data_4QZI # _model_server_result.job_id fJ7l7ZlFuE2u1mPPh7-lJw _model_server_result.datetime_utc '2024-11-27 22:07:21' _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 4qzi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":605}' # _entry.id 4QZI # _exptl.entry_id 4QZI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 451.158 _entity.id 7 _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 94.17 _cell.angle_gamma 90 _cell.entry_id 4QZI _cell.length_a 57.7 _cell.length_b 71.523 _cell.length_c 113.035 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4QZI _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,M _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 7 _struct_asym.id I _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 H NA NA . A NA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? metalc ? metalc2 A O VAL 145 A VAL 255 1_555 H NA NA . A NA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.757 ? metalc ? metalc3 A O VAL 148 A VAL 258 1_555 H NA NA . A NA 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc4 A OD2 ASP 233 A ASP 343 1_555 E ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.857 ? metalc ? metalc5 A OD1 ASP 233 A ASP 343 1_555 G MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc6 A OD1 ASP 235 A ASP 345 1_555 E ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.891 ? metalc ? metalc7 A OD2 ASP 235 A ASP 345 1_555 E ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.611 ? metalc ? metalc8 A OD2 ASP 235 A ASP 345 1_555 G MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.726 ? metalc ? metalc9 A OD2 ASP 324 A ASP 434 1_555 E ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc10 A OD2 ASP 363 A ASP 473 1_555 F ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc11 A ND1 HIS 365 A HIS 475 1_555 F ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.518 ? metalc ? metalc12 E ZN ZN . A ZN 601 1_555 D OP1 DC 6 U DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc13 G MG MG . A MG 603 1_555 I O2B DCT . A DCT 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc14 G MG MG . A MG 603 1_555 I O3G DCT . A DCT 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.89 ? metalc ? metalc15 G MG MG . A MG 603 1_555 J O HOH . A HOH 722 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc16 G MG MG . A MG 603 1_555 D OP1 DC 6 U DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.495 ? metalc ? metalc17 H NA NA . A NA 604 1_555 D OP1 DA 4 U DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 C N1 DG 6 T DG 6 1_555 D N3 DC 6 U DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 C N2 DG 6 T DG 6 1_555 D O2 DC 6 U DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 C O6 DG 6 T DG 6 1_555 D N4 DC 6 U DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_8_PAIR hydrog14 C N1 DG 7 T DG 7 1_555 D N1 DA 5 U DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_8_PAIR hydrog15 C O6 DG 7 T DG 7 1_555 D N6 DA 5 U DA 5 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 4QZI _atom_sites.fract_transf_matrix[1][1] 0.017331 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001264 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013982 _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] 0.00887 _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 ZN A 1 601 1 ZN ZN . F 4 ZN A 1 602 2 ZN ZN . G 5 MG A 1 603 3 MG MG . H 6 NA A 1 604 4 NA NA . I 7 DCT A 1 605 1 DCT DCT . J 8 HOH A 1 701 1 HOH HOH . J 8 HOH A 2 702 2 HOH HOH . J 8 HOH A 3 703 3 HOH HOH . J 8 HOH A 4 704 4 HOH HOH . J 8 HOH A 5 705 5 HOH HOH . J 8 HOH A 6 706 6 HOH HOH . J 8 HOH A 7 707 7 HOH HOH . J 8 HOH A 8 708 8 HOH HOH . J 8 HOH A 9 709 9 HOH HOH . J 8 HOH A 10 710 10 HOH HOH . J 8 HOH A 11 711 11 HOH HOH . J 8 HOH A 12 712 12 HOH HOH . J 8 HOH A 13 713 13 HOH HOH . J 8 HOH A 14 714 14 HOH HOH . J 8 HOH A 15 715 15 HOH HOH . J 8 HOH A 16 716 17 HOH HOH . J 8 HOH A 17 717 18 HOH HOH . J 8 HOH A 18 718 19 HOH HOH . J 8 HOH A 19 719 20 HOH HOH . J 8 HOH A 20 720 21 HOH HOH . J 8 HOH A 21 721 22 HOH HOH . J 8 HOH A 22 722 23 HOH HOH . J 8 HOH A 23 723 24 HOH HOH . J 8 HOH A 24 724 25 HOH HOH . J 8 HOH A 25 725 26 HOH HOH . J 8 HOH A 26 726 28 HOH HOH . J 8 HOH A 27 727 29 HOH HOH . J 8 HOH A 28 728 30 HOH HOH . J 8 HOH A 29 729 31 HOH HOH . J 8 HOH A 30 730 32 HOH HOH . J 8 HOH A 31 731 33 HOH HOH . J 8 HOH A 32 732 34 HOH HOH . J 8 HOH A 33 733 35 HOH HOH . J 8 HOH A 34 734 37 HOH HOH . J 8 HOH A 35 735 38 HOH HOH . J 8 HOH A 36 736 39 HOH HOH . J 8 HOH A 37 737 41 HOH HOH . J 8 HOH A 38 738 42 HOH HOH . J 8 HOH A 39 739 43 HOH HOH . J 8 HOH A 40 740 44 HOH HOH . J 8 HOH A 41 741 47 HOH HOH . J 8 HOH A 42 742 48 HOH HOH . J 8 HOH A 43 743 50 HOH HOH . J 8 HOH A 44 744 51 HOH HOH . J 8 HOH A 45 745 52 HOH HOH . J 8 HOH A 46 746 53 HOH HOH . J 8 HOH A 47 747 54 HOH HOH . J 8 HOH A 48 748 55 HOH HOH . J 8 HOH A 49 749 57 HOH HOH . J 8 HOH A 50 750 58 HOH HOH . J 8 HOH A 51 751 59 HOH HOH . J 8 HOH A 52 752 60 HOH HOH . J 8 HOH A 53 753 61 HOH HOH . J 8 HOH A 54 754 62 HOH HOH . J 8 HOH A 55 755 63 HOH HOH . J 8 HOH A 56 756 64 HOH HOH . J 8 HOH A 57 757 65 HOH HOH . J 8 HOH A 58 758 66 HOH HOH . J 8 HOH A 59 759 67 HOH HOH . J 8 HOH A 60 760 68 HOH HOH . J 8 HOH A 61 761 70 HOH HOH . K 8 HOH D 1 101 40 HOH HOH . K 8 HOH D 2 102 56 HOH HOH . L 8 HOH T 1 101 16 HOH HOH . L 8 HOH T 2 102 27 HOH HOH . L 8 HOH T 3 103 36 HOH HOH . L 8 HOH T 4 104 49 HOH HOH . L 8 HOH T 5 105 69 HOH HOH . M 8 HOH U 1 101 45 HOH HOH . M 8 HOH U 2 102 46 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 O O3A DCT . . . I 7 6.583 4.803 33.32 1 107.26 ? O3A DCT 605 A 1 HETATM 2 P PB DCT . . . I 7 6.569 3.342 33.546 1 106.73 ? PB DCT 605 A 1 HETATM 3 O O1B DCT . . . I 7 7.135 2.957 32.119 1 105.82 ? O1B DCT 605 A 1 HETATM 4 O O2B DCT . . . I 7 7.864 3.011 34.478 1 104.26 ? O2B DCT 605 A 1 HETATM 5 O O3B DCT . . . I 7 5.283 2.889 34.478 1 107.54 ? O3B DCT 605 A 1 HETATM 6 P PG DCT . . . I 7 4.373 3.869 35.474 1 106.53 ? PG DCT 605 A 1 HETATM 7 O O1G DCT . . . I 7 4.794 5.418 35.272 1 105.6 ? O1G DCT 605 A 1 HETATM 8 O O2G DCT . . . I 7 2.919 3.752 35.297 1 106.26 ? O2G DCT 605 A 1 HETATM 9 O O3G DCT . . . I 7 4.73 3.537 37.03 1 107.7 ? O3G DCT 605 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 9 #