data_3CYI # _model_server_result.job_id bmAEByqcszAdYRDs5Px2qg _model_server_result.datetime_utc '2025-01-24 23:04:18' _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 3cyi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1}' # _entry.id 3CYI # _exptl.entry_id 3CYI _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 90 _cell.angle_gamma 120 _cell.entry_id 3CYI _cell.length_a 68.53 _cell.length_b 68.53 _cell.length_c 51.09 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CYI _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _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 3 _struct_asym.id C _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 C O1A ATP . A ATP 1 1_555 B MG MG . A MG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc2 C O1G ATP . A ATP 1 1_555 B MG MG . A MG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc3 C O2B ATP . A ATP 1 1_555 B MG MG . A MG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc4 B MG MG . A MG 2 1_555 D O HOH . A HOH 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc5 B MG MG . A MG 2 1_555 D O HOH . A HOH 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc6 B MG MG . A MG 2 1_555 D O HOH . A HOH 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? # _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 3CYI _atom_sites.fract_transf_matrix[1][1] 0.014592 _atom_sites.fract_transf_matrix[1][2] 0.008425 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01685 _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] 0.019573 _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 2 2 MG MG . C 3 ATP A 1 1 1 ATP ATP . D 4 HOH A 1 138 1 HOH HOH . D 4 HOH A 2 139 2 HOH HOH . D 4 HOH A 3 140 3 HOH HOH . D 4 HOH A 4 141 4 HOH HOH . D 4 HOH A 5 142 5 HOH HOH . D 4 HOH A 6 143 6 HOH HOH . D 4 HOH A 7 144 7 HOH HOH . D 4 HOH A 8 145 8 HOH HOH . D 4 HOH A 9 146 9 HOH HOH . D 4 HOH A 10 147 10 HOH HOH . D 4 HOH A 11 148 11 HOH HOH . D 4 HOH A 12 149 12 HOH HOH . D 4 HOH A 13 150 13 HOH HOH . D 4 HOH A 14 151 14 HOH HOH . D 4 HOH A 15 152 15 HOH HOH . D 4 HOH A 16 153 16 HOH HOH . D 4 HOH A 17 154 17 HOH HOH . D 4 HOH A 18 155 18 HOH HOH . D 4 HOH A 19 156 19 HOH HOH . D 4 HOH A 20 157 20 HOH HOH . D 4 HOH A 21 158 21 HOH HOH . D 4 HOH A 22 159 22 HOH HOH . D 4 HOH A 23 160 23 HOH HOH . D 4 HOH A 24 161 24 HOH HOH . D 4 HOH A 25 162 25 HOH HOH . D 4 HOH A 26 163 26 HOH HOH . D 4 HOH A 27 164 27 HOH HOH . D 4 HOH A 28 165 28 HOH HOH . D 4 HOH A 29 166 29 HOH HOH . D 4 HOH A 30 167 30 HOH HOH . D 4 HOH A 31 168 31 HOH HOH . D 4 HOH A 32 169 32 HOH HOH . D 4 HOH A 33 170 33 HOH HOH . D 4 HOH A 34 171 34 HOH HOH . D 4 HOH A 35 172 35 HOH HOH . D 4 HOH A 36 173 36 HOH HOH . D 4 HOH A 37 174 37 HOH HOH . D 4 HOH A 38 175 38 HOH HOH . D 4 HOH A 39 176 39 HOH HOH . D 4 HOH A 40 177 40 HOH HOH . D 4 HOH A 41 178 41 HOH HOH . D 4 HOH A 42 179 42 HOH HOH . D 4 HOH A 43 180 43 HOH HOH . D 4 HOH A 44 181 44 HOH HOH . D 4 HOH A 45 182 45 HOH HOH . D 4 HOH A 46 183 46 HOH HOH . D 4 HOH A 47 184 47 HOH HOH . D 4 HOH A 48 185 48 HOH HOH . D 4 HOH A 49 186 49 HOH HOH . D 4 HOH A 50 187 50 HOH HOH . D 4 HOH A 51 188 51 HOH HOH . D 4 HOH A 52 189 52 HOH HOH . D 4 HOH A 53 190 53 HOH HOH . D 4 HOH A 54 191 54 HOH HOH . D 4 HOH A 55 192 55 HOH HOH . D 4 HOH A 56 193 56 HOH HOH . D 4 HOH A 57 194 57 HOH HOH . D 4 HOH A 58 195 58 HOH HOH . D 4 HOH A 59 196 59 HOH HOH . D 4 HOH A 60 197 60 HOH HOH . D 4 HOH A 61 198 61 HOH HOH . D 4 HOH A 62 199 62 HOH HOH . D 4 HOH A 63 200 63 HOH HOH . D 4 HOH A 64 201 64 HOH HOH . D 4 HOH A 65 202 65 HOH HOH . D 4 HOH A 66 203 66 HOH HOH . D 4 HOH A 67 204 67 HOH HOH . D 4 HOH A 68 205 68 HOH HOH . D 4 HOH A 69 206 69 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 . . . C 3 21.63 -8.33 -1.683 1 33.55 ? PG ATP 1 A 1 HETATM 2 O O1G ATP . . . C 3 21.369 -8.782 -3.089 1 32.45 ? O1G ATP 1 A 1 HETATM 3 O O2G ATP . . . C 3 22.666 -9.155 -0.949 1 31.47 ? O2G ATP 1 A 1 HETATM 4 O O3G ATP . . . C 3 21.886 -6.814 -1.684 1 30.31 ? O3G ATP 1 A 1 HETATM 5 P PB ATP . . . C 3 19.004 -9.319 -1.261 1 28.71 ? PB ATP 1 A 1 HETATM 6 O O1B ATP . . . C 3 18.072 -9.438 -0.087 1 26.16 ? O1B ATP 1 A 1 HETATM 7 O O2B ATP . . . C 3 19.505 -10.578 -1.954 1 28.67 ? O2B ATP 1 A 1 HETATM 8 O O3B ATP . . . C 3 20.22 -8.386 -0.867 1 28.04 ? O3B ATP 1 A 1 HETATM 9 P PA ATP . . . C 3 17.797 -8.97 -3.838 1 35.67 ? PA ATP 1 A 1 HETATM 10 O O1A ATP . . . C 3 18.899 -9.749 -4.498 1 35.97 ? O1A ATP 1 A 1 HETATM 11 O O2A ATP . . . C 3 17.219 -7.762 -4.534 1 36.1 ? O2A ATP 1 A 1 HETATM 12 O O3A ATP . . . C 3 18.245 -8.444 -2.374 1 29.91 ? O3A ATP 1 A 1 HETATM 13 O O5' ATP . . . C 3 16.647 -10.042 -3.494 1 37.51 ? O5' ATP 1 A 1 HETATM 14 C C5' ATP . . . C 3 15.413 -9.69 -2.9 1 37.19 ? C5' ATP 1 A 1 HETATM 15 C C4' ATP . . . C 3 14.343 -10.73 -3.223 1 36.84 ? C4' ATP 1 A 1 HETATM 16 O O4' ATP . . . C 3 13.135 -10.32 -2.566 1 37.23 ? O4' ATP 1 A 1 HETATM 17 C C3' ATP . . . C 3 14.018 -10.757 -4.721 1 37.38 ? C3' ATP 1 A 1 HETATM 18 O O3' ATP . . . C 3 13.604 -12.094 -5.064 1 35.53 ? O3' ATP 1 A 1 HETATM 19 C C2' ATP . . . C 3 12.837 -9.82 -4.881 1 38.56 ? C2' ATP 1 A 1 HETATM 20 O O2' ATP . . . C 3 11.951 -10.258 -5.932 1 37.3 ? O2' ATP 1 A 1 HETATM 21 C C1' ATP . . . C 3 12.134 -10.018 -3.556 1 38.51 ? C1' ATP 1 A 1 HETATM 22 N N9 ATP . . . C 3 11.333 -8.901 -3.05 1 38.42 ? N9 ATP 1 A 1 HETATM 23 C C8 ATP . . . C 3 10.065 -9.038 -2.629 1 39.99 ? C8 ATP 1 A 1 HETATM 24 N N7 ATP . . . C 3 9.583 -7.864 -2.174 1 38.35 ? N7 ATP 1 A 1 HETATM 25 C C5 ATP . . . C 3 10.556 -6.951 -2.333 1 39.47 ? C5 ATP 1 A 1 HETATM 26 C C6 ATP . . . C 3 10.69 -5.512 -2.043 1 38.53 ? C6 ATP 1 A 1 HETATM 27 N N6 ATP . . . C 3 9.652 -4.847 -1.509 1 39.09 ? N6 ATP 1 A 1 HETATM 28 N N1 ATP . . . C 3 11.862 -4.909 -2.347 1 39.35 ? N1 ATP 1 A 1 HETATM 29 C C2 ATP . . . C 3 12.898 -5.599 -2.865 1 39.06 ? C2 ATP 1 A 1 HETATM 30 N N3 ATP . . . C 3 12.845 -6.928 -3.14 1 40.59 ? N3 ATP 1 A 1 HETATM 31 C C4 ATP . . . C 3 11.718 -7.639 -2.892 1 38.81 ? C4 ATP 1 A 1 # _model_server_stats.io_time_ms 102 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #