data_3ZR0 # _model_server_result.job_id OA98z9Xemkcr3IHwuMccIg _model_server_result.datetime_utc '2024-10-11 07:23:03' _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 3zr0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1157}' # _entry.id 3ZR0 # _exptl.entry_id 3ZR0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 363.221 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 3ZR0 _cell.length_a 59.5 _cell.length_b 67.24 _cell.length_c 79.99 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ZR0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,J 1 1 B,F,G,H,I,K 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 F N N # _chem_comp.formula 'C10 H14 N5 O8 P' _chem_comp.formula_weight 363.221 _chem_comp.id 8OG _chem_comp.mon_nstd_flag n _chem_comp.name "8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE" _chem_comp.type 'dna linking' _chem_comp.pdbx_synonyms "8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE" # 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 OP3 P 8OG sing 1 n n OP3 HOP3 8OG sing 2 n n P OP1 8OG doub 3 n n P OP2 8OG sing 4 n n P O5' 8OG sing 5 n n OP2 HOP2 8OG sing 6 n n O5' C5' 8OG sing 7 n n C5' C4' 8OG sing 8 n n C5' H5' 8OG sing 9 n n C5' "H5''" 8OG sing 10 n n C4' O4' 8OG sing 11 n n C4' C3' 8OG sing 12 n n C4' H4' 8OG sing 13 n n O4' C1' 8OG sing 14 n n C3' O3' 8OG sing 15 n n C3' C2' 8OG sing 16 n n C3' H3' 8OG sing 17 n n O3' HO3' 8OG sing 18 n n C2' C1' 8OG sing 19 n n C2' H2' 8OG sing 20 n n C2' "H2''" 8OG sing 21 n n C1' N9 8OG sing 22 n n C1' H1' 8OG sing 23 n n N9 C8 8OG sing 24 n n N9 C4 8OG sing 25 n n C8 N7 8OG sing 26 n n C8 O8 8OG doub 27 n n N7 C5 8OG sing 28 n n N7 H7 8OG sing 29 n n C5 C6 8OG sing 30 n n C5 C4 8OG doub 31 n n C6 O6 8OG doub 32 n n C6 N1 8OG sing 33 n n N1 C2 8OG sing 34 n n N1 H1 8OG sing 35 n n C2 N2 8OG sing 36 n n C2 N3 8OG doub 37 n n N2 H21 8OG sing 38 n n N2 H22 8OG sing 39 n n N3 C4 8OG sing 40 n n # _atom_sites.entry_id 3ZR0 _atom_sites.fract_transf_matrix[1][1] 0.016807 _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] 0.014872 _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] 0.012502 _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 C 2 8OG A 1 1157 1157 8OG 8OG . D 3 SO4 A 1 1158 1158 SO4 SO4 . E 3 SO4 A 1 1159 1159 SO4 SO4 . F 2 8OG B 1 1157 1157 8OG 8OG . G 3 SO4 B 1 1158 1158 SO4 SO4 . H 3 SO4 B 1 1159 1159 SO4 SO4 . I 3 SO4 B 1 1160 1160 SO4 SO4 . J 4 HOH A 1 2001 2001 HOH HOH . J 4 HOH A 2 2002 2002 HOH HOH . J 4 HOH A 3 2003 2003 HOH HOH . J 4 HOH A 4 2004 2004 HOH HOH . J 4 HOH A 5 2005 2005 HOH HOH . J 4 HOH A 6 2006 2006 HOH HOH . J 4 HOH A 7 2007 2007 HOH HOH . J 4 HOH A 8 2008 2008 HOH HOH . J 4 HOH A 9 2009 2009 HOH HOH . J 4 HOH A 10 2010 2010 HOH HOH . J 4 HOH A 11 2011 2011 HOH HOH . J 4 HOH A 12 2012 2012 HOH HOH . J 4 HOH A 13 2013 2013 HOH HOH . J 4 HOH A 14 2014 2014 HOH HOH . J 4 HOH A 15 2015 2015 HOH HOH . J 4 HOH A 16 2016 2016 HOH HOH . J 4 HOH A 17 2017 2017 HOH HOH . J 4 HOH A 18 2018 2018 HOH HOH . J 4 HOH A 19 2019 2019 HOH HOH . J 4 HOH A 20 2020 2020 HOH HOH . J 4 HOH A 21 2021 2021 HOH HOH . J 4 HOH A 22 2022 2022 HOH HOH . J 4 HOH A 23 2023 2023 HOH HOH . J 4 HOH A 24 2024 2024 HOH HOH . J 4 HOH A 25 2025 2025 HOH HOH . J 4 HOH A 26 2026 2026 HOH HOH . J 4 HOH A 27 2027 2027 HOH HOH . J 4 HOH A 28 2028 2028 HOH HOH . J 4 HOH A 29 2029 2029 HOH HOH . J 4 HOH A 30 2030 2030 HOH HOH . J 4 HOH A 31 2031 2031 HOH HOH . J 4 HOH A 32 2032 2032 HOH HOH . J 4 HOH A 33 2033 2033 HOH HOH . J 4 HOH A 34 2034 2034 HOH HOH . J 4 HOH A 35 2035 2035 HOH HOH . J 4 HOH A 36 2036 2036 HOH HOH . J 4 HOH A 37 2037 2037 HOH HOH . J 4 HOH A 38 2038 2038 HOH HOH . J 4 HOH A 39 2039 2039 HOH HOH . J 4 HOH A 40 2040 2040 HOH HOH . J 4 HOH A 41 2041 2041 HOH HOH . J 4 HOH A 42 2042 2042 HOH HOH . J 4 HOH A 43 2043 2043 HOH HOH . J 4 HOH A 44 2044 2044 HOH HOH . J 4 HOH A 45 2045 2045 HOH HOH . J 4 HOH A 46 2046 2046 HOH HOH . J 4 HOH A 47 2047 2047 HOH HOH . J 4 HOH A 48 2048 2048 HOH HOH . J 4 HOH A 49 2049 2049 HOH HOH . J 4 HOH A 50 2050 2050 HOH HOH . J 4 HOH A 51 2051 2051 HOH HOH . J 4 HOH A 52 2052 2052 HOH HOH . J 4 HOH A 53 2053 2053 HOH HOH . J 4 HOH A 54 2054 2054 HOH HOH . J 4 HOH A 55 2055 2055 HOH HOH . J 4 HOH A 56 2056 2056 HOH HOH . J 4 HOH A 57 2057 2057 HOH HOH . J 4 HOH A 58 2058 2058 HOH HOH . J 4 HOH A 59 2059 2059 HOH HOH . J 4 HOH A 60 2060 2060 HOH HOH . J 4 HOH A 61 2061 2061 HOH HOH . J 4 HOH A 62 2062 2062 HOH HOH . J 4 HOH A 63 2063 2063 HOH HOH . J 4 HOH A 64 2064 2064 HOH HOH . J 4 HOH A 65 2065 2065 HOH HOH . J 4 HOH A 66 2066 2066 HOH HOH . J 4 HOH A 67 2067 2067 HOH HOH . J 4 HOH A 68 2068 2068 HOH HOH . J 4 HOH A 69 2069 2069 HOH HOH . J 4 HOH A 70 2070 2070 HOH HOH . J 4 HOH A 71 2071 2071 HOH HOH . J 4 HOH A 72 2072 2072 HOH HOH . J 4 HOH A 73 2073 2073 HOH HOH . J 4 HOH A 74 2074 2074 HOH HOH . J 4 HOH A 75 2075 2075 HOH HOH . J 4 HOH A 76 2076 2076 HOH HOH . J 4 HOH A 77 2077 2077 HOH HOH . J 4 HOH A 78 2078 2078 HOH HOH . J 4 HOH A 79 2079 2079 HOH HOH . J 4 HOH A 80 2080 2080 HOH HOH . J 4 HOH A 81 2081 2081 HOH HOH . J 4 HOH A 82 2082 2082 HOH HOH . J 4 HOH A 83 2083 2083 HOH HOH . J 4 HOH A 84 2084 2084 HOH HOH . J 4 HOH A 85 2085 2085 HOH HOH . J 4 HOH A 86 2086 2086 HOH HOH . J 4 HOH A 87 2087 2087 HOH HOH . J 4 HOH A 88 2088 2088 HOH HOH . J 4 HOH A 89 2089 2089 HOH HOH . J 4 HOH A 90 2090 2090 HOH HOH . J 4 HOH A 91 2091 2091 HOH HOH . J 4 HOH A 92 2092 2092 HOH HOH . J 4 HOH A 93 2093 2093 HOH HOH . J 4 HOH A 94 2094 2094 HOH HOH . J 4 HOH A 95 2095 2095 HOH HOH . J 4 HOH A 96 2096 2096 HOH HOH . J 4 HOH A 97 2097 2097 HOH HOH . J 4 HOH A 98 2098 2098 HOH HOH . J 4 HOH A 99 2099 2099 HOH HOH . J 4 HOH A 100 2100 2100 HOH HOH . J 4 HOH A 101 2101 2101 HOH HOH . J 4 HOH A 102 2102 2102 HOH HOH . J 4 HOH A 103 2103 2103 HOH HOH . J 4 HOH A 104 2104 2104 HOH HOH . J 4 HOH A 105 2105 2105 HOH HOH . J 4 HOH A 106 2106 2106 HOH HOH . J 4 HOH A 107 2107 2107 HOH HOH . J 4 HOH A 108 2108 2108 HOH HOH . J 4 HOH A 109 2109 2109 HOH HOH . J 4 HOH A 110 2110 2110 HOH HOH . J 4 HOH A 111 2111 2111 HOH HOH . J 4 HOH A 112 2112 2112 HOH HOH . J 4 HOH A 113 2113 2113 HOH HOH . J 4 HOH A 114 2114 2114 HOH HOH . J 4 HOH A 115 2115 2115 HOH HOH . J 4 HOH A 116 2116 2116 HOH HOH . J 4 HOH A 117 2117 2117 HOH HOH . J 4 HOH A 118 2118 2118 HOH HOH . J 4 HOH A 119 2119 2119 HOH HOH . J 4 HOH A 120 2120 2120 HOH HOH . J 4 HOH A 121 2121 2121 HOH HOH . J 4 HOH A 122 2122 2122 HOH HOH . J 4 HOH A 123 2123 2123 HOH HOH . J 4 HOH A 124 2124 2124 HOH HOH . J 4 HOH A 125 2125 2125 HOH HOH . J 4 HOH A 126 2126 2126 HOH HOH . J 4 HOH A 127 2127 2127 HOH HOH . J 4 HOH A 128 2128 2128 HOH HOH . J 4 HOH A 129 2129 2129 HOH HOH . J 4 HOH A 130 2130 2130 HOH HOH . J 4 HOH A 131 2131 2131 HOH HOH . J 4 HOH A 132 2132 2132 HOH HOH . J 4 HOH A 133 2133 2133 HOH HOH . J 4 HOH A 134 2134 2134 HOH HOH . K 4 HOH B 1 2001 2001 HOH HOH . K 4 HOH B 2 2002 2002 HOH HOH . K 4 HOH B 3 2003 2003 HOH HOH . K 4 HOH B 4 2004 2004 HOH HOH . K 4 HOH B 5 2005 2005 HOH HOH . K 4 HOH B 6 2006 2006 HOH HOH . K 4 HOH B 7 2007 2007 HOH HOH . K 4 HOH B 8 2008 2008 HOH HOH . K 4 HOH B 9 2009 2009 HOH HOH . K 4 HOH B 10 2010 2010 HOH HOH . K 4 HOH B 11 2011 2011 HOH HOH . K 4 HOH B 12 2012 2012 HOH HOH . K 4 HOH B 13 2013 2013 HOH HOH . K 4 HOH B 14 2014 2014 HOH HOH . K 4 HOH B 15 2015 2015 HOH HOH . K 4 HOH B 16 2016 2016 HOH HOH . K 4 HOH B 17 2017 2017 HOH HOH . K 4 HOH B 18 2018 2018 HOH HOH . K 4 HOH B 19 2019 2019 HOH HOH . K 4 HOH B 20 2020 2020 HOH HOH . K 4 HOH B 21 2021 2021 HOH HOH . K 4 HOH B 22 2022 2022 HOH HOH . K 4 HOH B 23 2023 2023 HOH HOH . K 4 HOH B 24 2024 2024 HOH HOH . K 4 HOH B 25 2025 2025 HOH HOH . K 4 HOH B 26 2026 2026 HOH HOH . K 4 HOH B 27 2027 2027 HOH HOH . K 4 HOH B 28 2028 2028 HOH HOH . K 4 HOH B 29 2029 2029 HOH HOH . K 4 HOH B 30 2030 2030 HOH HOH . K 4 HOH B 31 2031 2031 HOH HOH . K 4 HOH B 32 2032 2032 HOH HOH . K 4 HOH B 33 2033 2033 HOH HOH . K 4 HOH B 34 2034 2034 HOH HOH . K 4 HOH B 35 2035 2035 HOH HOH . K 4 HOH B 36 2036 2036 HOH HOH . K 4 HOH B 37 2037 2037 HOH HOH . K 4 HOH B 38 2038 2038 HOH HOH . K 4 HOH B 39 2039 2039 HOH HOH . K 4 HOH B 40 2040 2040 HOH HOH . K 4 HOH B 41 2041 2041 HOH HOH . K 4 HOH B 42 2042 2042 HOH HOH . K 4 HOH B 43 2043 2043 HOH HOH . K 4 HOH B 44 2044 2044 HOH HOH . K 4 HOH B 45 2045 2045 HOH HOH . K 4 HOH B 46 2046 2046 HOH HOH . K 4 HOH B 47 2047 2047 HOH HOH . K 4 HOH B 48 2048 2048 HOH HOH . K 4 HOH B 49 2049 2049 HOH HOH . K 4 HOH B 50 2050 2050 HOH HOH . K 4 HOH B 51 2051 2051 HOH HOH . K 4 HOH B 52 2052 2052 HOH HOH . K 4 HOH B 53 2053 2053 HOH HOH . K 4 HOH B 54 2054 2054 HOH HOH . K 4 HOH B 55 2055 2055 HOH HOH . K 4 HOH B 56 2056 2056 HOH HOH . K 4 HOH B 57 2057 2057 HOH HOH . K 4 HOH B 58 2058 2058 HOH HOH . K 4 HOH B 59 2059 2059 HOH HOH . K 4 HOH B 60 2060 2060 HOH HOH . K 4 HOH B 61 2061 2061 HOH HOH . K 4 HOH B 62 2062 2062 HOH HOH . K 4 HOH B 63 2063 2063 HOH HOH . K 4 HOH B 64 2064 2064 HOH HOH . K 4 HOH B 65 2065 2065 HOH HOH . K 4 HOH B 66 2066 2066 HOH HOH . K 4 HOH B 67 2067 2067 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 O OP3 8OG . . . F 2 35.676 14.254 -14.359 1 53.37 -1 OP3 8OG 1157 B 1 HETATM 2 P P 8OG . . . F 2 35.75 12.914 -15.058 1 55.41 ? P 8OG 1157 B 1 HETATM 3 O OP1 8OG . . . F 2 37.146 12.299 -14.863 1 56.47 -1 OP1 8OG 1157 B 1 HETATM 4 O OP2 8OG . . . F 2 35.436 12.93 -16.541 1 55.93 ? OP2 8OG 1157 B 1 HETATM 5 O O5' 8OG . . . F 2 34.704 11.938 -14.378 1 50.78 ? O5' 8OG 1157 B 1 HETATM 6 C C5' 8OG . . . F 2 33.321 12.013 -14.549 1 43.12 ? C5' 8OG 1157 B 1 HETATM 7 C C4' 8OG . . . F 2 32.52 12.175 -13.255 1 38.92 ? C4' 8OG 1157 B 1 HETATM 8 O O4' 8OG . . . F 2 31.027 12.208 -13.327 1 37.72 ? O4' 8OG 1157 B 1 HETATM 9 C C3' 8OG . . . F 2 32.754 11.104 -12.302 1 35.49 ? C3' 8OG 1157 B 1 HETATM 10 O O3' 8OG . . . F 2 32.616 11.676 -11.032 1 31.19 ? O3' 8OG 1157 B 1 HETATM 11 C C2' 8OG . . . F 2 31.679 10.135 -12.701 1 35.33 ? C2' 8OG 1157 B 1 HETATM 12 C C1' 8OG . . . F 2 30.495 11.021 -12.793 1 33.29 ? C1' 8OG 1157 B 1 HETATM 13 N N9 8OG . . . F 2 29.442 10.874 -13.762 1 35.7 ? N9 8OG 1157 B 1 HETATM 14 C C8 8OG . . . F 2 29.353 10.434 -15.01 1 35.75 ? C8 8OG 1157 B 1 HETATM 15 N N7 8OG . . . F 2 28.118 10.451 -15.63 1 38.67 ? N7 8OG 1157 B 1 HETATM 16 C C5 8OG . . . F 2 27.196 10.989 -14.661 1 31.82 ? C5 8OG 1157 B 1 HETATM 17 C C6 8OG . . . F 2 25.798 11.277 -14.631 1 27.94 ? C6 8OG 1157 B 1 HETATM 18 O O6 8OG . . . F 2 25.082 11.078 -15.56 1 34.93 ? O6 8OG 1157 B 1 HETATM 19 N N1 8OG . . . F 2 25.298 11.802 -13.47 1 28.1 ? N1 8OG 1157 B 1 HETATM 20 C C2 8OG . . . F 2 26.103 12.07 -12.305 1 30.77 ? C2 8OG 1157 B 1 HETATM 21 N N2 8OG . . . F 2 25.543 12.595 -11.177 1 26.85 ? N2 8OG 1157 B 1 HETATM 22 N N3 8OG . . . F 2 27.538 11.788 -12.301 1 33.86 ? N3 8OG 1157 B 1 HETATM 23 C C4 8OG . . . F 2 28.068 11.259 -13.455 1 32.8 ? C4 8OG 1157 B 1 HETATM 24 O O8 8OG . . . F 2 30.366 10.03 -15.562 1 44.81 ? O8 8OG 1157 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 24 #