data_4TO1 # _model_server_result.job_id jUKabVHrWmc0EtsVZUDlqA _model_server_result.datetime_utc '2024-11-28 18:17:40' _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":"F","auth_seq_id":702}' # _entry.id 4TO1 # _exptl.entry_id 4TO1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 491.182 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYADENOSINE 5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 ? 3 F N N ? 3 J 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 'C10 H16 N5 O12 P3' _chem_comp.formula_weight 491.182 _chem_comp.id DTP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYADENOSINE 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 PG O1G DTP doub 128 n n PG O2G DTP sing 129 n n PG O3G DTP sing 130 n n PG O3B DTP sing 131 n n O2G HOG2 DTP sing 132 n n O3G HOG3 DTP sing 133 n n PB O1B DTP doub 134 n n PB O2B DTP sing 135 n n PB O3B DTP sing 136 n n PB O3A DTP sing 137 n n O2B HOB2 DTP sing 138 n n PA O1A DTP doub 139 n n PA O2A DTP sing 140 n n PA O3A DTP sing 141 n n PA O5' DTP sing 142 n n O2A HOA2 DTP sing 143 n n O5' C5' DTP sing 144 n n C5' C4' DTP sing 145 n n C5' "H5'1" DTP sing 146 n n C5' "H5'2" DTP sing 147 n n C4' O4' DTP sing 148 n n C4' C3' DTP sing 149 n n C4' H4' DTP sing 150 n n O4' C1' DTP sing 151 n n C3' O3' DTP sing 152 n n C3' C2' DTP sing 153 n n C3' H3' DTP sing 154 n n O3' HO3' DTP sing 155 n n C2' C1' DTP sing 156 n n C2' "H2'1" DTP sing 157 n n C2' "H2'2" DTP sing 158 n n C1' N9 DTP sing 159 n n C1' H1' DTP sing 160 n n N9 C8 DTP sing 161 n y N9 C4 DTP sing 162 n y C8 N7 DTP doub 163 n y C8 H8 DTP sing 164 n n N7 C5 DTP sing 165 n y C5 C6 DTP sing 166 n y C5 C4 DTP doub 167 n y C6 N6 DTP sing 168 n n C6 N1 DTP doub 169 n y N6 HN61 DTP sing 170 n n N6 HN62 DTP sing 171 n n N1 C2 DTP sing 172 n y C2 N3 DTP doub 173 n y C2 H2 DTP sing 174 n n N3 C4 DTP sing 175 n y # _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 P PG DTP . . . F 3 -33.489 9.441 91.301 1 23.14 ? PG DTP 702 A 1 HETATM 2 O O1G DTP . . . F 3 -34.96 9.263 91.071 1 21.06 ? O1G DTP 702 A 1 HETATM 3 O O2G DTP . . . F 3 -33.226 9.843 92.717 1 21.09 ? O2G DTP 702 A 1 HETATM 4 O O3G DTP . . . F 3 -32.644 10.206 90.329 1 20.35 ? O3G DTP 702 A 1 HETATM 5 P PB DTP . . . F 3 -31.687 7.299 90.599 1 19.55 ? PB DTP 702 A 1 HETATM 6 O O1B DTP . . . F 3 -30.825 8.348 90 1 19.06 ? O1B DTP 702 A 1 HETATM 7 O O2B DTP . . . F 3 -32.012 6.161 89.642 1 20.7 ? O2B DTP 702 A 1 HETATM 8 O O3B DTP . . . F 3 -32.989 7.892 91.263 1 21.11 ? O3B DTP 702 A 1 HETATM 9 P PA DTP . . . F 3 -31.113 5.428 92.673 1 18.25 ? PA DTP 702 A 1 HETATM 10 O O1A DTP . . . F 3 -31.386 5.595 94.153 1 15.98 ? O1A DTP 702 A 1 HETATM 11 O O2A DTP . . . F 3 -32.012 4.491 91.921 1 20.15 ? O2A DTP 702 A 1 HETATM 12 O O3A DTP . . . F 3 -30.938 6.804 91.914 1 18.7 ? O3A DTP 702 A 1 HETATM 13 O O5' DTP . . . F 3 -29.671 4.82 92.435 1 20.47 ? O5' DTP 702 A 1 HETATM 14 C C5' DTP . . . F 3 -28.509 5.299 93.11 1 19.47 ? C5' DTP 702 A 1 HETATM 15 C C4' DTP . . . F 3 -27.525 4.165 93.378 1 19.43 ? C4' DTP 702 A 1 HETATM 16 O O4' DTP . . . F 3 -28.128 3.203 94.198 1 19.46 ? O4' DTP 702 A 1 HETATM 17 C C3' DTP . . . F 3 -27.069 3.396 92.161 1 20.31 ? C3' DTP 702 A 1 HETATM 18 O O3' DTP . . . F 3 -25.674 2.987 92.312 1 20.26 ? O3' DTP 702 A 1 HETATM 19 C C2' DTP . . . F 3 -28.023 2.206 92.059 1 21.15 ? C2' DTP 702 A 1 HETATM 20 C C1' DTP . . . F 3 -28.239 1.939 93.523 1 22.49 ? C1' DTP 702 A 1 HETATM 21 N N9 DTP . . . F 3 -29.544 1.467 93.954 1 26.03 ? N9 DTP 702 A 1 HETATM 22 C C8 DTP . . . F 3 -30.751 1.796 93.44 1 28.01 ? C8 DTP 702 A 1 HETATM 23 N N7 DTP . . . F 3 -31.785 1.219 94.146 1 28.05 ? N7 DTP 702 A 1 HETATM 24 C C5 DTP . . . F 3 -31.211 0.545 95.12 1 28.4 ? C5 DTP 702 A 1 HETATM 25 C C6 DTP . . . F 3 -31.75 -0.239 96.186 1 36.96 ? C6 DTP 702 A 1 HETATM 26 N N6 DTP . . . F 3 -33.119 -0.329 96.203 1 37.76 ? N6 DTP 702 A 1 HETATM 27 N N1 DTP . . . F 3 -30.831 -0.842 97.047 1 42.9 ? N1 DTP 702 A 1 HETATM 28 C C2 DTP . . . F 3 -29.477 -0.639 96.858 1 39.71 ? C2 DTP 702 A 1 HETATM 29 N N3 DTP . . . F 3 -28.916 0.111 95.86 1 28.34 ? N3 DTP 702 A 1 HETATM 30 C C4 DTP . . . F 3 -29.739 0.695 95.007 1 26.98 ? C4 DTP 702 A 1 # _model_server_stats.io_time_ms 47 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 428 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 30 #