data_4D4X # _model_server_result.job_id dEnm2IORSvQ8Pt9d1sDt5g _model_server_result.datetime_utc '2024-11-07 16:34:20' _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 4d4x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":128}' # _entry.id 4D4X # _exptl.entry_id 4D4X _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 618.503 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'HEME C' _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 4D4X _cell.length_a 53.155 _cell.length_b 53.155 _cell.length_c 180.501 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4D4X _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 1,2 # 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' 10_555 -y,-x,-z+1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 0 0 30.0835 # _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 covale ? covale1 A C PCA 1 A PCA 1 1_555 A N PHE 2 A PHE 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 A SG CYS 116 A CYS 116 1_555 B CAB HEC . A HEC 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.911 ? covale ? covale3 A SG CYS 119 A CYS 119 1_555 B CAC HEC . A HEC 128 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.687 ? metalc ? metalc1 B FE HEC . A HEC 128 1_555 C O NO . A NO 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? metalc ? metalc2 B FE HEC . A HEC 128 1_555 C N NO . A NO 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.803 ? # _chem_comp.formula 'C34 H34 Fe N4 O4' _chem_comp.formula_weight 618.503 _chem_comp.id HEC _chem_comp.mon_nstd_flag . _chem_comp.name 'HEME C' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 4D4X _atom_sites.fract_transf_matrix[1][1] 0.018813 _atom_sites.fract_transf_matrix[1][2] 0.010862 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021723 _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] 0.00554 _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 HEC A 1 128 128 HEC HEC . C 3 NO A 1 129 129 NO NO . D 4 HOH A 1 2001 2001 HOH HOH . D 4 HOH A 2 2002 2002 HOH HOH . D 4 HOH A 3 2003 2003 HOH HOH . D 4 HOH A 4 2004 2004 HOH HOH . D 4 HOH A 5 2005 2005 HOH HOH . D 4 HOH A 6 2006 2006 HOH HOH . D 4 HOH A 7 2007 2007 HOH HOH . D 4 HOH A 8 2008 2008 HOH HOH . D 4 HOH A 9 2009 2009 HOH HOH . D 4 HOH A 10 2010 2010 HOH HOH . D 4 HOH A 11 2011 2011 HOH HOH . D 4 HOH A 12 2012 2012 HOH HOH . D 4 HOH A 13 2013 2013 HOH HOH . D 4 HOH A 14 2014 2014 HOH HOH . D 4 HOH A 15 2015 2015 HOH HOH . D 4 HOH A 16 2016 2016 HOH HOH . D 4 HOH A 17 2017 2017 HOH HOH . D 4 HOH A 18 2018 2018 HOH HOH . D 4 HOH A 19 2019 2019 HOH HOH . D 4 HOH A 20 2020 2020 HOH HOH . D 4 HOH A 21 2021 2021 HOH HOH . D 4 HOH A 22 2022 2022 HOH HOH . D 4 HOH A 23 2023 2023 HOH HOH . D 4 HOH A 24 2024 2024 HOH HOH . D 4 HOH A 25 2025 2025 HOH HOH . D 4 HOH A 26 2026 2026 HOH HOH . D 4 HOH A 27 2027 2027 HOH HOH . D 4 HOH A 28 2028 2028 HOH HOH . D 4 HOH A 29 2029 2029 HOH HOH . D 4 HOH A 30 2030 2030 HOH HOH . D 4 HOH A 31 2031 2031 HOH HOH . D 4 HOH A 32 2032 2032 HOH HOH . D 4 HOH A 33 2033 2033 HOH HOH . D 4 HOH A 34 2034 2034 HOH HOH . D 4 HOH A 35 2035 2035 HOH HOH . D 4 HOH A 36 2036 2036 HOH HOH . D 4 HOH A 37 2037 2037 HOH HOH . D 4 HOH A 38 2038 2038 HOH HOH . D 4 HOH A 39 2039 2039 HOH HOH . D 4 HOH A 40 2040 2040 HOH HOH . D 4 HOH A 41 2041 2041 HOH HOH . D 4 HOH A 42 2042 2042 HOH HOH . D 4 HOH A 43 2043 2043 HOH HOH . D 4 HOH A 44 2044 2044 HOH HOH . D 4 HOH A 45 2045 2045 HOH HOH . D 4 HOH A 46 2046 2046 HOH HOH . D 4 HOH A 47 2047 2047 HOH HOH . D 4 HOH A 48 2048 2048 HOH HOH . D 4 HOH A 49 2049 2049 HOH HOH . D 4 HOH A 50 2050 2050 HOH HOH . D 4 HOH A 51 2051 2051 HOH HOH . D 4 HOH A 52 2052 2052 HOH HOH . D 4 HOH A 53 2053 2053 HOH HOH . D 4 HOH A 54 2054 2054 HOH HOH . D 4 HOH A 55 2055 2055 HOH HOH . D 4 HOH A 56 2056 2056 HOH HOH . D 4 HOH A 57 2057 2057 HOH HOH . D 4 HOH A 58 2058 2058 HOH HOH . D 4 HOH A 59 2059 2059 HOH HOH . D 4 HOH A 60 2060 2060 HOH HOH . D 4 HOH A 61 2061 2061 HOH HOH . D 4 HOH A 62 2062 2062 HOH HOH . D 4 HOH A 63 2063 2063 HOH HOH . D 4 HOH A 64 2064 2064 HOH HOH . D 4 HOH A 65 2065 2065 HOH HOH . D 4 HOH A 66 2066 2066 HOH HOH . D 4 HOH A 67 2067 2067 HOH HOH . D 4 HOH A 68 2068 2068 HOH HOH . D 4 HOH A 69 2069 2069 HOH HOH . D 4 HOH A 70 2070 2070 HOH HOH . D 4 HOH A 71 2071 2071 HOH HOH . D 4 HOH A 72 2072 2072 HOH HOH . D 4 HOH A 73 2073 2073 HOH HOH . D 4 HOH A 74 2074 2074 HOH HOH . D 4 HOH A 75 2075 2075 HOH HOH . D 4 HOH A 76 2076 2076 HOH HOH . D 4 HOH A 77 2077 2077 HOH HOH . D 4 HOH A 78 2078 2078 HOH HOH . D 4 HOH A 79 2079 2079 HOH HOH . D 4 HOH A 80 2080 2080 HOH HOH . D 4 HOH A 81 2081 2081 HOH HOH . D 4 HOH A 82 2082 2082 HOH HOH . D 4 HOH A 83 2083 2083 HOH HOH . D 4 HOH A 84 2084 2084 HOH HOH . D 4 HOH A 85 2085 2085 HOH HOH . D 4 HOH A 86 2086 2086 HOH HOH . D 4 HOH A 87 2087 2087 HOH HOH . D 4 HOH A 88 2088 2088 HOH HOH . D 4 HOH A 89 2089 2089 HOH HOH . D 4 HOH A 90 2090 2090 HOH HOH . D 4 HOH A 91 2091 2091 HOH HOH . D 4 HOH A 92 2092 2092 HOH HOH . D 4 HOH A 93 2093 2093 HOH HOH . D 4 HOH A 94 2095 2095 HOH HOH . D 4 HOH A 95 2096 2096 HOH HOH . D 4 HOH A 96 2097 2097 HOH HOH . D 4 HOH A 97 2098 2098 HOH HOH . D 4 HOH A 98 2099 2099 HOH HOH . D 4 HOH A 99 2100 2100 HOH HOH . D 4 HOH A 100 2101 2101 HOH HOH . D 4 HOH A 101 2102 2102 HOH HOH . D 4 HOH A 102 2103 2103 HOH HOH . D 4 HOH A 103 2104 2104 HOH HOH . D 4 HOH A 104 2105 2105 HOH HOH . D 4 HOH A 105 2106 2106 HOH HOH . D 4 HOH A 106 2107 2107 HOH HOH . D 4 HOH A 107 2108 2108 HOH HOH . D 4 HOH A 108 2109 2109 HOH HOH . D 4 HOH A 109 2110 2110 HOH HOH . D 4 HOH A 110 2111 2111 HOH HOH . D 4 HOH A 111 2112 2112 HOH HOH . D 4 HOH A 112 2113 2113 HOH HOH . D 4 HOH A 113 2114 2114 HOH HOH . D 4 HOH A 114 2115 2115 HOH HOH . D 4 HOH A 115 2116 2116 HOH HOH . D 4 HOH A 116 2117 2117 HOH HOH . D 4 HOH A 117 2118 2118 HOH HOH . D 4 HOH A 118 2119 2119 HOH HOH . D 4 HOH A 119 2120 2120 HOH HOH . D 4 HOH A 120 2121 2121 HOH HOH . D 4 HOH A 121 2122 2122 HOH HOH . D 4 HOH A 122 2123 2123 HOH HOH . D 4 HOH A 123 2124 2124 HOH HOH . D 4 HOH A 124 2125 2125 HOH HOH . D 4 HOH A 125 2126 2126 HOH HOH . D 4 HOH A 126 2127 2127 HOH HOH . D 4 HOH A 127 2128 2128 HOH HOH . D 4 HOH A 128 2129 2129 HOH HOH . D 4 HOH A 129 2130 2130 HOH HOH . D 4 HOH A 130 2131 2131 HOH HOH . D 4 HOH A 131 2132 2132 HOH HOH . D 4 HOH A 132 2133 2133 HOH HOH . D 4 HOH A 133 2134 2134 HOH HOH . D 4 HOH A 134 2135 2135 HOH HOH . D 4 HOH A 135 2136 2136 HOH HOH . D 4 HOH A 136 2137 2137 HOH HOH . D 4 HOH A 137 2138 2138 HOH HOH . D 4 HOH A 138 2139 2139 HOH HOH . D 4 HOH A 139 2140 2140 HOH HOH . D 4 HOH A 140 2141 2141 HOH HOH . D 4 HOH A 141 2142 2142 HOH HOH . D 4 HOH A 142 2143 2143 HOH HOH . D 4 HOH A 143 2144 2144 HOH HOH . D 4 HOH A 144 2145 2145 HOH HOH . D 4 HOH A 145 2146 2146 HOH HOH . D 4 HOH A 146 2147 2147 HOH HOH . D 4 HOH A 147 2148 2148 HOH HOH . D 4 HOH A 148 2149 2149 HOH HOH . D 4 HOH A 149 2150 2150 HOH HOH . D 4 HOH A 150 2151 2151 HOH HOH . D 4 HOH A 151 2152 2152 HOH HOH . D 4 HOH A 152 2153 2153 HOH HOH . D 4 HOH A 153 2154 2154 HOH HOH . D 4 HOH A 154 2155 2155 HOH HOH . D 4 HOH A 155 2156 2156 HOH HOH . D 4 HOH A 156 2157 2157 HOH HOH . D 4 HOH A 157 2158 2158 HOH HOH . D 4 HOH A 158 2159 2159 HOH HOH . D 4 HOH A 159 2160 2160 HOH HOH . D 4 HOH A 160 2161 2161 HOH HOH . D 4 HOH A 161 2163 2163 HOH HOH . D 4 HOH A 162 2164 2164 HOH HOH . D 4 HOH A 163 2165 2165 HOH HOH . D 4 HOH A 164 2166 2166 HOH HOH . D 4 HOH A 165 2167 2167 HOH HOH . D 4 HOH A 166 2168 2168 HOH HOH . D 4 HOH A 167 2169 2169 HOH HOH . D 4 HOH A 168 2170 2170 HOH HOH . D 4 HOH A 169 2171 2171 HOH HOH . D 4 HOH A 170 2172 2172 HOH HOH . D 4 HOH A 171 2173 2173 HOH HOH . D 4 HOH A 172 2174 2174 HOH HOH . D 4 HOH A 173 2175 2175 HOH HOH . D 4 HOH A 174 2176 2176 HOH HOH . D 4 HOH A 175 2177 2177 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 FE FE HEC . . . B 2 22.863 -25.435 8.577 1 16.71 ? FE HEC 128 A 1 HETATM 2 C CHA HEC . . . B 2 26.259 -25.18 8.771 1 18.51 ? CHA HEC 128 A 1 HETATM 3 C CHB HEC . . . B 2 22.692 -25.832 11.91 1 17.31 ? CHB HEC 128 A 1 HETATM 4 C CHC HEC . . . B 2 19.52 -24.769 8.484 1 14.7 ? CHC HEC 128 A 1 HETATM 5 C CHD HEC . . . B 2 23.018 -25.008 5.277 1 17.88 ? CHD HEC 128 A 1 HETATM 6 N NA HEC . . . B 2 24.224 -25.451 10.07 1 17.24 ? NA HEC 128 A 1 HETATM 7 C C1A HEC . . . B 2 25.579 -25.314 9.979 1 17.17 ? C1A HEC 128 A 1 HETATM 8 C C2A HEC . . . B 2 26.186 -25.406 11.247 1 19.09 ? C2A HEC 128 A 1 HETATM 9 C C3A HEC . . . B 2 25.156 -25.607 12.148 1 18.48 ? C3A HEC 128 A 1 HETATM 10 C C4A HEC . . . B 2 23.971 -25.591 11.395 1 16.96 ? C4A HEC 128 A 1 HETATM 11 C CMA HEC . . . B 2 25.251 -25.815 13.655 1 19.76 ? CMA HEC 128 A 1 HETATM 12 C CAA HEC . . . B 2 27.647 -25.256 11.59 1 19.92 ? CAA HEC 128 A 1 HETATM 13 C CBA HEC . . . B 2 28.075 -23.774 11.634 1 20.5 ? CBA HEC 128 A 1 HETATM 14 C CGA HEC . . . B 2 29.533 -23.588 12.007 1 19.51 ? CGA HEC 128 A 1 HETATM 15 O O1A HEC . . . B 2 30.426 -23.827 11.207 1 22.97 ? O1A HEC 128 A 1 HETATM 16 O O2A HEC . . . B 2 29.827 -23.116 13.088 1 24.93 ? O2A HEC 128 A 1 HETATM 17 N NB HEC . . . B 2 21.42 -25.307 9.923 1 16.71 ? NB HEC 128 A 1 HETATM 18 C C1B HEC . . . B 2 21.474 -25.636 11.249 1 16.8 ? C1B HEC 128 A 1 HETATM 19 C C2B HEC . . . B 2 20.224 -25.714 11.882 1 17.53 ? C2B HEC 128 A 1 HETATM 20 C C3B HEC . . . B 2 19.336 -25.315 10.895 1 18.06 ? C3B HEC 128 A 1 HETATM 21 C C4B HEC . . . B 2 20.099 -25.133 9.712 1 15.47 ? C4B HEC 128 A 1 HETATM 22 C CMB HEC . . . B 2 19.949 -26.131 13.318 1 20.05 ? CMB HEC 128 A 1 HETATM 23 C CAB HEC . . . B 2 17.831 -25.095 11.011 1 17.36 ? CAB HEC 128 A 1 HETATM 24 C CBB HEC . . . B 2 17.385 -24.339 12.248 1 16.6 ? CBB HEC 128 A 1 HETATM 25 N NC HEC . . . B 2 21.543 -24.888 7.163 1 15.06 ? NC HEC 128 A 1 HETATM 26 C C1C HEC . . . B 2 20.212 -24.739 7.262 1 15.77 ? C1C HEC 128 A 1 HETATM 27 C C2C HEC . . . B 2 19.537 -24.58 6.045 1 15.87 ? C2C HEC 128 A 1 HETATM 28 C C3C HEC . . . B 2 20.519 -24.726 5.098 1 17.24 ? C3C HEC 128 A 1 HETATM 29 C C4C HEC . . . B 2 21.737 -24.911 5.813 1 15.39 ? C4C HEC 128 A 1 HETATM 30 C CMC HEC . . . B 2 18.037 -24.365 5.856 1 16.51 ? CMC HEC 128 A 1 HETATM 31 C CAC HEC . . . B 2 20.424 -24.684 3.606 1 18.62 ? CAC HEC 128 A 1 HETATM 32 C CBC HEC . . . B 2 19.433 -23.798 2.95 1 21.51 ? CBC HEC 128 A 1 HETATM 33 N ND HEC . . . B 2 24.37 -25.124 7.318 1 16.97 ? ND HEC 128 A 1 HETATM 34 C C1D HEC . . . B 2 24.293 -25.048 5.946 1 18.44 ? C1D HEC 128 A 1 HETATM 35 C C2D HEC . . . B 2 25.519 -24.991 5.296 1 18.14 ? C2D HEC 128 A 1 HETATM 36 C C3D HEC . . . B 2 26.464 -25.008 6.325 1 17.22 ? C3D HEC 128 A 1 HETATM 37 C C4D HEC . . . B 2 25.723 -25.115 7.502 1 16.93 ? C4D HEC 128 A 1 HETATM 38 C CMD HEC . . . B 2 25.793 -24.917 3.817 1 19.25 ? CMD HEC 128 A 1 HETATM 39 C CAD HEC . . . B 2 27.951 -24.926 6.15 1 17.26 ? CAD HEC 128 A 1 HETATM 40 C CBD HEC . . . B 2 28.453 -23.462 6.218 1 19.27 ? CBD HEC 128 A 1 HETATM 41 C CGD HEC . . . B 2 29.951 -23.351 6.023 1 19.49 ? CGD HEC 128 A 1 HETATM 42 O O1D HEC . . . B 2 30.723 -24.048 6.761 1 19.9 ? O1D HEC 128 A 1 HETATM 43 O O2D HEC . . . B 2 30.335 -22.59 5.124 1 20.03 ? O2D HEC 128 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 43 #