data_1DY3 # _model_server_result.job_id mF5RdesbVq-TSxN3tWLwTw _model_server_result.datetime_utc '2024-12-26 21:42:00' _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":"C","auth_seq_id":201}' # _entry.id 1DY3 # _exptl.entry_id 1DY3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 313.354 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 7,8-DIHYDRO-6-HYDROXYMETHYL-7-METHYL-7-[2-PHENYLETHYL]-PTERIN _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 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 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 'C16 H19 N5 O2' _chem_comp.formula_weight 313.354 _chem_comp.id 87Y _chem_comp.mon_nstd_flag . _chem_comp.name 7,8-DIHYDRO-6-HYDROXYMETHYL-7-METHYL-7-[2-PHENYLETHYL]-PTERIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 2-AMINO-6-HYDROXYMETHYL-7-METHYL-7-PHENETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE;7,8-DIHYDRO-6-HYDROXYMETHYL-7-METHYL-7-[2-PHENYLETHYL]-PTERIN # 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 N2 C3 87Y sing 1 n y N2 C1 87Y sing 2 n y N2 H2 87Y sing 3 n n C3 O8 87Y doub 4 n n C3 C7 87Y sing 5 n y C7 N10 87Y sing 6 n n C7 C6 87Y doub 7 n y N10 C12 87Y doub 8 n n C12 C15 87Y sing 9 n n C12 C11 87Y sing 10 n n C15 O16 87Y sing 11 n n C15 H152 87Y sing 12 n n C15 H151 87Y sing 13 n n O16 H16 87Y sing 14 n n C11 C14 87Y sing 15 n n C11 C13 87Y sing 16 n n C11 N9 87Y sing 17 n n C14 C17 87Y sing 18 n n C14 H142 87Y sing 19 n n C14 H141 87Y sing 20 n n C13 H133 87Y sing 21 n n C13 H132 87Y sing 22 n n C13 H131 87Y sing 23 n n N9 C6 87Y sing 24 n n N9 H9 87Y sing 25 n n C6 N4 87Y sing 26 n y N4 C1 87Y doub 27 n y C1 N5 87Y sing 28 n n N5 H52 87Y sing 29 n n N5 H51 87Y sing 30 n n C17 C18 87Y sing 31 n n C17 H172 87Y sing 32 n n C17 H171 87Y sing 33 n n C18 C19 87Y doub 34 n y C18 C23 87Y sing 35 n y C19 C20 87Y sing 36 n y C19 H19 87Y sing 37 n n C20 C21 87Y doub 38 n y C20 H20 87Y sing 39 n n C21 C22 87Y sing 40 n y C21 H21 87Y sing 41 n n C22 C23 87Y doub 42 n y C22 H22 87Y sing 43 n n C23 H23 87Y sing 44 n n # _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 N N2 87Y . . . C 3 16.636 30.962 15.501 1 7.79 ? N2 87Y 201 A 1 HETATM 2 C C3 87Y . . . C 3 17.399 31.751 16.293 1 10.29 ? C3 87Y 201 A 1 HETATM 3 O O8 87Y . . . C 3 18.472 32.21 15.789 1 9.92 ? O8 87Y 201 A 1 HETATM 4 C C7 87Y . . . C 3 16.942 31.867 17.673 1 10.87 ? C7 87Y 201 A 1 HETATM 5 N N10 87Y . . . C 3 17.718 32.599 18.607 1 12.74 ? N10 87Y 201 A 1 HETATM 6 C C12 87Y . . . C 3 17.288 32.844 19.784 1 13.48 ? C12 87Y 201 A 1 HETATM 7 C C15 87Y . . . C 3 17.924 33.745 20.807 1 16.76 ? C15 87Y 201 A 1 HETATM 8 O O16 87Y . . . C 3 19.271 33.683 20.389 1 19.97 ? O16 87Y 201 A 1 HETATM 9 C C11 87Y . . . C 3 15.929 32.422 20.289 1 14.39 ? C11 87Y 201 A 1 HETATM 10 C C14 87Y . . . C 3 15.764 32.037 21.735 1 14.42 ? C14 87Y 201 A 1 HETATM 11 C C13 87Y . . . C 3 15.181 33.836 20.108 1 10.34 ? C13 87Y 201 A 1 HETATM 12 N N9 87Y . . . C 3 15.193 31.601 19.313 1 13.18 ? N9 87Y 201 A 1 HETATM 13 C C6 87Y . . . C 3 15.741 31.402 18.103 1 11.45 ? C6 87Y 201 A 1 HETATM 14 N N4 87Y . . . C 3 15.043 30.628 17.143 1 10.33 ? N4 87Y 201 A 1 HETATM 15 C C1 87Y . . . C 3 15.512 30.392 15.941 1 9.31 ? C1 87Y 201 A 1 HETATM 16 N N5 87Y . . . C 3 14.825 29.597 15.134 1 8.19 ? N5 87Y 201 A 1 HETATM 17 C C17 87Y . . . C 3 16.578 30.697 21.847 1 17.14 ? C17 87Y 201 A 1 HETATM 18 C C18 87Y . . . C 3 16.097 30.055 23.122 1 21.01 ? C18 87Y 201 A 1 HETATM 19 C C19 87Y . . . C 3 16.283 30.607 24.376 1 22.71 ? C19 87Y 201 A 1 HETATM 20 C C20 87Y . . . C 3 15.882 30.041 25.589 1 24.35 ? C20 87Y 201 A 1 HETATM 21 C C21 87Y . . . C 3 15.235 28.798 25.525 1 25.1 ? C21 87Y 201 A 1 HETATM 22 C C22 87Y . . . C 3 15.053 28.238 24.256 1 23.39 ? C22 87Y 201 A 1 HETATM 23 C C23 87Y . . . C 3 15.459 28.797 23.039 1 22.62 ? C23 87Y 201 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 23 #