 1301 A 1 HETATM 4 C C4 DCP . . . F 5 128.96 140.647 166.397 1 108.98 ? C4 DCP 1301 A 1 HETATM 5 C C5 DCP . . . F 5 128.718 139.476 165.624 1 107.21 ? C5 DCP 1301 A 1 HETATM 6 C C6 DCP . . . F 5 129.504 138.385 165.878 1 103.81 ? C6 DCP 1301 A 1 HETATM 7 O O2 DCP . . . F 5 131.561 139.711 168.474 1 108.03 ? O2 DCP 1301 A 1 HETATM 8 N N4 DCP . . . F 5 128.182 141.776 166.169 1 107.12 ? N4 DCP 1301 A 1 HETATM 9 C C1' DCP . . . F 5 131.275 137.179 167.026 1 106.57 ? C1' DCP 1301 A 1 HETATM 10 C C2' DCP . . . F 5 131.341 136.511 168.42 1 108.13 ? C2' DCP 1301 A 1 HETATM 11 C C3' DCP . . . F 5 131.484 135.018 168.033 1 106.47 ? C3' DCP 1301 A 1 HETATM 12 C C4' DCP . . . F 5 131.632 135.091 166.491 1 105.87 ? C4' DCP 1301 A 1 HETATM 13 O O4' DCP . . . F 5 130.772 136.18 166.189 1 102.84 ? O4' DCP 1301 A 1 HETATM 14 O O3' DCP . . . F 5 132.598 134.464 168.661 1 106.57 ? O3' DCP 1301 A 1 HETATM 15 C C5' DCP . . . F 5 131.225 133.787 165.746 1 103.9 ? C5' DCP 1301 A 1 HETATM 16 O O5' DCP . . . F 5 129.982 133.45 166.044 1 102.69 ? O5' DCP 1301 A 1 HETATM 17 P PA DCP . . . F 5 129.049 132.241 165.084 1 107.35 ? PA DCP 1301 A 1 HETATM 18 O O1A DCP . . . F 5 128.269 133.081 164.117 1 105.49 ? O1A DCP 1301 A 1 HETATM 19 O O2A DCP . . . F 5 130.185 131.504 164.428 1 109.44 ? O2A DCP 1301 A 1 HETATM 20 O O3A DCP . . . F 5 128.458 131.603 166.341 1 113.62 ? O3A DCP 1301 A 1 HETATM 21 P PB DCP . . . F 5 128.855 130.243 167.298 1 120.71 ? PB DCP 1301 A 1 HETATM 22 O O1B DCP . . . F 5 130.27 130.51 167.708 1 103.35 ? O1B DCP 1301 A 1 HETATM 23 O O2B DCP . . . F 5 127.799 130.362 168.368 1 113.69 ? O2B DCP 1301 A 1 HETATM 24 O O3B DCP . . . F 5 128.446 129.237 166.191 1 111.56 ? O3B DCP 1301 A 1 HETATM 25 P PG DCP . . . F 5 127.006 128.816 165.499 1 109.66 ? PG DCP 1301 A 1 HETATM 26 O O1G DCP . . . F 5 126.866 129.734 164.292 1 103.14 ? O1G DCP 1301 A 1 HETATM 27 O O2G DCP . . . F 5 126.097 129.2 166.652 1 106.96 ? O2G DCP 1301 A 1 HETATM 28 O O3G DCP . . . F 5 127.09 127.332 165.184 1 102.23 ? O3G DCP 1301 A 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #