data_1DY3 # _model_server_result.job_id LAzVyFaacO_8zLJtbvfawg _model_server_result.datetime_utc '2024-12-26 20:49:29' _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 1dy3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":200}' # _entry.id 1DY3 # _exptl.entry_id 1DY3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 2 _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 1DY3 _cell.length_a 40.96 _cell.length_b 69.01 _cell.length_c 115.49 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DY3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PQS _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,E,F _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 2 _struct_asym.id B _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 OD2 ASP 95 A ASP 95 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc2 A OD1 ASP 95 A ASP 95 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? metalc ? metalc3 A OD2 ASP 97 A ASP 97 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc4 A OD1 ASP 97 A ASP 97 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc5 B O1G ATP . A ATP 200 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? metalc ? metalc6 B O2B ATP . A ATP 200 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc7 B O2B ATP . A ATP 200 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc8 B O1A ATP . A ATP 200 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc9 C O16 87Y . A 87Y 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.63 ? metalc ? metalc10 D MG MG . A MG 202 1_555 F O HOH . A HOH 2141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? metalc ? metalc11 E MG MG . A MG 203 1_555 F O HOH . A HOH 2068 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? metalc ? metalc12 E MG MG . A MG 203 1_555 F O HOH . A HOH 2136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? # _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 114 n n PG O2G ATP sing 115 n n PG O3G ATP sing 116 n n PG O3B ATP sing 117 n n O2G HOG2 ATP sing 118 n n O3G HOG3 ATP sing 119 n n PB O1B ATP doub 120 n n PB O2B ATP sing 121 n n PB O3B ATP sing 122 n n PB O3A ATP sing 123 n n O2B HOB2 ATP sing 124 n n PA O1A ATP doub 125 n n PA O2A ATP sing 126 n n PA O3A ATP sing 127 n n PA O5' ATP sing 128 n n O2A HOA2 ATP sing 129 n n O5' C5' ATP sing 130 n n C5' C4' ATP sing 131 n n C5' "H5'1" ATP sing 132 n n C5' "H5'2" ATP sing 133 n n C4' O4' ATP sing 134 n n C4' C3' ATP sing 135 n n C4' H4' ATP sing 136 n n O4' C1' ATP sing 137 n n C3' O3' ATP sing 138 n n C3' C2' ATP sing 139 n n C3' H3' ATP sing 140 n n O3' HO3' ATP sing 141 n n C2' O2' ATP sing 142 n n C2' C1' ATP sing 143 n n C2' H2' ATP sing 144 n n O2' HO2' ATP sing 145 n n C1' N9 ATP sing 146 n n C1' H1' ATP sing 147 n n N9 C8 ATP sing 148 n y N9 C4 ATP sing 149 n y C8 N7 ATP doub 150 n y C8 H8 ATP sing 151 n n N7 C5 ATP sing 152 n y C5 C6 ATP sing 153 n y C5 C4 ATP doub 154 n y C6 N6 ATP sing 155 n n C6 N1 ATP doub 156 n y N6 HN61 ATP sing 157 n n N6 HN62 ATP sing 158 n n N1 C2 ATP sing 159 n y C2 N3 ATP doub 160 n y C2 H2 ATP sing 161 n n N3 C4 ATP sing 162 n y # _atom_sites.entry_id 1DY3 _atom_sites.fract_transf_matrix[1][1] 0.024414 _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] 0.014503 _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] 0.008659 _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 ATP A 1 200 200 ATP ATP . C 3 87Y A 1 201 201 87Y 87Y . D 4 MG A 1 202 202 MG MG . E 4 MG A 1 203 203 MG MG . F 5 HOH A 1 2001 2001 HOH HOH . F 5 HOH A 2 2002 2002 HOH HOH . F 5 HOH A 3 2003 2003 HOH HOH . F 5 HOH A 4 2004 2004 HOH HOH . F 5 HOH A 5 2005 2005 HOH HOH . F 5 HOH A 6 2006 2006 HOH HOH . F 5 HOH A 7 2007 2007 HOH HOH . F 5 HOH A 8 2008 2008 HOH HOH . F 5 HOH A 9 2009 2009 HOH HOH . F 5 HOH A 10 2010 2010 HOH HOH . F 5 HOH A 11 2011 2011 HOH HOH . F 5 HOH A 12 2012 2012 HOH HOH . F 5 HOH A 13 2013 2013 HOH HOH . F 5 HOH A 14 2014 2014 HOH HOH . F 5 HOH A 15 2015 2015 HOH HOH . F 5 HOH A 16 2016 2016 HOH HOH . F 5 HOH A 17 2017 2017 HOH HOH . F 5 HOH A 18 2018 2018 HOH HOH . F 5 HOH A 19 2019 2019 HOH HOH . F 5 HOH A 20 2020 2020 HOH HOH . F 5 HOH A 21 2021 2021 HOH HOH . F 5 HOH A 22 2022 2022 HOH HOH . F 5 HOH A 23 2023 2023 HOH HOH . F 5 HOH A 24 2024 2024 HOH HOH . F 5 HOH A 25 2025 2025 HOH HOH . F 5 HOH A 26 2026 2026 HOH HOH . F 5 HOH A 27 2027 2027 HOH HOH . F 5 HOH A 28 2028 2028 HOH HOH . F 5 HOH A 29 2029 2029 HOH HOH . F 5 HOH A 30 2030 2030 HOH HOH . F 5 HOH A 31 2031 2031 HOH HOH . F 5 HOH A 32 2032 2032 HOH HOH . F 5 HOH A 33 2033 2033 HOH HOH . F 5 HOH A 34 2034 2034 HOH HOH . F 5 HOH A 35 2035 2035 HOH HOH . F 5 HOH A 36 2036 2036 HOH HOH . F 5 HOH A 37 2037 2037 HOH HOH . F 5 HOH A 38 2038 2038 HOH HOH . F 5 HOH A 39 2039 2039 HOH HOH . F 5 HOH A 40 2040 2040 HOH HOH . F 5 HOH A 41 2041 2041 HOH HOH . F 5 HOH A 42 2042 2042 HOH HOH . F 5 HOH A 43 2043 2043 HOH HOH . F 5 HOH A 44 2044 2044 HOH HOH . F 5 HOH A 45 2045 2045 HOH HOH . F 5 HOH A 46 2046 2046 HOH HOH . F 5 HOH A 47 2047 2047 HOH HOH . F 5 HOH A 48 2048 2048 HOH HOH . F 5 HOH A 49 2049 2049 HOH HOH . F 5 HOH A 50 2050 2050 HOH HOH . F 5 HOH A 51 2051 2051 HOH HOH . F 5 HOH A 52 2052 2052 HOH HOH . F 5 HOH A 53 2053 2053 HOH HOH . F 5 HOH A 54 2054 2054 HOH HOH . F 5 HOH A 55 2055 2055 HOH HOH . F 5 HOH A 56 2056 2056 HOH HOH . F 5 HOH A 57 2057 2057 HOH HOH . F 5 HOH A 58 2058 2058 HOH HOH . F 5 HOH A 59 2059 2059 HOH HOH . F 5 HOH A 60 2060 2060 HOH HOH . F 5 HOH A 61 2061 2061 HOH HOH . F 5 HOH A 62 2062 2062 HOH HOH . F 5 HOH A 63 2063 2063 HOH HOH . F 5 HOH A 64 2064 2064 HOH HOH . F 5 HOH A 65 2065 2065 HOH HOH . F 5 HOH A 66 2066 2066 HOH HOH . F 5 HOH A 67 2067 2067 HOH HOH . F 5 HOH A 68 2068 2068 HOH HOH . F 5 HOH A 69 2069 2069 HOH HOH . F 5 HOH A 70 2070 2070 HOH HOH . F 5 HOH A 71 2071 2071 HOH HOH . F 5 HOH A 72 2072 2072 HOH HOH . F 5 HOH A 73 2073 2073 HOH HOH . F 5 HOH A 74 2074 2074 HOH HOH . F 5 HOH A 75 2075 2075 HOH HOH . F 5 HOH A 76 2076 2076 HOH HOH . F 5 HOH A 77 2077 2077 HOH HOH . F 5 HOH A 78 2078 2078 HOH HOH . F 5 HOH A 79 2079 2079 HOH HOH . F 5 HOH A 80 2080 2080 HOH HOH . F 5 HOH A 81 2081 2081 HOH HOH . F 5 HOH A 82 2082 2082 HOH HOH . F 5 HOH A 83 2083 2083 HOH HOH . F 5 HOH A 84 2084 2084 HOH HOH . F 5 HOH A 85 2085 2085 HOH HOH . F 5 HOH A 86 2086 2086 HOH HOH . F 5 HOH A 87 2087 2087 HOH HOH . F 5 HOH A 88 2088 2088 HOH HOH . F 5 HOH A 89 2089 2089 HOH HOH . F 5 HOH A 90 2090 2090 HOH HOH . F 5 HOH A 91 2091 2091 HOH HOH . F 5 HOH A 92 2092 2092 HOH HOH . F 5 HOH A 93 2093 2093 HOH HOH . F 5 HOH A 94 2094 2094 HOH HOH . F 5 HOH A 95 2095 2095 HOH HOH . F 5 HOH A 96 2096 2096 HOH HOH . F 5 HOH A 97 2097 2097 HOH HOH . F 5 HOH A 98 2098 2098 HOH HOH . F 5 HOH A 99 2099 2099 HOH HOH . F 5 HOH A 100 2100 2100 HOH HOH . F 5 HOH A 101 2101 2101 HOH HOH . F 5 HOH A 102 2102 2102 HOH HOH . F 5 HOH A 103 2103 2103 HOH HOH . F 5 HOH A 104 2104 2104 HOH HOH . F 5 HOH A 105 2105 2105 HOH HOH . F 5 HOH A 106 2106 2106 HOH HOH . F 5 HOH A 107 2107 2107 HOH HOH . F 5 HOH A 108 2108 2108 HOH HOH . F 5 HOH A 109 2109 2109 HOH HOH . F 5 HOH A 110 2110 2110 HOH HOH . F 5 HOH A 111 2111 2111 HOH HOH . F 5 HOH A 112 2112 2112 HOH HOH . F 5 HOH A 113 2113 2113 HOH HOH . F 5 HOH A 114 2114 2114 HOH HOH . F 5 HOH A 115 2115 2115 HOH HOH . F 5 HOH A 116 2116 2116 HOH HOH . F 5 HOH A 117 2117 2117 HOH HOH . F 5 HOH A 118 2118 2118 HOH HOH . F 5 HOH A 119 2119 2119 HOH HOH . F 5 HOH A 120 2120 2120 HOH HOH . F 5 HOH A 121 2121 2121 HOH HOH . F 5 HOH A 122 2122 2122 HOH HOH . F 5 HOH A 123 2123 2123 HOH HOH . F 5 HOH A 124 2124 2124 HOH HOH . F 5 HOH A 125 2125 2125 HOH HOH . F 5 HOH A 126 2126 2126 HOH HOH . F 5 HOH A 127 2127 2127 HOH HOH . F 5 HOH A 128 2128 2128 HOH HOH . F 5 HOH A 129 2129 2129 HOH HOH . F 5 HOH A 130 2130 2130 HOH HOH . F 5 HOH A 131 2131 2131 HOH HOH . F 5 HOH A 132 2132 2132 HOH HOH . F 5 HOH A 133 2133 2133 HOH HOH . F 5 HOH A 134 2134 2134 HOH HOH . F 5 HOH A 135 2135 2135 HOH HOH . F 5 HOH A 136 2136 2136 HOH HOH . F 5 HOH A 137 2137 2137 HOH HOH . F 5 HOH A 138 2138 2138 HOH HOH . F 5 HOH A 139 2139 2139 HOH HOH . F 5 HOH A 140 2140 2140 HOH HOH . F 5 HOH A 141 2141 2141 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 . . . B 2 21.458 33.569 23.543 1 14.98 ? PG ATP 200 A 1 HETATM 2 O O1G ATP . . . B 2 21.649 32.73 22.351 1 14.01 ? O1G ATP 200 A 1 HETATM 3 O O2G ATP . . . B 2 20.773 32.806 24.614 1 13.48 ? O2G ATP 200 A 1 HETATM 4 O O3G ATP . . . B 2 22.79 34.015 24.029 1 16.16 ? O3G ATP 200 A 1 HETATM 5 P PB ATP . . . B 2 20.948 36.119 22.341 1 17.71 ? PB ATP 200 A 1 HETATM 6 O O1B ATP . . . B 2 19.803 36.794 21.727 1 20.59 ? O1B ATP 200 A 1 HETATM 7 O O2B ATP . . . B 2 21.951 35.701 21.408 1 15.08 ? O2B ATP 200 A 1 HETATM 8 O O3B ATP . . . B 2 20.553 34.848 23.238 1 15.75 ? O3B ATP 200 A 1 HETATM 9 P PA ATP . . . B 2 22.515 38.342 23.089 1 17.5 ? PA ATP 200 A 1 HETATM 10 O O1A ATP . . . B 2 22.895 38.568 21.735 1 11.54 ? O1A ATP 200 A 1 HETATM 11 O O2A ATP . . . B 2 21.826 39.645 23.436 1 14.2 ? O2A ATP 200 A 1 HETATM 12 O O3A ATP . . . B 2 21.652 37.049 23.443 1 15.18 ? O3A ATP 200 A 1 HETATM 13 O O5' ATP . . . B 2 23.713 38.06 24.089 1 20.5 ? O5' ATP 200 A 1 HETATM 14 C C5' ATP . . . B 2 24.724 39.054 24.181 1 21.21 ? C5' ATP 200 A 1 HETATM 15 C C4' ATP . . . B 2 25.438 38.837 25.536 1 18.74 ? C4' ATP 200 A 1 HETATM 16 O O4' ATP . . . B 2 25.947 37.496 25.559 1 20.34 ? O4' ATP 200 A 1 HETATM 17 C C3' ATP . . . B 2 26.603 39.805 25.628 1 23.43 ? C3' ATP 200 A 1 HETATM 18 O O3' ATP . . . B 2 26.678 40.287 27.003 1 34.49 ? O3' ATP 200 A 1 HETATM 19 C C2' ATP . . . B 2 27.795 38.856 25.24 1 20.31 ? C2' ATP 200 A 1 HETATM 20 O O2' ATP . . . B 2 28.916 39.322 26.042 1 19.31 ? O2' ATP 200 A 1 HETATM 21 C C1' ATP . . . B 2 27.308 37.51 25.843 1 18.98 ? C1' ATP 200 A 1 HETATM 22 N N9 ATP . . . B 2 27.96 36.34 25.287 1 15.97 ? N9 ATP 200 A 1 HETATM 23 C C8 ATP . . . B 2 28.441 35.285 25.986 1 11.82 ? C8 ATP 200 A 1 HETATM 24 N N7 ATP . . . B 2 28.887 34.286 25.29 1 15.86 ? N7 ATP 200 A 1 HETATM 25 C C5 ATP . . . B 2 28.718 34.675 24.048 1 12.19 ? C5 ATP 200 A 1 HETATM 26 C C6 ATP . . . B 2 29.01 34.011 22.879 1 15.01 ? C6 ATP 200 A 1 HETATM 27 N N6 ATP . . . B 2 29.553 32.8 22.777 1 14.58 ? N6 ATP 200 A 1 HETATM 28 N N1 ATP . . . B 2 28.732 34.654 21.721 1 15.16 ? N1 ATP 200 A 1 HETATM 29 C C2 ATP . . . B 2 28.165 35.91 21.77 1 15.27 ? C2 ATP 200 A 1 HETATM 30 N N3 ATP . . . B 2 27.843 36.603 22.847 1 14.89 ? N3 ATP 200 A 1 HETATM 31 C C4 ATP . . . B 2 28.141 35.929 23.97 1 13.97 ? C4 ATP 200 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 580 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #