data_8GY3 # _model_server_result.job_id rjNmKuyrsHfsPC7eQz01sA _model_server_result.datetime_utc '2025-07-05 00:57:30' _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 8gy3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 8GY3 # _exptl.entry_id 8GY3 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 618.503 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'HEME C' _entity.pdbx_number_of_molecules 3 _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 8GY3 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GY3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _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 ? _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 ? 4 D N N ? 4 E N N ? 4 F N 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 SG CYS 57 A CYS 57 1_555 D CAB HEC . A HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.765 ? covale ? covale2 A SG CYS 60 A CYS 60 1_555 D CAC HEC . A HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? covale ? covale3 A SG CYS 207 A CYS 207 1_555 E CAB HEC . A HEC 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? covale ? covale4 A SG CYS 210 A CYS 210 1_555 E CAC HEC . A HEC 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? covale ? covale5 A SG CYS 341 A CYS 341 1_555 F CAB HEC . A HEC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? covale ? covale6 A SG CYS 344 A CYS 344 1_555 F CAC HEC . A HEC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.765 ? metalc ? metalc1 A NE2 HIS 61 A HIS 61 1_555 D FE HEC . A HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc2 A NE2 HIS 211 A HIS 211 1_555 E FE HEC . A HEC 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc3 A NE2 HIS 345 A HIS 345 1_555 F FE HEC . A HEC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc4 B SG CYS 39 B CYS 39 1_555 H FE1 FES . B FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc5 B SG CYS 44 B CYS 44 1_555 H FE1 FES . B FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc6 B SG CYS 47 B CYS 47 1_555 H FE2 FES . B FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc7 B SG CYS 59 B CYS 59 1_555 H FE2 FES . B FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc8 B SG CYS 97 B CYS 97 1_555 I FE1 FES . B FES 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc9 B SG CYS 100 B CYS 100 1_555 I FE2 FES . B FES 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc10 B SG CYS 132 B CYS 132 1_555 I FE2 FES . B FES 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc11 B SG CYS 134 B CYS 134 1_555 I FE1 FES . B FES 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? # _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 ? # 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 FE NA HEC sing 133 n n FE NB HEC sing 134 n n FE NC HEC sing 135 n n FE ND HEC sing 136 n n CHA C1A HEC doub 137 n n CHA C4D HEC sing 138 n n CHA HHA HEC sing 139 n n CHB C4A HEC doub 140 n n CHB C1B HEC sing 141 n n CHB HHB HEC sing 142 n n CHC C4B HEC doub 143 n n CHC C1C HEC sing 144 n n CHC HHC HEC sing 145 n n CHD C4C HEC doub 146 n n CHD C1D HEC sing 147 n n CHD HHD HEC sing 148 n n NA C1A HEC sing 149 n y NA C4A HEC sing 150 n y C1A C2A HEC sing 151 n y C2A C3A HEC doub 152 n y C2A CAA HEC sing 153 n n C3A C4A HEC sing 154 n y C3A CMA HEC sing 155 n n CMA HMA1 HEC sing 156 n n CMA HMA2 HEC sing 157 n n CMA HMA3 HEC sing 158 n n CAA CBA HEC sing 159 n n CAA HAA1 HEC sing 160 n n CAA HAA2 HEC sing 161 n n CBA CGA HEC sing 162 n n CBA HBA1 HEC sing 163 n n CBA HBA2 HEC sing 164 n n CGA O1A HEC doub 165 n n CGA O2A HEC sing 166 n n O2A H2A HEC sing 167 n n NB C1B HEC sing 168 n y NB C4B HEC sing 169 n y C1B C2B HEC doub 170 n y C2B C3B HEC sing 171 n y C2B CMB HEC sing 172 n n C3B C4B HEC sing 173 n y C3B CAB HEC doub 174 e n CMB HMB1 HEC sing 175 n n CMB HMB2 HEC sing 176 n n CMB HMB3 HEC sing 177 n n CAB CBB HEC sing 178 n n CAB HAB HEC sing 179 n n CBB HBB1 HEC sing 180 n n CBB HBB2 HEC sing 181 n n CBB HBB3 HEC sing 182 n n NC C1C HEC sing 183 n y NC C4C HEC sing 184 n y C1C C2C HEC doub 185 n y C2C C3C HEC sing 186 n y C2C CMC HEC sing 187 n n C3C C4C HEC sing 188 n y C3C CAC HEC doub 189 e n CMC HMC1 HEC sing 190 n n CMC HMC2 HEC sing 191 n n CMC HMC3 HEC sing 192 n n CAC CBC HEC sing 193 n n CAC HAC HEC sing 194 n n CBC HBC1 HEC sing 195 n n CBC HBC2 HEC sing 196 n n CBC HBC3 HEC sing 197 n n ND C1D HEC sing 198 n y ND C4D HEC sing 199 n y C1D C2D HEC doub 200 n y C2D C3D HEC sing 201 n y C2D CMD HEC sing 202 n n C3D C4D HEC doub 203 n y C3D CAD HEC sing 204 n n CMD HMD1 HEC sing 205 n n CMD HMD2 HEC sing 206 n n CMD HMD3 HEC sing 207 n n CAD CBD HEC sing 208 n n CAD HAD1 HEC sing 209 n n CAD HAD2 HEC sing 210 n n CBD CGD HEC sing 211 n n CBD HBD1 HEC sing 212 n n CBD HBD2 HEC sing 213 n n CGD O1D HEC doub 214 n n CGD O2D HEC sing 215 n n O2D H2D HEC sing 216 n n # _atom_sites.entry_id 8GY3 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 D 4 HEC A 1 501 501 HEC HEC . E 4 HEC A 1 502 502 HEC HEC . F 4 HEC A 1 503 503 HEC HEC . G 5 U10 A 1 504 504 U10 U10 . H 6 FES B 1 201 201 FES FES . I 6 FES B 1 202 202 FES FES . J 7 PCD C 1 801 801 PCD PCD . # 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 . . . D 4 121.865 136.035 90.872 1 126.85 ? FE HEC 501 A 1 HETATM 2 C CHA HEC . . . D 4 118.559 135.799 89.974 1 102.98 ? CHA HEC 501 A 1 HETATM 3 C CHB HEC . . . D 4 122.745 134.493 87.975 1 104.07 ? CHB HEC 501 A 1 HETATM 4 C CHC HEC . . . D 4 125.184 136.552 91.61 1 99.86 ? CHC HEC 501 A 1 HETATM 5 C CHD HEC . . . D 4 120.997 137.222 93.913 1 100.8 ? CHD HEC 501 A 1 HETATM 6 N NA HEC . . . D 4 120.854 135.302 89.3 1 104.2 ? NA HEC 501 A 1 HETATM 7 C C1A HEC . . . D 4 119.49 135.292 89.095 1 103.42 ? C1A HEC 501 A 1 HETATM 8 C C2A HEC . . . D 4 119.193 134.665 87.823 1 102.75 ? C2A HEC 501 A 1 HETATM 9 C C3A HEC . . . D 4 120.359 134.307 87.276 1 103.94 ? C3A HEC 501 A 1 HETATM 10 C C4A HEC . . . D 4 121.404 134.698 88.185 1 103.15 ? C4A HEC 501 A 1 HETATM 11 C CMA HEC . . . D 4 120.639 133.604 85.929 1 103.66 ? CMA HEC 501 A 1 HETATM 12 C CAA HEC . . . D 4 117.761 134.489 87.271 1 99.48 ? CAA HEC 501 A 1 HETATM 13 C CBA HEC . . . D 4 117.318 133.023 87.082 1 104 ? CBA HEC 501 A 1 HETATM 14 C CGA HEC . . . D 4 115.819 132.874 86.978 1 108.22 ? CGA HEC 501 A 1 HETATM 15 O O1A HEC . . . D 4 115.396 131.697 86.831 1 107.74 ? O1A HEC 501 A 1 HETATM 16 O O2A HEC . . . D 4 115.19 133.954 86.843 1 109.63 ? O2A HEC 501 A 1 HETATM 17 N NB HEC . . . D 4 123.606 135.608 89.978 1 106.03 ? NB HEC 501 A 1 HETATM 18 C C1B HEC . . . D 4 123.756 134.958 88.774 1 104.28 ? C1B HEC 501 A 1 HETATM 19 C C2B HEC . . . D 4 125.151 134.841 88.477 1 103.19 ? C2B HEC 501 A 1 HETATM 20 C C3B HEC . . . D 4 125.819 135.415 89.489 1 101.8 ? C3B HEC 501 A 1 HETATM 21 C C4B HEC . . . D 4 124.864 135.9 90.438 1 99.33 ? C4B HEC 501 A 1 HETATM 22 C CMB HEC . . . D 4 125.677 134.159 87.196 1 103.15 ? CMB HEC 501 A 1 HETATM 23 C CAB HEC . . . D 4 127.376 135.524 89.606 1 106.16 ? CAB HEC 501 A 1 HETATM 24 C CBB HEC . . . D 4 127.854 136.591 88.828 1 103.79 ? CBB HEC 501 A 1 HETATM 25 N NC HEC . . . D 4 122.873 136.744 92.446 1 99.15 ? NC HEC 501 A 1 HETATM 26 C C1C HEC . . . D 4 124.244 136.883 92.56 1 100.84 ? C1C HEC 501 A 1 HETATM 27 C C2C HEC . . . D 4 124.583 137.439 93.861 1 103.33 ? C2C HEC 501 A 1 HETATM 28 C C3C HEC . . . D 4 123.418 137.62 94.494 1 101.99 ? C3C HEC 501 A 1 HETATM 29 C C4C HEC . . . D 4 122.345 137.202 93.645 1 97.54 ? C4C HEC 501 A 1 HETATM 30 C CMC HEC . . . D 4 126.025 137.725 94.321 1 104.52 ? CMC HEC 501 A 1 HETATM 31 C CAC HEC . . . D 4 123.247 138.204 95.952 1 101.89 ? CAC HEC 501 A 1 HETATM 32 C CBC HEC . . . D 4 123.305 139.566 96.011 1 99.58 ? CBC HEC 501 A 1 HETATM 33 N ND HEC . . . D 4 120.115 136.428 91.761 1 101.85 ? ND HEC 501 A 1 HETATM 34 C C1D HEC . . . D 4 119.965 136.92 93.047 1 104.43 ? C1D HEC 501 A 1 HETATM 35 C C2D HEC . . . D 4 118.556 137.063 93.315 1 103.54 ? C2D HEC 501 A 1 HETATM 36 C C3D HEC . . . D 4 117.882 136.677 92.241 1 102.24 ? C3D HEC 501 A 1 HETATM 37 C C4D HEC . . . D 4 118.855 136.268 91.237 1 101.59 ? C4D HEC 501 A 1 HETATM 38 C CMD HEC . . . D 4 118.027 137.592 94.67 1 99.74 ? CMD HEC 501 A 1 HETATM 39 C CAD HEC . . . D 4 116.361 136.635 92.014 1 101.46 ? CAD HEC 501 A 1 HETATM 40 C CBD HEC . . . D 4 115.679 137.812 91.334 1 99.08 ? CBD HEC 501 A 1 HETATM 41 C CGD HEC . . . D 4 114.202 137.634 91.142 1 104.95 ? CGD HEC 501 A 1 HETATM 42 O O1D HEC . . . D 4 113.626 137.025 92.085 1 107.21 ? O1D HEC 501 A 1 HETATM 43 O O2D HEC . . . D 4 113.664 138.147 90.128 1 110.79 ? O2D HEC 501 A 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #