data_9DO4 # _model_server_result.job_id j4phoauAcl6c7tNCbtC_Tw _model_server_result.datetime_utc '2024-12-23 16:19:07' _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 9do4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 9DO4 # _exptl.entry_id 9DO4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 3 _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 116.37 _cell.angle_gamma 90 _cell.entry_id 9DO4 _cell.length_a 104.197 _cell.length_b 40.114 _cell.length_c 107.032 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9DO4 _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 3 _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 ASP 293 B ASP 272 1_555 B MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? metalc ? metalc2 A OD2 ASP 293 B ASP 272 1_555 B MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc3 B MG MG . B MG 401 1_555 D O1B ATP . B ATP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.888 ? metalc ? metalc4 B MG MG . B MG 401 1_555 E O HOH . B HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc5 B MG MG . B MG 401 1_555 E O HOH . B HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc6 B MG MG . B MG 401 1_555 E O HOH . B HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc7 C MG MG . B MG 402 1_555 D O2A ATP . B ATP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.716 ? metalc ? metalc8 C MG MG . B MG 402 1_555 E O HOH . B HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc9 C MG MG . B MG 402 1_555 E O HOH . B HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc10 C MG MG . B MG 402 1_555 E O HOH . B HOH 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc11 C MG MG . B MG 402 1_555 E O HOH . B HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc12 C MG MG . B MG 402 1_555 E O HOH . B HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? # _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 70 n n PG O2G ATP sing 71 n n PG O3G ATP sing 72 n n PG O3B ATP sing 73 n n O2G HOG2 ATP sing 74 n n O3G HOG3 ATP sing 75 n n PB O1B ATP doub 76 n n PB O2B ATP sing 77 n n PB O3B ATP sing 78 n n PB O3A ATP sing 79 n n O2B HOB2 ATP sing 80 n n PA O1A ATP doub 81 n n PA O2A ATP sing 82 n n PA O3A ATP sing 83 n n PA O5' ATP sing 84 n n O2A HOA2 ATP sing 85 n n O5' C5' ATP sing 86 n n C5' C4' ATP sing 87 n n C5' "H5'1" ATP sing 88 n n C5' "H5'2" ATP sing 89 n n C4' O4' ATP sing 90 n n C4' C3' ATP sing 91 n n C4' H4' ATP sing 92 n n O4' C1' ATP sing 93 n n C3' O3' ATP sing 94 n n C3' C2' ATP sing 95 n n C3' H3' ATP sing 96 n n O3' HO3' ATP sing 97 n n C2' O2' ATP sing 98 n n C2' C1' ATP sing 99 n n C2' H2' ATP sing 100 n n O2' HO2' ATP sing 101 n n C1' N9 ATP sing 102 n n C1' H1' ATP sing 103 n n N9 C8 ATP sing 104 n y N9 C4 ATP sing 105 n y C8 N7 ATP doub 106 n y C8 H8 ATP sing 107 n n N7 C5 ATP sing 108 n y C5 C6 ATP sing 109 n y C5 C4 ATP doub 110 n y C6 N6 ATP sing 111 n n C6 N1 ATP doub 112 n y N6 HN61 ATP sing 113 n n N6 HN62 ATP sing 114 n n N1 C2 ATP sing 115 n y C2 N3 ATP doub 116 n y C2 H2 ATP sing 117 n n N3 C4 ATP sing 118 n y # _atom_sites.entry_id 9DO4 _atom_sites.fract_transf_matrix[1][1] 0.009597 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004757 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024929 _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] 0.010428 _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 B 1 401 401 MG MG . C 2 MG B 1 402 402 MG MG . D 3 ATP B 1 403 403 ATP ATP . E 4 HOH B 1 501 3 HOH HOH . E 4 HOH B 2 502 6 HOH HOH . E 4 HOH B 3 503 8 HOH HOH . E 4 HOH B 4 504 4 HOH HOH . E 4 HOH B 5 505 28 HOH HOH . E 4 HOH B 6 506 1 HOH HOH . E 4 HOH B 7 507 7 HOH HOH . E 4 HOH B 8 508 5 HOH HOH . E 4 HOH B 9 509 2 HOH HOH . E 4 HOH B 10 510 15 HOH HOH . E 4 HOH B 11 511 18 HOH HOH . E 4 HOH B 12 512 9 HOH HOH . E 4 HOH B 13 513 29 HOH HOH . E 4 HOH B 14 514 27 HOH HOH . E 4 HOH B 15 515 19 HOH HOH . E 4 HOH B 16 516 26 HOH HOH . E 4 HOH B 17 517 24 HOH HOH . E 4 HOH B 18 518 23 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 ATP . . . D 3 9.867 15.914 23.471 1 69.9 ? PG ATP 403 B 1 HETATM 2 O O1G ATP . . . D 3 9.941 16.887 22.318 1 55.86 ? O1G ATP 403 B 1 HETATM 3 O O2G ATP . . . D 3 11.006 16.082 24.443 1 60.51 -1 O2G ATP 403 B 1 HETATM 4 O O3G ATP . . . D 3 8.517 15.909 24.145 1 65.49 ? O3G ATP 403 B 1 HETATM 5 P PB ATP . . . D 3 9.156 13.556 21.862 1 68.48 ? PB ATP 403 B 1 HETATM 6 O O1B ATP . . . D 3 7.941 13.101 22.601 1 71.41 -1 O1B ATP 403 B 1 HETATM 7 O O2B ATP . . . D 3 10.027 12.555 21.178 1 65.63 ? O2B ATP 403 B 1 HETATM 8 O O3B ATP . . . D 3 10.059 14.442 22.842 1 62.98 ? O3B ATP 403 B 1 HETATM 9 P PA ATP . . . D 3 7.655 14.64 19.596 1 54 ? PA ATP 403 B 1 HETATM 10 O O1A ATP . . . D 3 6.301 14.907 20.158 1 52.86 -1 O1A ATP 403 B 1 HETATM 11 O O2A ATP . . . D 3 7.837 13.39 18.8 1 46.13 ? O2A ATP 403 B 1 HETATM 12 O O3A ATP . . . D 3 8.719 14.661 20.792 1 57.18 ? O3A ATP 403 B 1 HETATM 13 O O5' ATP . . . D 3 8.132 15.912 18.742 1 47.19 ? O5' ATP 403 B 1 HETATM 14 C C5' ATP . . . D 3 9.546 16.221 18.686 1 42.41 ? C5' ATP 403 B 1 HETATM 15 C C4' ATP . . . D 3 10.232 15.186 17.832 1 43.09 ? C4' ATP 403 B 1 HETATM 16 O O4' ATP . . . D 3 9.584 15.137 16.541 1 42.71 ? O4' ATP 403 B 1 HETATM 17 C C3' ATP . . . D 3 11.71 15.43 17.505 1 42.43 ? C3' ATP 403 B 1 HETATM 18 O O3' ATP . . . D 3 12.551 14.749 18.428 1 48.17 ? O3' ATP 403 B 1 HETATM 19 C C2' ATP . . . D 3 11.876 14.889 16.075 1 37.05 ? C2' ATP 403 B 1 HETATM 20 O O2' ATP . . . D 3 12.767 13.797 16.023 1 36.39 ? O2' ATP 403 B 1 HETATM 21 C C1' ATP . . . D 3 10.46 14.479 15.661 1 36.63 ? C1' ATP 403 B 1 HETATM 22 N N9 ATP . . . D 3 10.071 14.815 14.29 1 33.3 ? N9 ATP 403 B 1 HETATM 23 C C8 ATP . . . D 3 9.486 13.973 13.383 1 35.09 ? C8 ATP 403 B 1 HETATM 24 N N7 ATP . . . D 3 9.243 14.556 12.232 1 35.9 ? N7 ATP 403 B 1 HETATM 25 C C5 ATP . . . D 3 9.689 15.861 12.401 1 32.01 ? C5 ATP 403 B 1 HETATM 26 C C6 ATP . . . D 3 9.714 16.975 11.541 1 29.87 ? C6 ATP 403 B 1 HETATM 27 N N6 ATP . . . D 3 9.255 16.956 10.293 1 32.5 ? N6 ATP 403 B 1 HETATM 28 N N1 ATP . . . D 3 10.238 18.125 12.028 1 31.13 ? N1 ATP 403 B 1 HETATM 29 C C2 ATP . . . D 3 10.697 18.137 13.286 1 27.9 ? C2 ATP 403 B 1 HETATM 30 N N3 ATP . . . D 3 10.722 17.156 14.183 1 33.54 ? N3 ATP 403 B 1 HETATM 31 C C4 ATP . . . D 3 10.202 16.029 13.67 1 31.98 ? C4 ATP 403 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #