data_5DT4 # _model_server_result.job_id zU40K3ymA4ZgMz5RS1Evng _model_server_result.datetime_utc '2024-11-24 08:57:34' _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 5dt4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 5DT4 # _exptl.entry_id 5DT4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-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 90 _cell.angle_gamma 120 _cell.entry_id 5DT4 _cell.length_a 82.5 _cell.length_b 82.5 _cell.length_c 170.02 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DT4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 4 _struct_asym.id D _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 OD1 ASN 138 A ASN 261 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc2 A OD2 ASP 151 A ASP 274 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? metalc ? metalc3 B MG MG . A MG 401 1_555 D O1B ATP . A ATP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-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 ATP doub 102 n n PG O2G ATP sing 103 n n PG O3G ATP sing 104 n n PG O3B ATP sing 105 n n O2G HOG2 ATP sing 106 n n O3G HOG3 ATP sing 107 n n PB O1B ATP doub 108 n n PB O2B ATP sing 109 n n PB O3B ATP sing 110 n n PB O3A ATP sing 111 n n O2B HOB2 ATP sing 112 n n PA O1A ATP doub 113 n n PA O2A ATP sing 114 n n PA O3A ATP sing 115 n n PA O5' ATP sing 116 n n O2A HOA2 ATP sing 117 n n O5' C5' ATP sing 118 n n C5' C4' ATP sing 119 n n C5' "H5'1" ATP sing 120 n n C5' "H5'2" ATP sing 121 n n C4' O4' ATP sing 122 n n C4' C3' ATP sing 123 n n C4' H4' ATP sing 124 n n O4' C1' ATP sing 125 n n C3' O3' ATP sing 126 n n C3' C2' ATP sing 127 n n C3' H3' ATP sing 128 n n O3' HO3' ATP sing 129 n n C2' O2' ATP sing 130 n n C2' C1' ATP sing 131 n n C2' H2' ATP sing 132 n n O2' HO2' ATP sing 133 n n C1' N9 ATP sing 134 n n C1' H1' ATP sing 135 n n N9 C8 ATP sing 136 n y N9 C4 ATP sing 137 n y C8 N7 ATP doub 138 n y C8 H8 ATP sing 139 n n N7 C5 ATP sing 140 n y C5 C6 ATP sing 141 n y C5 C4 ATP doub 142 n y C6 N6 ATP sing 143 n n C6 N1 ATP doub 144 n y N6 HN61 ATP sing 145 n n N6 HN62 ATP sing 146 n n N1 C2 ATP sing 147 n y C2 N3 ATP doub 148 n y C2 H2 ATP sing 149 n n N3 C4 ATP sing 150 n y # _atom_sites.entry_id 5DT4 _atom_sites.fract_transf_matrix[1][1] 0.012121 _atom_sites.fract_transf_matrix[1][2] 0.006998 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013996 _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] 0.005882 _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 B 2 MG A 1 401 1 MG MG . C 3 5DN A 1 402 1 5DN 035 . D 4 ATP A 1 403 1 ATP ATP . # 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 ATP . . . D 4 -11.855 -22.847 5.89 1 150.38 ? PG ATP 403 A 1 HETATM 2 O O1G ATP . . . D 4 -11.593 -21.812 4.822 1 153.62 ? O1G ATP 403 A 1 HETATM 3 O O2G ATP . . . D 4 -12.97 -23.812 5.563 1 151.39 ? O2G ATP 403 A 1 HETATM 4 O O3G ATP . . . D 4 -11.9 -22.295 7.295 1 150.03 ? O3G ATP 403 A 1 HETATM 5 P PB ATP . . . D 4 -9.703 -23.979 4.512 1 122.04 ? PB ATP 403 A 1 HETATM 6 O O1B ATP . . . D 4 -10.487 -24.916 3.625 1 120.68 ? O1B ATP 403 A 1 HETATM 7 O O2B ATP . . . D 4 -9.285 -22.624 3.994 1 119.36 ? O2B ATP 403 A 1 HETATM 8 O O3B ATP . . . D 4 -10.532 -23.764 5.875 1 137.57 ? O3B ATP 403 A 1 HETATM 9 P PA ATP . . . D 4 -8.499 -26.221 5.671 1 108.35 ? PA ATP 403 A 1 HETATM 10 O O1A ATP . . . D 4 -9.766 -26.866 5.162 1 108.21 ? O1A ATP 403 A 1 HETATM 11 O O2A ATP . . . D 4 -8.26 -26.099 7.157 1 102.76 ? O2A ATP 403 A 1 HETATM 12 O O3A ATP . . . D 4 -8.385 -24.752 5.021 1 116.35 ? O3A ATP 403 A 1 HETATM 13 O O5' ATP . . . D 4 -7.244 -26.992 5.021 1 106.78 ? O5' ATP 403 A 1 HETATM 14 C C5' ATP . . . D 4 -6.668 -26.536 3.799 1 105.42 ? C5' ATP 403 A 1 HETATM 15 C C4' ATP . . . D 4 -5.957 -27.693 3.109 1 103.24 ? C4' ATP 403 A 1 HETATM 16 O O4' ATP . . . D 4 -4.717 -27.96 3.769 1 103.21 ? O4' ATP 403 A 1 HETATM 17 C C3' ATP . . . D 4 -6.793 -28.963 3.159 1 101.5 ? C3' ATP 403 A 1 HETATM 18 O O3' ATP . . . D 4 -7.081 -29.412 1.832 1 99.94 ? O3' ATP 403 A 1 HETATM 19 C C2' ATP . . . D 4 -5.956 -29.995 3.887 1 103.57 ? C2' ATP 403 A 1 HETATM 20 O O2' ATP . . . D 4 -5.7 -31.111 3.03 1 106.89 ? O2' ATP 403 A 1 HETATM 21 C C1' ATP . . . D 4 -4.649 -29.306 4.249 1 102.21 ? C1' ATP 403 A 1 HETATM 22 N N9 ATP . . . D 4 -4.476 -29.304 5.723 1 100.4 ? N9 ATP 403 A 1 HETATM 23 C C8 ATP . . . D 4 -5.099 -28.482 6.588 1 99.47 ? C8 ATP 403 A 1 HETATM 24 N N7 ATP . . . D 4 -4.722 -28.738 7.867 1 100.18 ? N7 ATP 403 A 1 HETATM 25 C C5 ATP . . . D 4 -3.835 -29.749 7.831 1 99.76 ? C5 ATP 403 A 1 HETATM 26 C C6 ATP . . . D 4 -3.044 -30.512 8.826 1 97.6 ? C6 ATP 403 A 1 HETATM 27 N N6 ATP . . . D 4 -3.13 -30.236 10.149 1 93.17 ? N6 ATP 403 A 1 HETATM 28 N N1 ATP . . . D 4 -2.234 -31.492 8.367 1 98.98 ? N1 ATP 403 A 1 HETATM 29 C C2 ATP . . . D 4 -2.139 -31.775 7.055 1 97.76 ? C2 ATP 403 A 1 HETATM 30 N N3 ATP . . . D 4 -2.826 -31.125 6.099 1 98.47 ? N3 ATP 403 A 1 HETATM 31 C C4 ATP . . . D 4 -3.676 -30.119 6.416 1 100.45 ? C4 ATP 403 A 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 343 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 31 #