data_8QXK # _model_server_result.job_id AForFWoHgmVSBDpBbHS2Kg _model_server_result.datetime_utc '2024-10-16 23:36:30' _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 8qxk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":707}' # _entry.id 8QXK # _exptl.entry_id 8QXK _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 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 8QXK _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8QXK _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_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,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 J N N ? 5 Q N N ? 5 Y N N ? 5 FA 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 A NE2 HIS 167 A HIS 167 1_555 F FE FE . A FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc2 A NE2 HIS 206 A HIS 206 1_555 F FE FE . A FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc3 A OD2 ASP 207 A ASP 207 1_555 F FE FE . A FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc4 A OD1 ASP 207 A ASP 207 1_555 G MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc5 A OD2 ASP 311 A ASP 311 1_555 F FE FE . A FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.78 ? metalc ? metalc6 E O3G GTP . A GTP 701 1_555 I MG MG . A MG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? metalc ? metalc7 E O1B GTP . A GTP 701 1_555 I MG MG . A MG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc8 G MG MG . A MG 703 1_555 J O2A DCP . A DCP 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.836 ? metalc ? metalc9 I MG MG . A MG 705 1_555 Z O1G DTP . D DTP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc10 I MG MG . A MG 705 1_555 Z O1B DTP . D DTP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc11 K O1G DTP . A DTP 707 1_555 EA MG MG . D MG 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc12 K O1B DTP . A DTP 707 1_555 EA MG MG . D MG 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc13 B NE2 HIS 167 C HIS 167 1_555 M FE FE . C FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc14 B NE2 HIS 206 C HIS 206 1_555 M FE FE . C FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc15 B OD2 ASP 207 C ASP 207 1_555 M FE FE . C FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc16 B OD1 ASP 207 C ASP 207 1_555 N MG MG . C MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.457 ? metalc ? metalc17 B OD2 ASP 311 C ASP 311 1_555 M FE FE . C FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.785 ? metalc ? metalc18 L O3G GTP . C GTP 701 1_555 P MG MG . C MG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.702 ? metalc ? metalc19 L O1B GTP . C GTP 701 1_555 P MG MG . C MG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.965 ? metalc ? metalc20 N MG MG . C MG 703 1_555 Q O1A DCP . C DCP 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.842 ? metalc ? metalc21 P MG MG . C MG 705 1_555 S O1G DTP . B DTP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc22 P MG MG . C MG 705 1_555 S O1B DTP . B DTP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc23 R O1G DTP . C DTP 707 1_555 X MG MG . B MG 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc24 R O1B DTP . C DTP 707 1_555 X MG MG . B MG 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc25 C NE2 HIS 167 B HIS 167 1_555 U FE FE . B FE 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc26 C NE2 HIS 206 B HIS 206 1_555 U FE FE . B FE 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc27 C OD1 ASP 207 B ASP 207 1_555 V MG MG . B MG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? metalc ? metalc28 C OD2 ASP 311 B ASP 311 1_555 U FE FE . B FE 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.781 ? metalc ? metalc29 T O3G GTP . B GTP 702 1_555 X MG MG . B MG 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.699 ? metalc ? metalc30 T O1B GTP . B GTP 702 1_555 X MG MG . B MG 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? metalc ? metalc31 V MG MG . B MG 704 1_555 Y O1A DCP . B DCP 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.854 ? metalc ? metalc32 D NE2 HIS 167 D HIS 167 1_555 BA FE FE . D FE 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc33 D NE2 HIS 206 D HIS 206 1_555 BA FE FE . D FE 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc34 D OD2 ASP 207 D ASP 207 1_555 BA FE FE . D FE 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc35 D OD1 ASP 207 D ASP 207 1_555 CA MG MG . D MG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? metalc ? metalc36 D OD2 ASP 311 D ASP 311 1_555 BA FE FE . D FE 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? metalc ? metalc37 AA O3G GTP . D GTP 702 1_555 EA MG MG . D MG 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.694 ? metalc ? metalc38 AA O1B GTP . D GTP 702 1_555 EA MG MG . D MG 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? # _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 83 n n N1 C6 DCP sing 84 n n N1 C1' DCP sing 85 n n C2 N3 DCP sing 86 n n C2 O2 DCP doub 87 n n N3 C4 DCP doub 88 n n C4 C5 DCP sing 89 n n C4 N4 DCP sing 90 n n C5 C6 DCP doub 91 n n C5 H5 DCP sing 92 n n C6 H6 DCP sing 93 n n N4 HN41 DCP sing 94 n n N4 HN42 DCP sing 95 n n C1' C2' DCP sing 96 n n C1' O4' DCP sing 97 n n C1' H1' DCP sing 98 n n C2' C3' DCP sing 99 n n C2' "H2'1" DCP sing 100 n n C2' "H2'2" DCP sing 101 n n C3' C4' DCP sing 102 n n C3' O3' DCP sing 103 n n C3' H3' DCP sing 104 n n C4' O4' DCP sing 105 n n C4' C5' DCP sing 106 n n C4' H4' DCP sing 107 n n O3' HO3' DCP sing 108 n n C5' O5' DCP sing 109 n n C5' "H5'1" DCP sing 110 n n C5' "H5'2" DCP sing 111 n n O5' PA DCP sing 112 n n PA O1A DCP doub 113 n n PA O2A DCP sing 114 n n PA O3A DCP sing 115 n n O2A HOA2 DCP sing 116 n n O3A PB DCP sing 117 n n PB O1B DCP doub 118 n n PB O2B DCP sing 119 n n PB O3B DCP sing 120 n n O2B HOB2 DCP sing 121 n n O3B PG DCP sing 122 n n PG O1G DCP doub 123 n n PG O2G DCP sing 124 n n PG O3G DCP sing 125 n n O2G HOG2 DCP sing 126 n n O3G HOG3 DCP sing 127 n n # _atom_sites.entry_id 8QXK _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 GTP A 1 701 702 GTP GTP . F 3 FE A 1 702 801 FE FE . G 4 MG A 1 703 802 MG MG . H 4 MG A 1 704 803 MG MG . I 4 MG A 1 705 804 MG MG . J 5 DCP A 1 706 805 DCP DCP . K 6 DTP A 1 707 703 DTP DTP . L 2 GTP C 1 701 702 GTP GTP . M 3 FE C 1 702 801 FE FE . N 4 MG C 1 703 802 MG MG . O 4 MG C 1 704 803 MG MG . P 4 MG C 1 705 804 MG MG . Q 5 DCP C 1 706 805 DCP DCP . R 6 DTP C 1 707 703 DTP DTP . S 6 DTP B 1 701 703 DTP DTP . T 2 GTP B 1 702 702 GTP GTP . U 3 FE B 1 703 801 FE FE . V 4 MG B 1 704 802 MG MG . W 4 MG B 1 705 803 MG MG . X 4 MG B 1 706 804 MG MG . Y 5 DCP B 1 707 805 DCP DCP . Z 6 DTP D 1 701 703 DTP DTP . AA 2 GTP D 1 702 702 GTP GTP . BA 3 FE D 1 703 801 FE FE . CA 4 MG D 1 704 802 MG MG . DA 4 MG D 1 705 803 MG MG . EA 4 MG D 1 706 804 MG MG . FA 5 DCP D 1 707 805 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 . . . Y 5 143.328 146.14 158.87 1 4.74 ? N1 DCP 707 B 1 HETATM 2 C C2 DCP . . . Y 5 142.764 145.978 160.119 1 4.74 ? C2 DCP 707 B 1 HETATM 3 N N3 DCP . . . Y 5 142.485 144.712 160.591 1 4.74 ? N3 DCP 707 B 1 HETATM 4 C C4 DCP . . . Y 5 142.557 143.635 159.735 1 4.74 ? C4 DCP 707 B 1 HETATM 5 C C5 DCP . . . Y 5 142.983 143.824 158.427 1 4.74 ? C5 DCP 707 B 1 HETATM 6 C C6 DCP . . . Y 5 143.498 145.058 158.055 1 4.74 ? C6 DCP 707 B 1 HETATM 7 O O2 DCP . . . Y 5 142.514 146.957 160.815 1 4.74 ? O2 DCP 707 B 1 HETATM 8 N N4 DCP . . . Y 5 142.219 142.421 160.157 1 4.74 ? N4 DCP 707 B 1 HETATM 9 C C1' DCP . . . Y 5 143.64 147.485 158.358 1 4.74 ? C1' DCP 707 B 1 HETATM 10 C C2' DCP . . . Y 5 145.137 147.732 158.448 1 4.74 ? C2' DCP 707 B 1 HETATM 11 C C3' DCP . . . Y 5 145.523 148.302 157.098 1 4.74 ? C3' DCP 707 B 1 HETATM 12 C C4' DCP . . . Y 5 144.297 148.137 156.205 1 4.74 ? C4' DCP 707 B 1 HETATM 13 O O4' DCP . . . Y 5 143.267 147.578 156.997 1 4.74 ? O4' DCP 707 B 1 HETATM 14 O O3' DCP . . . Y 5 145.885 149.655 157.245 1 4.74 ? O3' DCP 707 B 1 HETATM 15 C C5' DCP . . . Y 5 144.541 147.248 154.986 1 4.74 ? C5' DCP 707 B 1 HETATM 16 O O5' DCP . . . Y 5 144.005 147.868 153.836 1 4.74 ? O5' DCP 707 B 1 HETATM 17 P PA DCP . . . Y 5 143.018 147.099 152.817 1 4.74 ? PA DCP 707 B 1 HETATM 18 O O1A DCP . . . Y 5 143.313 147.527 151.401 1 4.74 ? O1A DCP 707 B 1 HETATM 19 O O2A DCP . . . Y 5 141.579 147.4 153.143 1 4.74 ? O2A DCP 707 B 1 HETATM 20 O O3A DCP . . . Y 5 143.298 145.522 153.007 1 4.74 ? O3A DCP 707 B 1 HETATM 21 P PB DCP . . . Y 5 144.24 144.679 152.008 1 4.74 ? PB DCP 707 B 1 HETATM 22 O O1B DCP . . . Y 5 144.719 145.529 150.858 1 4.74 ? O1B DCP 707 B 1 HETATM 23 O O2B DCP . . . Y 5 143.503 143.469 151.498 1 4.74 ? O2B DCP 707 B 1 HETATM 24 O O3B DCP . . . Y 5 145.499 144.236 152.904 1 4.74 ? O3B DCP 707 B 1 HETATM 25 P PG DCP . . . Y 5 146.607 143.229 152.31 1 4.74 ? PG DCP 707 B 1 HETATM 26 O O1G DCP . . . Y 5 146.021 142.522 151.113 1 4.74 ? O1G DCP 707 B 1 HETATM 27 O O2G DCP . . . Y 5 146.959 142.21 153.364 1 4.74 ? O2G DCP 707 B 1 HETATM 28 O O3G DCP . . . Y 5 147.847 143.988 151.907 1 4.74 ? O3G DCP 707 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #