data_5YUD # _model_server_result.job_id vXoM-03YF87YhVRpktmmoA _model_server_result.datetime_utc '2025-08-30 23:59:52' _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 5yud # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1501}' # _entry.id 5YUD # _exptl.entry_id 5YUD _exptl.method 'ELECTRON MICROSCOPY' # _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 90 _cell.angle_gamma 90 _cell.entry_id 5YUD _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YUD _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 5YUD _atom_sites.fract_transf_matrix[1][1] 0.003827 _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] 0.003827 _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] 0.003827 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 3 _pdbx_nonpoly_scheme.mon_id ATP _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 1501 _pdbx_nonpoly_scheme.auth_seq_num 355 _pdbx_nonpoly_scheme.pdb_mon_id ATP _pdbx_nonpoly_scheme.auth_mon_id ATP _pdbx_nonpoly_scheme.pdb_ins_code . # 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 . . . C 3 106.613 154.518 142.642 1 18.11 ? PG ATP 1501 A 1 HETATM 2 O O1G ATP . . . C 3 107.335 155.243 141.542 1 6.59 ? O1G ATP 1501 A 1 HETATM 3 O O2G ATP . . . C 3 107.283 153.268 143.15 1 15.57 -1 O2G ATP 1501 A 1 HETATM 4 O O3G ATP . . . C 3 105.133 154.355 142.423 1 17.95 ? O3G ATP 1501 A 1 HETATM 5 P PB ATP . . . C 3 105.598 155.204 144.987 1 22.96 ? PB ATP 1501 A 1 HETATM 6 O O1B ATP . . . C 3 104.239 155.502 144.42 1 13.08 -1 O1B ATP 1501 A 1 HETATM 7 O O2B ATP . . . C 3 106.007 155.805 146.3 1 19.59 ? O2B ATP 1501 A 1 HETATM 8 O O3B ATP . . . C 3 106.697 155.518 143.882 1 13.8 ? O3B ATP 1501 A 1 HETATM 9 P PA ATP . . . C 3 104.555 152.709 145.53 1 19.49 ? PA ATP 1501 A 1 HETATM 10 O O1A ATP . . . C 3 103.31 153.549 145.44 1 13.47 -1 O1A ATP 1501 A 1 HETATM 11 O O2A ATP . . . C 3 104.944 152.051 146.824 1 25 ? O2A ATP 1501 A 1 HETATM 12 O O3A ATP . . . C 3 105.771 153.614 145.033 1 21.72 ? O3A ATP 1501 A 1 HETATM 13 O O5' ATP . . . C 3 104.48 151.572 144.412 1 14.92 ? O5' ATP 1501 A 1 HETATM 14 C C5' ATP . . . C 3 104.331 150.235 144.86 1 58.54 ? C5' ATP 1501 A 1 HETATM 15 C C4' ATP . . . C 3 103.084 149.599 144.274 1 15.72 ? C4' ATP 1501 A 1 HETATM 16 O O4' ATP . . . C 3 103.173 148.178 144.357 1 30.04 ? O4' ATP 1501 A 1 HETATM 17 C C3' ATP . . . C 3 101.867 150.019 145.065 1 9.26 ? C3' ATP 1501 A 1 HETATM 18 O O3' ATP . . . C 3 101.001 150.779 144.224 1 33.78 ? O3' ATP 1501 A 1 HETATM 19 C C2' ATP . . . C 3 101.188 148.74 145.51 1 1 ? C2' ATP 1501 A 1 HETATM 20 O O2' ATP . . . C 3 99.879 148.651 144.952 1 48.53 ? O2' ATP 1501 A 1 HETATM 21 C C1' ATP . . . C 3 102.031 147.602 144.986 1 12.71 ? C1' ATP 1501 A 1 HETATM 22 N N9 ATP . . . C 3 102.532 146.808 146.124 1 19.15 ? N9 ATP 1501 A 1 HETATM 23 C C8 ATP . . . C 3 103.75 146.949 146.659 1 45.84 ? C8 ATP 1501 A 1 HETATM 24 N N7 ATP . . . C 3 103.946 146.089 147.684 1 35.77 ? N7 ATP 1501 A 1 HETATM 25 C C5 ATP . . . C 3 102.829 145.371 147.815 1 24 ? C5 ATP 1501 A 1 HETATM 26 C C6 ATP . . . C 3 102.374 144.297 148.711 1 26.67 ? C6 ATP 1501 A 1 HETATM 27 N N6 ATP . . . C 3 103.172 143.804 149.682 1 31.35 ? N6 ATP 1501 A 1 HETATM 28 N N1 ATP . . . C 3 101.133 143.826 148.519 1 19.73 ? N1 ATP 1501 A 1 HETATM 29 C C2 ATP . . . C 3 100.332 144.307 147.555 1 28.79 ? C2 ATP 1501 A 1 HETATM 30 N N3 ATP . . . C 3 100.68 145.285 146.705 1 18.18 ? N3 ATP 1501 A 1 HETATM 31 C C4 ATP . . . C 3 101.898 145.849 146.786 1 37.89 ? C4 ATP 1501 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 31 #