data_9IBX # _model_server_result.job_id pAzYZPz6B78gRsLhxk025Q _model_server_result.datetime_utc '2025-07-03 08:50:09' _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 9ibx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1301}' # _entry.id 9IBX # _exptl.entry_id 9IBX _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 467.157 _entity.id 6 _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 ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 9IBX _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9IBX _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 pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_and_software_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 x,y,z _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 6 _struct_asym.id G _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 metalc ? metalc1 A OD1 ASP 850 A ASP 868 1_555 F CA CA . A CA 1300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.539 ? metalc ? metalc2 A O VAL 851 A VAL 869 1_555 F CA CA . A CA 1300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc3 A OD1 ASP 1095 A ASP 1113 1_555 F CA CA . A CA 1300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.624 ? metalc ? metalc4 F CA CA . A CA 1300 1_555 G O1B DCP . A DCP 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? metalc ? metalc5 F CA CA . A CA 1300 1_555 G O1A DCP . A DCP 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc6 F CA CA . A CA 1300 1_555 G O2G DCP . A DCP 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? hydrog WATSON-CRICK hydrog1 D N1 DG 8 P DG 8 1_555 E N3 DC 33 T DC 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 D N2 DG 8 P DG 8 1_555 E O2 DC 33 T DC 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 D O6 DG 8 P DG 8 1_555 E N4 DC 33 T DC 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 D N3 DT 9 P DT 9 1_555 E N1 DA 32 T DA 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 D O4 DT 9 P DT 9 1_555 E N6 DA 32 T DA 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 D N3 DC 10 P DC 10 1_555 E N1 DG 31 T DG 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 D N4 DC 10 P DC 10 1_555 E O6 DG 31 T DG 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 D O2 DC 10 P DC 10 1_555 E N2 DG 31 T DG 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 D N1 DG 11 P DG 11 1_555 E N3 DC 30 T DC 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 D N2 DG 11 P DG 11 1_555 E O2 DC 30 T DC 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 D O6 DG 11 P DG 11 1_555 E N4 DC 30 T DC 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 D N1 DA 12 P DA 12 1_555 E N3 DT 29 T DT 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 D N6 DA 12 P DA 12 1_555 E O4 DT 29 T DT 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 D N1 DG 13 P DG 13 1_555 E N3 DC 28 T DC 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 D N2 DG 13 P DG 13 1_555 E O2 DC 28 T DC 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 D O6 DG 13 P DG 13 1_555 E N4 DC 28 T DC 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 D N3 DT 14 P DT 14 1_555 E N1 DA 27 T DA 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 D O4 DT 14 P DT 14 1_555 E N6 DA 27 T DA 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 D N3 DC 15 P DC 15 1_555 E N1 DG 26 T DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 D N4 DC 15 P DC 15 1_555 E O6 DG 26 T DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 D O2 DC 15 P DC 15 1_555 E N2 DG 26 T DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 D N3 DT 16 P DT 16 1_555 E N1 DA 25 T DA 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 D O4 DT 16 P DT 16 1_555 E N6 DA 25 T DA 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 D N1 DA 17 P DA 17 1_555 E N3 DT 24 T DT 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 D N6 DA 17 P DA 17 1_555 E O4 DT 24 T DT 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 D N1 DG 18 P DG 18 1_555 E N3 DC 23 T DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 D N2 DG 18 P DG 18 1_555 E O2 DC 23 T DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 D O6 DG 18 P DG 18 1_555 E N4 DC 23 T DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 D N1 DA 19 P DA 19 1_555 E N3 DT 22 T DT 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 D N6 DA 19 P DA 19 1_555 E O4 DT 22 T DT 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 D N1 DG 20 P DG 20 1_555 E N3 DC 21 T DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 D N2 DG 20 P DG 20 1_555 E O2 DC 21 T DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 D O6 DG 20 P DG 20 1_555 E N4 DC 21 T DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 D N1 DG 21 P DG 21 1_555 E N3 DC 20 T DC 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 D N2 DG 21 P DG 21 1_555 E O2 DC 20 T DC 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 D O6 DG 21 P DG 21 1_555 E N4 DC 20 T DC 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 D N1 DA 22 P DA 22 1_555 E N3 DT 19 T DT 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 D N6 DA 22 P DA 22 1_555 E O4 DT 19 T DT 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 D N1 DG 23 P DG 23 1_555 E N3 DC 18 T DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 D N2 DG 23 P DG 23 1_555 E O2 DC 18 T DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 D O6 DG 23 P DG 23 1_555 E N4 DC 18 T DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 D N3 DC 24 P DC 24 1_555 E N1 DG 17 T DG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 D N4 DC 24 P DC 24 1_555 E O6 DG 17 T DG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 D O2 DC 24 P DC 24 1_555 E N2 DG 17 T DG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_27_PAIR hydrog45 D N3 DT 25 P DT 25 1_555 E O6 DG 16 T DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_27_PAIR hydrog46 D O4 DT 25 P DT 25 1_555 E N1 DG 16 T DG 16 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 ? # 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 DCP sing 156 n n N1 C6 DCP sing 157 n n N1 C1' DCP sing 158 n n C2 N3 DCP sing 159 n n C2 O2 DCP doub 160 n n N3 C4 DCP doub 161 n n C4 C5 DCP sing 162 n n C4 N4 DCP sing 163 n n C5 C6 DCP doub 164 n n C5 H5 DCP sing 165 n n C6 H6 DCP sing 166 n n N4 HN41 DCP sing 167 n n N4 HN42 DCP sing 168 n n C1' C2' DCP sing 169 n n C1' O4' DCP sing 170 n n C1' H1' DCP sing 171 n n C2' C3' DCP sing 172 n n C2' "H2'1" DCP sing 173 n n C2' "H2'2" DCP sing 174 n n C3' C4' DCP sing 175 n n C3' O3' DCP sing 176 n n C3' H3' DCP sing 177 n n C4' O4' DCP sing 178 n n C4' C5' DCP sing 179 n n C4' H4' DCP sing 180 n n O3' HO3' DCP sing 181 n n C5' O5' DCP sing 182 n n C5' "H5'1" DCP sing 183 n n C5' "H5'2" DCP sing 184 n n O5' PA DCP sing 185 n n PA O1A DCP doub 186 n n PA O2A DCP sing 187 n n PA O3A DCP sing 188 n n O2A HOA2 DCP sing 189 n n O3A PB DCP sing 190 n n PB O1B DCP doub 191 n n PB O2B DCP sing 192 n n PB O3B DCP sing 193 n n O2B HOB2 DCP sing 194 n n O3B PG DCP sing 195 n n PG O1G DCP doub 196 n n PG O2G DCP sing 197 n n PG O3G DCP sing 198 n n O2G HOG2 DCP sing 199 n n O3G HOG3 DCP sing 200 n n # _atom_sites.entry_id 9IBX _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 CA A 1 1300 1300 CA CA . G 6 DCP A 1 1301 1301 DCP DCP . # 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 . . . G 6 144.038 131.919 99.261 1 134.96 ? N1 DCP 1301 A 1 HETATM 2 C C2 DCP . . . G 6 144.329 133.255 98.929 1 135.67 ? C2 DCP 1301 A 1 HETATM 3 N N3 DCP . . . G 6 144.905 134.071 99.833 1 130.43 ? N3 DCP 1301 A 1 HETATM 4 C C4 DCP . . . G 6 145.207 133.612 101.061 1 131.51 ? C4 DCP 1301 A 1 HETATM 5 C C5 DCP . . . G 6 144.928 132.298 101.403 1 131.9 ? C5 DCP 1301 A 1 HETATM 6 C C6 DCP . . . G 6 144.334 131.456 100.476 1 136.78 ? C6 DCP 1301 A 1 HETATM 7 O O2 DCP . . . G 6 144.052 133.686 97.792 1 137.31 ? O2 DCP 1301 A 1 HETATM 8 N N4 DCP . . . G 6 145.786 134.436 101.962 1 136.64 ? N4 DCP 1301 A 1 HETATM 9 C C1' DCP . . . G 6 143.415 131.043 98.271 1 135.69 ? C1' DCP 1301 A 1 HETATM 10 C C2' DCP . . . G 6 144.478 130.543 97.308 1 137.71 ? C2' DCP 1301 A 1 HETATM 11 C C3' DCP . . . G 6 144.612 129.066 97.614 1 136.57 ? C3' DCP 1301 A 1 HETATM 12 C C4' DCP . . . G 6 143.325 128.696 98.314 1 135.49 ? C4' DCP 1301 A 1 HETATM 13 O O4' DCP . . . G 6 142.845 129.9 98.909 1 137.88 ? O4' DCP 1301 A 1 HETATM 14 O O3' DCP . . . G 6 144.785 128.294 96.427 1 138.99 ? O3' DCP 1301 A 1 HETATM 15 C C5' DCP . . . G 6 143.573 127.63 99.365 1 137.53 ? C5' DCP 1301 A 1 HETATM 16 O O5' DCP . . . G 6 144.518 128.148 100.297 1 142.91 ? O5' DCP 1301 A 1 HETATM 17 P PA DCP . . . G 6 145.736 127.236 100.81 1 142.46 ? PA DCP 1301 A 1 HETATM 18 O O1A DCP . . . G 6 145.374 125.79 100.582 1 138.2 ? O1A DCP 1301 A 1 HETATM 19 O O2A DCP . . . G 6 146.122 127.715 102.186 1 137.65 ? O2A DCP 1301 A 1 HETATM 20 O O3A DCP . . . G 6 146.911 127.634 99.787 1 138.14 ? O3A DCP 1301 A 1 HETATM 21 P PB DCP . . . G 6 147.778 126.487 99.067 1 144.77 ? PB DCP 1301 A 1 HETATM 22 O O1B DCP . . . G 6 146.838 125.552 98.346 1 142.44 ? O1B DCP 1301 A 1 HETATM 23 O O2B DCP . . . G 6 148.906 127.156 98.322 1 138.73 ? O2B DCP 1301 A 1 HETATM 24 O O3B DCP . . . G 6 148.399 125.705 100.327 1 144.04 ? O3B DCP 1301 A 1 HETATM 25 P PG DCP . . . G 6 148.793 124.148 100.238 1 143.05 ? PG DCP 1301 A 1 HETATM 26 O O1G DCP . . . G 6 149.497 123.887 101.546 1 139.98 ? O1G DCP 1301 A 1 HETATM 27 O O2G DCP . . . G 6 147.464 123.447 100.088 1 137.83 ? O2G DCP 1301 A 1 HETATM 28 O O3G DCP . . . G 6 149.685 124.06 99.027 1 134.92 ? O3G DCP 1301 A 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 34 _model_server_stats.query_time_ms 599 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #