data_2JAO # _model_server_result.job_id rHHdVx9sCN4JvhysnurGyA _model_server_result.datetime_utc '2024-11-07 14:32:51' _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 2jao # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1201}' # _entry.id 2JAO # _exptl.entry_id 2JAO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" _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 2JAO _cell.length_a 76.25 _cell.length_b 76.25 _cell.length_c 85.76 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2JAO _symmetry.cell_setting ? _symmetry.Int_Tables_number 171 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 62' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_445 -x-1,-y-1,z -1 0 0 0 -1 0 0 0 1 -38.125 -66.034437 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 OD1 ASN 12 A ASN 12 1_555 D MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? metalc ? metalc2 A O ASP 14 A ASP 14 1_555 D MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc3 A OD1 ASP 147 A ASP 147 1_555 D MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc4 C OP3 DGP . A DGP 1201 1_555 D MG MG . A MG 1202 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.948 ? metalc ? metalc5 C OP3 DGP . A DGP 1201 1_555 D MG MG . A MG 1202 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc6 D MG MG . A MG 1202 1_555 E O HOH . A HOH 2174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc7 D MG MG . A MG 1202 1_555 E O HOH . A HOH 2175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? # _chem_comp.formula 'C10 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id DGP _chem_comp.mon_nstd_flag n _chem_comp.name "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" _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 P OP1 DGP doub 83 n n P OP2 DGP sing 84 n n P OP3 DGP sing 85 n n P O5' DGP sing 86 n n OP2 HOP2 DGP sing 87 n n OP3 HOP3 DGP sing 88 n n O5' C5' DGP sing 89 n n C5' C4' DGP sing 90 n n C5' H5' DGP sing 91 n n C5' "H5''" DGP sing 92 n n C4' O4' DGP sing 93 n n C4' C3' DGP sing 94 n n C4' H4' DGP sing 95 n n O4' C1' DGP sing 96 n n C3' O3' DGP sing 97 n n C3' C2' DGP sing 98 n n C3' H3' DGP sing 99 n n O3' HO3' DGP sing 100 n n C2' C1' DGP sing 101 n n C2' H2' DGP sing 102 n n C2' "H2''" DGP sing 103 n n C1' N9 DGP sing 104 n n C1' H1' DGP sing 105 n n N9 C8 DGP sing 106 n y N9 C4 DGP sing 107 n y C8 N7 DGP doub 108 n y C8 H8 DGP sing 109 n n N7 C5 DGP sing 110 n y C5 C6 DGP sing 111 n n C5 C4 DGP doub 112 n y C6 O6 DGP doub 113 n n C6 N1 DGP sing 114 n n N1 C2 DGP sing 115 n n N1 HN1 DGP sing 116 n n C2 N2 DGP sing 117 n n C2 N3 DGP doub 118 n n N2 HN21 DGP sing 119 n n N2 HN22 DGP sing 120 n n N3 C4 DGP sing 121 n n # _atom_sites.entry_id 2JAO _atom_sites.fract_transf_matrix[1][1] 0.013115 _atom_sites.fract_transf_matrix[1][2] 0.007572 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015144 _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] 0.01166 _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 GOL A 1 1200 1200 GOL GOL . C 3 DGP A 1 1201 1201 DGP DGP . D 4 MG A 1 1202 1202 MG MG . E 5 HOH A 1 2001 2001 HOH HOH . E 5 HOH A 2 2002 2002 HOH HOH . E 5 HOH A 3 2003 2003 HOH HOH . E 5 HOH A 4 2004 2004 HOH HOH . E 5 HOH A 5 2005 2005 HOH HOH . E 5 HOH A 6 2006 2006 HOH HOH . E 5 HOH A 7 2007 2007 HOH HOH . E 5 HOH A 8 2008 2008 HOH HOH . E 5 HOH A 9 2009 2009 HOH HOH . E 5 HOH A 10 2010 2010 HOH HOH . E 5 HOH A 11 2011 2011 HOH HOH . E 5 HOH A 12 2012 2012 HOH HOH . E 5 HOH A 13 2013 2013 HOH HOH . E 5 HOH A 14 2014 2014 HOH HOH . E 5 HOH A 15 2015 2015 HOH HOH . E 5 HOH A 16 2016 2016 HOH HOH . E 5 HOH A 17 2017 2017 HOH HOH . E 5 HOH A 18 2018 2018 HOH HOH . E 5 HOH A 19 2019 2019 HOH HOH . E 5 HOH A 20 2020 2020 HOH HOH . E 5 HOH A 21 2021 2021 HOH HOH . E 5 HOH A 22 2022 2022 HOH HOH . E 5 HOH A 23 2023 2023 HOH HOH . E 5 HOH A 24 2024 2024 HOH HOH . E 5 HOH A 25 2025 2025 HOH HOH . E 5 HOH A 26 2026 2026 HOH HOH . E 5 HOH A 27 2027 2027 HOH HOH . E 5 HOH A 28 2028 2028 HOH HOH . E 5 HOH A 29 2029 2029 HOH HOH . E 5 HOH A 30 2030 2030 HOH HOH . E 5 HOH A 31 2031 2031 HOH HOH . E 5 HOH A 32 2032 2032 HOH HOH . E 5 HOH A 33 2033 2033 HOH HOH . E 5 HOH A 34 2034 2034 HOH HOH . E 5 HOH A 35 2035 2035 HOH HOH . E 5 HOH A 36 2036 2036 HOH HOH . E 5 HOH A 37 2037 2037 HOH HOH . E 5 HOH A 38 2038 2038 HOH HOH . E 5 HOH A 39 2039 2039 HOH HOH . E 5 HOH A 40 2040 2040 HOH HOH . E 5 HOH A 41 2041 2041 HOH HOH . E 5 HOH A 42 2042 2042 HOH HOH . E 5 HOH A 43 2043 2043 HOH HOH . E 5 HOH A 44 2044 2044 HOH HOH . E 5 HOH A 45 2045 2045 HOH HOH . E 5 HOH A 46 2046 2046 HOH HOH . E 5 HOH A 47 2047 2047 HOH HOH . E 5 HOH A 48 2048 2048 HOH HOH . E 5 HOH A 49 2049 2049 HOH HOH . E 5 HOH A 50 2050 2050 HOH HOH . E 5 HOH A 51 2051 2051 HOH HOH . E 5 HOH A 52 2052 2052 HOH HOH . E 5 HOH A 53 2053 2053 HOH HOH . E 5 HOH A 54 2054 2054 HOH HOH . E 5 HOH A 55 2055 2055 HOH HOH . E 5 HOH A 56 2056 2056 HOH HOH . E 5 HOH A 57 2057 2057 HOH HOH . E 5 HOH A 58 2058 2058 HOH HOH . E 5 HOH A 59 2059 2059 HOH HOH . E 5 HOH A 60 2060 2060 HOH HOH . E 5 HOH A 61 2061 2061 HOH HOH . E 5 HOH A 62 2062 2062 HOH HOH . E 5 HOH A 63 2063 2063 HOH HOH . E 5 HOH A 64 2064 2064 HOH HOH . E 5 HOH A 65 2065 2065 HOH HOH . E 5 HOH A 66 2066 2066 HOH HOH . E 5 HOH A 67 2067 2067 HOH HOH . E 5 HOH A 68 2068 2068 HOH HOH . E 5 HOH A 69 2069 2069 HOH HOH . E 5 HOH A 70 2070 2070 HOH HOH . E 5 HOH A 71 2071 2071 HOH HOH . E 5 HOH A 72 2072 2072 HOH HOH . E 5 HOH A 73 2073 2073 HOH HOH . E 5 HOH A 74 2074 2074 HOH HOH . E 5 HOH A 75 2075 2075 HOH HOH . E 5 HOH A 76 2076 2076 HOH HOH . E 5 HOH A 77 2077 2077 HOH HOH . E 5 HOH A 78 2078 2078 HOH HOH . E 5 HOH A 79 2079 2079 HOH HOH . E 5 HOH A 80 2080 2080 HOH HOH . E 5 HOH A 81 2081 2081 HOH HOH . E 5 HOH A 82 2082 2082 HOH HOH . E 5 HOH A 83 2083 2083 HOH HOH . E 5 HOH A 84 2084 2084 HOH HOH . E 5 HOH A 85 2085 2085 HOH HOH . E 5 HOH A 86 2086 2086 HOH HOH . E 5 HOH A 87 2087 2087 HOH HOH . E 5 HOH A 88 2088 2088 HOH HOH . E 5 HOH A 89 2089 2089 HOH HOH . E 5 HOH A 90 2090 2090 HOH HOH . E 5 HOH A 91 2091 2091 HOH HOH . E 5 HOH A 92 2092 2092 HOH HOH . E 5 HOH A 93 2093 2093 HOH HOH . E 5 HOH A 94 2094 2094 HOH HOH . E 5 HOH A 95 2095 2095 HOH HOH . E 5 HOH A 96 2096 2096 HOH HOH . E 5 HOH A 97 2097 2097 HOH HOH . E 5 HOH A 98 2098 2098 HOH HOH . E 5 HOH A 99 2099 2099 HOH HOH . E 5 HOH A 100 2100 2100 HOH HOH . E 5 HOH A 101 2101 2101 HOH HOH . E 5 HOH A 102 2102 2102 HOH HOH . E 5 HOH A 103 2103 2103 HOH HOH . E 5 HOH A 104 2104 2104 HOH HOH . E 5 HOH A 105 2105 2105 HOH HOH . E 5 HOH A 106 2106 2106 HOH HOH . E 5 HOH A 107 2107 2107 HOH HOH . E 5 HOH A 108 2108 2108 HOH HOH . E 5 HOH A 109 2109 2109 HOH HOH . E 5 HOH A 110 2110 2110 HOH HOH . E 5 HOH A 111 2111 2111 HOH HOH . E 5 HOH A 112 2112 2112 HOH HOH . E 5 HOH A 113 2113 2113 HOH HOH . E 5 HOH A 114 2114 2114 HOH HOH . E 5 HOH A 115 2115 2115 HOH HOH . E 5 HOH A 116 2116 2116 HOH HOH . E 5 HOH A 117 2117 2117 HOH HOH . E 5 HOH A 118 2118 2118 HOH HOH . E 5 HOH A 119 2119 2119 HOH HOH . E 5 HOH A 120 2120 2120 HOH HOH . E 5 HOH A 121 2121 2121 HOH HOH . E 5 HOH A 122 2122 2122 HOH HOH . E 5 HOH A 123 2123 2123 HOH HOH . E 5 HOH A 124 2124 2124 HOH HOH . E 5 HOH A 125 2125 2125 HOH HOH . E 5 HOH A 126 2126 2126 HOH HOH . E 5 HOH A 127 2127 2127 HOH HOH . E 5 HOH A 128 2128 2128 HOH HOH . E 5 HOH A 129 2129 2129 HOH HOH . E 5 HOH A 130 2130 2130 HOH HOH . E 5 HOH A 131 2131 2131 HOH HOH . E 5 HOH A 132 2132 2132 HOH HOH . E 5 HOH A 133 2133 2133 HOH HOH . E 5 HOH A 134 2134 2134 HOH HOH . E 5 HOH A 135 2135 2135 HOH HOH . E 5 HOH A 136 2136 2136 HOH HOH . E 5 HOH A 137 2137 2137 HOH HOH . E 5 HOH A 138 2138 2138 HOH HOH . E 5 HOH A 139 2139 2139 HOH HOH . E 5 HOH A 140 2140 2140 HOH HOH . E 5 HOH A 141 2141 2141 HOH HOH . E 5 HOH A 142 2142 2142 HOH HOH . E 5 HOH A 143 2143 2143 HOH HOH . E 5 HOH A 144 2144 2144 HOH HOH . E 5 HOH A 145 2145 2145 HOH HOH . E 5 HOH A 146 2146 2146 HOH HOH . E 5 HOH A 147 2147 2147 HOH HOH . E 5 HOH A 148 2148 2148 HOH HOH . E 5 HOH A 149 2149 2149 HOH HOH . E 5 HOH A 150 2150 2150 HOH HOH . E 5 HOH A 151 2151 2151 HOH HOH . E 5 HOH A 152 2152 2152 HOH HOH . E 5 HOH A 153 2153 2153 HOH HOH . E 5 HOH A 154 2154 2154 HOH HOH . E 5 HOH A 155 2155 2155 HOH HOH . E 5 HOH A 156 2156 2156 HOH HOH . E 5 HOH A 157 2157 2157 HOH HOH . E 5 HOH A 158 2158 2158 HOH HOH . E 5 HOH A 159 2159 2159 HOH HOH . E 5 HOH A 160 2160 2160 HOH HOH . E 5 HOH A 161 2161 2161 HOH HOH . E 5 HOH A 162 2162 2162 HOH HOH . E 5 HOH A 163 2163 2163 HOH HOH . E 5 HOH A 164 2164 2164 HOH HOH . E 5 HOH A 165 2165 2165 HOH HOH . E 5 HOH A 166 2166 2166 HOH HOH . E 5 HOH A 167 2167 2167 HOH HOH . E 5 HOH A 168 2168 2168 HOH HOH . E 5 HOH A 169 2169 2169 HOH HOH . E 5 HOH A 170 2170 2170 HOH HOH . E 5 HOH A 171 2171 2171 HOH HOH . E 5 HOH A 172 2172 2172 HOH HOH . E 5 HOH A 173 2173 2173 HOH HOH . E 5 HOH A 174 2174 2174 HOH HOH . E 5 HOH A 175 2175 2175 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 P DGP . A . C 3 -8.023 -27.425 -0.148 0.5 22.38 ? P DGP 1201 A 1 HETATM 2 P P DGP . B . C 3 -8.148 -28.979 -1.557 0.5 22.6 ? P DGP 1201 A 1 HETATM 3 O OP1 DGP . A . C 3 -9.131 -28.569 -0.048 0.5 20.73 ? OP1 DGP 1201 A 1 HETATM 4 O OP1 DGP . B . C 3 -8.35 -30.46 -2.169 0.5 22.04 ? OP1 DGP 1201 A 1 HETATM 5 O OP2 DGP . A . C 3 -8.025 -26.664 1.284 0.5 22.38 ? OP2 DGP 1201 A 1 HETATM 6 O OP2 DGP . B . C 3 -9.201 -28.742 -0.376 0.5 20.9 ? OP2 DGP 1201 A 1 HETATM 7 O OP3 DGP . A . C 3 -6.72 -28.062 -0.494 0.5 23.51 ? OP3 DGP 1201 A 1 HETATM 8 O OP3 DGP . B . C 3 -6.78 -28.731 -1.024 0.5 21.75 ? OP3 DGP 1201 A 1 HETATM 9 O O5' DGP . A . C 3 -8.516 -26.348 -1.188 0.5 22.77 ? O5' DGP 1201 A 1 HETATM 10 O O5' DGP . B . C 3 -8.568 -28.023 -2.725 0.5 24.94 ? O5' DGP 1201 A 1 HETATM 11 C C5' DGP . . . C 3 -8.311 -26.651 -2.538 1 29.13 ? C5' DGP 1201 A 1 HETATM 12 C C4' DGP . . . C 3 -9.055 -25.703 -3.468 1 33.99 ? C4' DGP 1201 A 1 HETATM 13 O O4' DGP . . . C 3 -8.137 -24.586 -3.439 1 36.46 ? O4' DGP 1201 A 1 HETATM 14 C C3' DGP . . . C 3 -8.964 -26.297 -4.875 1 35.33 ? C3' DGP 1201 A 1 HETATM 15 O O3' DGP . . . C 3 -10.296 -26.498 -5.386 1 36.12 ? O3' DGP 1201 A 1 HETATM 16 C C2' DGP . . . C 3 -8.262 -25.212 -5.677 1 35.78 ? C2' DGP 1201 A 1 HETATM 17 C C1' DGP . . . C 3 -8.244 -24.015 -4.732 1 40.87 ? C1' DGP 1201 A 1 HETATM 18 N N9 DGP . . . C 3 -7.086 -23.138 -5.088 1 42.49 ? N9 DGP 1201 A 1 HETATM 19 C C8 DGP . . . C 3 -5.791 -23.472 -5.13 1 43.31 ? C8 DGP 1201 A 1 HETATM 20 N N7 DGP . . . C 3 -5.067 -22.407 -5.519 1 43.16 ? N7 DGP 1201 A 1 HETATM 21 C C5 DGP . . . C 3 -5.899 -21.394 -5.731 1 43.14 ? C5 DGP 1201 A 1 HETATM 22 C C6 DGP . . . C 3 -5.696 -20.077 -6.125 1 43.1 ? C6 DGP 1201 A 1 HETATM 23 O O6 DGP . . . C 3 -4.57 -19.63 -6.384 1 42.3 ? O6 DGP 1201 A 1 HETATM 24 N N1 DGP . . . C 3 -6.828 -19.256 -6.237 1 43.67 ? N1 DGP 1201 A 1 HETATM 25 C C2 DGP . . . C 3 -8.118 -19.767 -5.954 1 43.67 ? C2 DGP 1201 A 1 HETATM 26 N N2 DGP . . . C 3 -9.169 -18.957 -6.081 1 43.31 ? N2 DGP 1201 A 1 HETATM 27 N N3 DGP . . . C 3 -8.276 -21.055 -5.573 1 42.61 ? N3 DGP 1201 A 1 HETATM 28 C C4 DGP . . . C 3 -7.196 -21.857 -5.455 1 43.33 ? C4 DGP 1201 A 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #