data_4TO1 # _model_server_result.job_id COVw4ZNFJOIVlHpWSawOYQ _model_server_result.datetime_utc '2024-11-07 01:39:23' _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 4to1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":701}' # _entry.id 4TO1 # _exptl.entry_id 4TO1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 467.157 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 115.79 _cell.angle_gamma 90 _cell.entry_id 4TO1 _cell.length_a 86.204 _cell.length_b 141.586 _cell.length_c 98.187 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4TO1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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,N,O,P,Q,R,S,T,U,V,W,X _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 ? 2 E N N ? 2 I N N ? 2 K N N ? 2 O N N ? 2 R N N ? 2 S 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 F O3G DTP . A DTP 702 1_555 G MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.936 ? metalc ? metalc2 F O1B DTP . A DTP 702 1_555 G MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc3 G MG MG . A MG 703 1_555 P O2B GTP . C GTP 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc4 G MG MG . A MG 703 1_555 P O1A GTP . C GTP 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc5 G MG MG . A MG 703 1_555 P O3G GTP . C GTP 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.852 ? metalc ? metalc6 G MG MG . A MG 703 1_555 W O HOH . C HOH 808 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc7 H MG MG . A MG 704 1_555 U O HOH . A HOH 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc8 H MG MG . A MG 704 1_555 J O1B DTP . B DTP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc9 H MG MG . A MG 704 1_555 J O2G DTP . B DTP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.725 ? metalc ? metalc10 H MG MG . A MG 704 1_555 T O1G GTP . D GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.781 ? metalc ? metalc11 H MG MG . A MG 704 1_555 T O1B GTP . D GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc12 H MG MG . A MG 704 1_555 T O2A GTP . D GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc13 K O1B DCP . C DCP 701 1_555 L MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.849 ? metalc ? metalc14 K O2G DCP . C DCP 701 1_555 L MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc15 L MG MG . C MG 702 1_555 Q O3G GTP . D GTP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.916 ? metalc ? metalc16 L MG MG . C MG 702 1_555 Q O2B GTP . D GTP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.908 ? metalc ? metalc17 L MG MG . C MG 702 1_555 Q O1A GTP . D GTP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc18 L MG MG . C MG 702 1_555 X O HOH . D HOH 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc19 M MG MG . C MG 703 1_555 N O1G GTP . C GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.835 ? metalc ? metalc20 M MG MG . C MG 703 1_555 N O1A GTP . C GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc21 M MG MG . C MG 703 1_555 N O1B GTP . C GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc22 M MG MG . C MG 703 1_555 W O HOH . C HOH 821 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc23 M MG MG . C MG 703 1_555 R O2G DCP . D DCP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.922 ? metalc ? metalc24 M MG MG . C MG 703 1_555 R O1B DCP . D DCP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.867 ? # _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 4TO1 _atom_sites.fract_transf_matrix[1][1] 0.0116 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005605 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007063 _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] 0.011311 _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 DCP A 1 701 700 DCP DCP . F 3 DTP A 1 702 800 DTP DTP . G 4 MG A 1 703 850 MG MG . H 4 MG A 1 704 850 MG MG . I 2 DCP B 1 701 700 DCP DCP . J 3 DTP B 1 702 800 DTP DTP . K 2 DCP C 1 701 800 DCP DCP . L 4 MG C 1 702 850 MG MG . M 4 MG C 1 703 850 MG MG . N 5 GTP C 1 704 900 GTP GTP . O 2 DCP C 1 705 700 DCP DCP . P 5 GTP C 1 706 900 GTP GTP . Q 5 GTP D 1 701 900 GTP GTP . R 2 DCP D 1 702 800 DCP DCP . S 2 DCP D 1 703 700 DCP DCP . T 5 GTP D 1 704 900 GTP GTP . U 6 HOH A 1 801 11 HOH HOH . U 6 HOH A 2 802 18 HOH HOH . U 6 HOH A 3 803 22 HOH HOH . U 6 HOH A 4 804 31 HOH HOH . U 6 HOH A 5 805 32 HOH HOH . U 6 HOH A 6 806 44 HOH HOH . U 6 HOH A 7 807 46 HOH HOH . V 6 HOH B 1 801 15 HOH HOH . V 6 HOH B 2 802 34 HOH HOH . V 6 HOH B 3 803 38 HOH HOH . V 6 HOH B 4 804 48 HOH HOH . V 6 HOH B 5 805 51 HOH HOH . V 6 HOH B 6 806 52 HOH HOH . W 6 HOH C 1 801 25 HOH HOH . W 6 HOH C 2 802 1 HOH HOH . W 6 HOH C 3 803 3 HOH HOH . W 6 HOH C 4 804 4 HOH HOH . W 6 HOH C 5 805 9 HOH HOH . W 6 HOH C 6 806 10 HOH HOH . W 6 HOH C 7 807 12 HOH HOH . W 6 HOH C 8 808 14 HOH HOH . W 6 HOH C 9 809 17 HOH HOH . W 6 HOH C 10 810 19 HOH HOH . W 6 HOH C 11 811 20 HOH HOH . W 6 HOH C 12 812 21 HOH HOH . W 6 HOH C 13 813 27 HOH HOH . W 6 HOH C 14 814 33 HOH HOH . W 6 HOH C 15 815 47 HOH HOH . W 6 HOH C 16 816 49 HOH HOH . W 6 HOH C 17 817 50 HOH HOH . W 6 HOH C 18 818 53 HOH HOH . W 6 HOH C 19 819 54 HOH HOH . W 6 HOH C 20 820 58 HOH HOH . W 6 HOH C 21 821 59 HOH HOH . W 6 HOH C 22 822 60 HOH HOH . X 6 HOH D 1 801 55 HOH HOH . X 6 HOH D 2 802 56 HOH HOH . X 6 HOH D 3 803 57 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 DCP . . . E 2 -35.767 -11.055 120.28 1 45.12 ? N1 DCP 701 A 1 HETATM 2 C C2 DCP . . . E 2 -35.626 -12.419 120.571 1 43.71 ? C2 DCP 701 A 1 HETATM 3 N N3 DCP . . . E 2 -36.733 -13.176 120.751 1 43.46 ? N3 DCP 701 A 1 HETATM 4 C C4 DCP . . . E 2 -37.965 -12.637 120.661 1 41.35 ? C4 DCP 701 A 1 HETATM 5 C C5 DCP . . . E 2 -38.133 -11.293 120.371 1 42.42 ? C5 DCP 701 A 1 HETATM 6 C C6 DCP . . . E 2 -37.004 -10.506 120.177 1 43.7 ? C6 DCP 701 A 1 HETATM 7 O O2 DCP . . . E 2 -34.486 -12.913 120.669 1 46.11 ? O2 DCP 701 A 1 HETATM 8 N N4 DCP . . . E 2 -39.044 -13.411 120.849 1 43.77 ? N4 DCP 701 A 1 HETATM 9 C C1' DCP . . . E 2 -34.559 -10.238 120.074 1 44.54 ? C1' DCP 701 A 1 HETATM 10 C C2' DCP . . . E 2 -34.244 -10.135 118.599 1 40.47 ? C2' DCP 701 A 1 HETATM 11 C C3' DCP . . . E 2 -33.76 -8.733 118.434 1 40.58 ? C3' DCP 701 A 1 HETATM 12 C C4' DCP . . . E 2 -34.298 -7.945 119.601 1 43.57 ? C4' DCP 701 A 1 HETATM 13 O O4' DCP . . . E 2 -34.744 -8.904 120.545 1 45.54 ? O4' DCP 701 A 1 HETATM 14 O O3' DCP . . . E 2 -32.348 -8.767 118.461 1 38.08 ? O3' DCP 701 A 1 HETATM 15 C C5' DCP . . . E 2 -35.448 -7.019 119.196 1 52.92 ? C5' DCP 701 A 1 HETATM 16 O O5' DCP . . . E 2 -36.309 -6.773 120.318 1 62.34 ? O5' DCP 701 A 1 HETATM 17 P PA DCP . . . E 2 -35.987 -5.587 121.362 1 65.1 ? PA DCP 701 A 1 HETATM 18 O O1A DCP . . . E 2 -36.502 -5.982 122.707 1 61.33 ? O1A DCP 701 A 1 HETATM 19 O O2A DCP . . . E 2 -34.543 -5.148 121.179 1 58.33 ? O2A DCP 701 A 1 HETATM 20 O O3A DCP . . . E 2 -36.948 -4.39 120.832 1 70.53 ? O3A DCP 701 A 1 HETATM 21 P PB DCP . . . E 2 -38.465 -4.6 120.329 1 64.65 ? PB DCP 701 A 1 HETATM 22 O O1B DCP . . . E 2 -39.204 -5.497 121.283 1 63.61 ? O1B DCP 701 A 1 HETATM 23 O O2B DCP . . . E 2 -39.023 -3.221 120.03 1 75.52 ? O2B DCP 701 A 1 HETATM 24 O O3B DCP . . . E 2 -38.229 -5.384 118.93 1 67.96 ? O3B DCP 701 A 1 HETATM 25 P PG DCP . . . E 2 -39.022 -4.909 117.6 1 61.1 ? PG DCP 701 A 1 HETATM 26 O O1G DCP . . . E 2 -40.427 -5.463 117.784 1 64.46 ? O1G DCP 701 A 1 HETATM 27 O O2G DCP . . . E 2 -38.934 -3.403 117.675 1 60.69 ? O2G DCP 701 A 1 HETATM 28 O O3G DCP . . . E 2 -38.242 -5.53 116.485 1 59.16 ? O3G DCP 701 A 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 32 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #