data_4QZG # _model_server_result.job_id jdPPz8dxJ_TxQIVaWpV7WA _model_server_result.datetime_utc '2024-11-24 03:48:17' _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 4qzg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":604}' # _entry.id 4QZG # _exptl.entry_id 4QZG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 451.158 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2',3'-DIDEOXYCYTIDINE 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 96.16 _cell.angle_gamma 90 _cell.entry_id 4QZG _cell.length_a 56.992 _cell.length_b 70.851 _cell.length_c 114.893 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4QZG _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,H,I,J,K,L _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 H _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 O THR 143 A THR 253 1_555 G NA NA . A NA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc2 A O VAL 145 A VAL 255 1_555 G NA NA . A NA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.897 ? metalc ? metalc3 A O VAL 148 A VAL 258 1_555 G NA NA . A NA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.859 ? metalc ? metalc4 A OD1 ASP 233 A ASP 343 1_555 E MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.901 ? metalc ? metalc5 A OD2 ASP 233 A ASP 343 1_555 F MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc6 A OD2 ASP 235 A ASP 345 1_555 E MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc7 A OD1 ASP 235 A ASP 345 1_555 F MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc8 A OD2 ASP 324 A ASP 434 1_555 F MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc9 E MG MG . A MG 601 1_555 H O2A DCT . A DCT 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc10 E MG MG . A MG 601 1_555 H O2B DCT . A DCT 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc11 E MG MG . A MG 601 1_555 H O2G DCT . A DCT 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? metalc ? metalc12 E MG MG . A MG 601 1_555 I O HOH . A HOH 715 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc13 F MG MG . A MG 602 1_555 H O2A DCT . A DCT 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.773 ? metalc ? metalc14 G NA NA . A NA 603 1_555 D OP1 DA 5 U DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? hydrog WATSON-CRICK hydrog1 B N1 DA 1 D DA 1 1_555 C N3 DT 5 T DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N6 DA 1 D DA 1 1_555 C O4 DT 5 T DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N1 DA 2 D DA 2 1_555 C N3 DT 4 T DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N6 DA 2 D DA 2 1_555 C O4 DT 4 T DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N1 DA 3 D DA 3 1_555 C N3 DT 3 T DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N6 DA 3 D DA 3 1_555 C O4 DT 3 T DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N1 DA 4 D DA 4 1_555 C N3 DT 2 T DT 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N6 DA 4 D DA 4 1_555 C O4 DT 2 T DT 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N1 DA 5 D DA 5 1_555 C N3 DT 1 T DT 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N6 DA 5 D DA 5 1_555 C O4 DT 1 T DT 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H16 N3 O12 P3' _chem_comp.formula_weight 451.158 _chem_comp.id DCT _chem_comp.mon_nstd_flag n _chem_comp.name "2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE" _chem_comp.type 'dna linking' _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 DCT sing 156 n n N1 C6 DCT sing 157 n n N1 C1' DCT sing 158 n n C2 N3 DCT sing 159 n n C2 O2 DCT doub 160 n n N3 C4 DCT doub 161 n n C4 C5 DCT sing 162 n n C4 N4 DCT sing 163 n n C5 C6 DCT doub 164 n n C5 H5 DCT sing 165 n n C6 H6 DCT sing 166 n n N4 HN41 DCT sing 167 n n N4 HN42 DCT sing 168 n n C1' C2' DCT sing 169 n n C1' O4' DCT sing 170 n n C1' H1' DCT sing 171 n n C2' C3' DCT sing 172 n n C2' H2' DCT sing 173 n n C2' "H2''" DCT sing 174 n n C3' C4' DCT sing 175 n n C3' "H3'1" DCT sing 176 n n C3' "H3'2" DCT sing 177 n n C4' O4' DCT sing 178 n n C4' C5' DCT sing 179 n n C4' H4' DCT sing 180 n n C5' O5' DCT sing 181 n n C5' H5' DCT sing 182 n n C5' "H5''" DCT sing 183 n n O5' PA DCT sing 184 n n PA O1A DCT doub 185 n n PA O2A DCT sing 186 n n PA O3A DCT sing 187 n n O2A HOA2 DCT sing 188 n n O3A PB DCT sing 189 n n PB O1B DCT doub 190 n n PB O2B DCT sing 191 n n PB O3B DCT sing 192 n n O2B HOB2 DCT sing 193 n n O3B PG DCT sing 194 n n PG O1G DCT doub 195 n n PG O2G DCT sing 196 n n PG O3G DCT sing 197 n n O2G HOG2 DCT sing 198 n n O3G HOG3 DCT sing 199 n n # _atom_sites.entry_id 4QZG _atom_sites.fract_transf_matrix[1][1] 0.017546 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001894 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014114 _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] 0.008754 _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 4 MG A 1 601 1 MG MG . F 4 MG A 1 602 2 MG MG . G 5 NA A 1 603 3 NA NA . H 6 DCT A 1 604 1 DCT DCT . I 7 HOH A 1 701 1 HOH HOH . I 7 HOH A 2 702 2 HOH HOH . I 7 HOH A 3 703 3 HOH HOH . I 7 HOH A 4 704 4 HOH HOH . I 7 HOH A 5 705 5 HOH HOH . I 7 HOH A 6 706 8 HOH HOH . I 7 HOH A 7 707 9 HOH HOH . I 7 HOH A 8 708 10 HOH HOH . I 7 HOH A 9 709 11 HOH HOH . I 7 HOH A 10 710 12 HOH HOH . I 7 HOH A 11 711 13 HOH HOH . I 7 HOH A 12 712 14 HOH HOH . I 7 HOH A 13 713 16 HOH HOH . I 7 HOH A 14 714 17 HOH HOH . I 7 HOH A 15 715 19 HOH HOH . I 7 HOH A 16 716 20 HOH HOH . I 7 HOH A 17 717 21 HOH HOH . I 7 HOH A 18 718 22 HOH HOH . I 7 HOH A 19 719 23 HOH HOH . I 7 HOH A 20 720 24 HOH HOH . I 7 HOH A 21 721 26 HOH HOH . I 7 HOH A 22 722 27 HOH HOH . I 7 HOH A 23 723 28 HOH HOH . I 7 HOH A 24 724 29 HOH HOH . I 7 HOH A 25 725 31 HOH HOH . I 7 HOH A 26 726 32 HOH HOH . I 7 HOH A 27 727 33 HOH HOH . I 7 HOH A 28 728 34 HOH HOH . I 7 HOH A 29 729 35 HOH HOH . I 7 HOH A 30 730 37 HOH HOH . I 7 HOH A 31 731 38 HOH HOH . I 7 HOH A 32 732 39 HOH HOH . I 7 HOH A 33 733 40 HOH HOH . I 7 HOH A 34 734 41 HOH HOH . I 7 HOH A 35 735 42 HOH HOH . I 7 HOH A 36 736 43 HOH HOH . J 7 HOH D 1 101 7 HOH HOH . K 7 HOH T 1 101 15 HOH HOH . K 7 HOH T 2 102 30 HOH HOH . K 7 HOH T 3 103 36 HOH HOH . L 7 HOH U 1 101 6 HOH HOH . L 7 HOH U 2 102 18 HOH HOH . L 7 HOH U 3 103 25 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 DCT . . . H 6 7.701 -1.605 30.937 1 54.47 ? N1 DCT 604 A 1 HETATM 2 C C2 DCT . . . H 6 7.621 -2.066 29.603 1 54.68 ? C2 DCT 604 A 1 HETATM 3 N N3 DCT . . . H 6 6.508 -2.797 29.2 1 51.94 ? N3 DCT 604 A 1 HETATM 4 C C4 DCT . . . H 6 5.517 -3.069 30.103 1 53.7 ? C4 DCT 604 A 1 HETATM 5 C C5 DCT . . . H 6 5.56 -2.624 31.469 1 53.78 ? C5 DCT 604 A 1 HETATM 6 C C6 DCT . . . H 6 6.643 -1.893 31.88 1 55.56 ? C6 DCT 604 A 1 HETATM 7 O O2 DCT . . . H 6 8.558 -1.781 28.822 1 54.83 ? O2 DCT 604 A 1 HETATM 8 N N4 DCT . . . H 6 4.453 -3.826 29.729 1 55.64 ? N4 DCT 604 A 1 HETATM 9 C C1' DCT . . . H 6 8.852 -0.842 31.293 1 47.52 ? C1' DCT 604 A 1 HETATM 10 C C2' DCT . . . H 6 8.805 0.485 30.67 1 43.64 ? C2' DCT 604 A 1 HETATM 11 C C3' DCT . . . H 6 7.997 1.23 31.7 1 44.66 ? C3' DCT 604 A 1 HETATM 12 C C4' DCT . . . H 6 8.79 0.775 32.94 1 47.49 ? C4' DCT 604 A 1 HETATM 13 O O4' DCT . . . H 6 9.016 -0.636 32.679 1 49.33 ? O4' DCT 604 A 1 HETATM 14 C C5' DCT . . . H 6 7.892 1.087 34.085 1 48.08 ? C5' DCT 604 A 1 HETATM 15 O O5' DCT . . . H 6 6.978 0.016 34.475 1 52.29 ? O5' DCT 604 A 1 HETATM 16 P PA DCT . . . H 6 5.522 0.65 34.837 1 53.96 ? PA DCT 604 A 1 HETATM 17 O O1A DCT . . . H 6 4.466 -0.515 34.622 1 56.15 ? O1A DCT 604 A 1 HETATM 18 O O2A DCT . . . H 6 5.462 1.129 36.273 1 57.44 ? O2A DCT 604 A 1 HETATM 19 O O3A DCT . . . H 6 5.472 1.881 33.876 1 52.82 ? O3A DCT 604 A 1 HETATM 20 P PB DCT . . . H 6 5.088 3.275 34.305 1 56.12 ? PB DCT 604 A 1 HETATM 21 O O1B DCT . . . H 6 5.76 4.23 33.336 1 51.27 ? O1B DCT 604 A 1 HETATM 22 O O2B DCT . . . H 6 6.082 3.55 35.483 1 57.73 ? O2B DCT 604 A 1 HETATM 23 O O3B DCT . . . H 6 3.629 3.794 34.717 1 59.26 ? O3B DCT 604 A 1 HETATM 24 P PG DCT . . . H 6 3.304 4.23 36.173 1 58.61 ? PG DCT 604 A 1 HETATM 25 O O1G DCT . . . H 6 1.742 4.188 36.117 1 61.23 ? O1G DCT 604 A 1 HETATM 26 O O2G DCT . . . H 6 3.965 3.315 37.145 1 55.17 ? O2G DCT 604 A 1 HETATM 27 O O3G DCT . . . H 6 3.826 5.794 36.362 1 61.22 ? O3G DCT 604 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #