data_3DMI # _model_server_result.job_id LHmgLLRk6UOzaJSMku2dAw _model_server_result.datetime_utc '2025-09-01 03:47:24' _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 3dmi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":146}' # _entry.id 3DMI # _exptl.entry_id 3DMI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 618.503 _entity.id 3 _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 90 _cell.entry_id 3DMI _cell.length_a 80.385 _cell.length_b 80.385 _cell.length_c 80.385 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DMI _symmetry.cell_setting ? _symmetry.Int_Tables_number 197 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 3' # _pdbx_struct_assembly.method_details PISA _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 _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 covale ? covale1 A SG CYS 14 A CYS 59 1_555 C CAB HEC . A HEC 146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.644 ? covale ? covale2 A SG CYS 17 A CYS 62 1_555 C CAC HEC . A HEC 146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.665 ? metalc ? metalc1 A NE2 HIS 18 A HIS 63 1_555 C FE HEC . A HEC 146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc2 A SD MET 60 A MET 105 1_555 C FE HEC . A HEC 146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc3 A OD2 ASP 69 A ASP 114 1_555 B MG MG . A MG 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc4 B MG MG . A MG 134 1_555 D O HOH . A HOH 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc5 B MG MG . A MG 134 1_555 D O HOH . A HOH 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc6 B MG MG . A MG 134 1_555 D O HOH . A HOH 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc7 B MG MG . A MG 134 1_555 D O HOH . A HOH 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc8 B MG MG . A MG 134 1_555 D O HOH . A HOH 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? # _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 129 n n FE NB HEC sing 130 n n FE NC HEC sing 131 n n FE ND HEC sing 132 n n CHA C1A HEC doub 133 n n CHA C4D HEC sing 134 n n CHA HHA HEC sing 135 n n CHB C4A HEC doub 136 n n CHB C1B HEC sing 137 n n CHB HHB HEC sing 138 n n CHC C4B HEC doub 139 n n CHC C1C HEC sing 140 n n CHC HHC HEC sing 141 n n CHD C4C HEC doub 142 n n CHD C1D HEC sing 143 n n CHD HHD HEC sing 144 n n NA C1A HEC sing 145 n y NA C4A HEC sing 146 n y C1A C2A HEC sing 147 n y C2A C3A HEC doub 148 n y C2A CAA HEC sing 149 n n C3A C4A HEC sing 150 n y C3A CMA HEC sing 151 n n CMA HMA1 HEC sing 152 n n CMA HMA2 HEC sing 153 n n CMA HMA3 HEC sing 154 n n CAA CBA HEC sing 155 n n CAA HAA1 HEC sing 156 n n CAA HAA2 HEC sing 157 n n CBA CGA HEC sing 158 n n CBA HBA1 HEC sing 159 n n CBA HBA2 HEC sing 160 n n CGA O1A HEC doub 161 n n CGA O2A HEC sing 162 n n O2A H2A HEC sing 163 n n NB C1B HEC sing 164 n y NB C4B HEC sing 165 n y C1B C2B HEC doub 166 n y C2B C3B HEC sing 167 n y C2B CMB HEC sing 168 n n C3B C4B HEC sing 169 n y C3B CAB HEC doub 170 e n CMB HMB1 HEC sing 171 n n CMB HMB2 HEC sing 172 n n CMB HMB3 HEC sing 173 n n CAB CBB HEC sing 174 n n CAB HAB HEC sing 175 n n CBB HBB1 HEC sing 176 n n CBB HBB2 HEC sing 177 n n CBB HBB3 HEC sing 178 n n NC C1C HEC sing 179 n y NC C4C HEC sing 180 n y C1C C2C HEC doub 181 n y C2C C3C HEC sing 182 n y C2C CMC HEC sing 183 n n C3C C4C HEC sing 184 n y C3C CAC HEC doub 185 e n CMC HMC1 HEC sing 186 n n CMC HMC2 HEC sing 187 n n CMC HMC3 HEC sing 188 n n CAC CBC HEC sing 189 n n CAC HAC HEC sing 190 n n CBC HBC1 HEC sing 191 n n CBC HBC2 HEC sing 192 n n CBC HBC3 HEC sing 193 n n ND C1D HEC sing 194 n y ND C4D HEC sing 195 n y C1D C2D HEC doub 196 n y C2D C3D HEC sing 197 n y C2D CMD HEC sing 198 n n C3D C4D HEC doub 199 n y C3D CAD HEC sing 200 n n CMD HMD1 HEC sing 201 n n CMD HMD2 HEC sing 202 n n CMD HMD3 HEC sing 203 n n CAD CBD HEC sing 204 n n CAD HAD1 HEC sing 205 n n CAD HAD2 HEC sing 206 n n CBD CGD HEC sing 207 n n CBD HBD1 HEC sing 208 n n CBD HBD2 HEC sing 209 n n CGD O1D HEC doub 210 n n CGD O2D HEC sing 211 n n O2D H2D HEC sing 212 n n # _atom_sites.entry_id 3DMI _atom_sites.fract_transf_matrix[1][1] 0.01244 _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] 0.01244 _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] 0.01244 _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 MG A 1 134 134 MG MG . C 3 HEC A 1 146 146 HEC HEM . D 4 HOH A 1 147 147 HOH HOH . D 4 HOH A 2 148 148 HOH HOH . D 4 HOH A 3 149 149 HOH HOH . D 4 HOH A 4 150 150 HOH HOH . D 4 HOH A 5 151 151 HOH HOH . D 4 HOH A 6 152 152 HOH HOH . D 4 HOH A 7 153 153 HOH HOH . D 4 HOH A 8 154 154 HOH HOH . D 4 HOH A 9 155 155 HOH HOH . D 4 HOH A 10 156 156 HOH HOH . D 4 HOH A 11 157 157 HOH HOH . D 4 HOH A 12 158 158 HOH HOH . D 4 HOH A 13 159 159 HOH HOH . D 4 HOH A 14 160 160 HOH HOH . D 4 HOH A 15 161 161 HOH HOH . D 4 HOH A 16 162 162 HOH HOH . D 4 HOH A 17 163 163 HOH HOH . D 4 HOH A 18 164 164 HOH HOH . D 4 HOH A 19 165 165 HOH HOH . D 4 HOH A 20 166 166 HOH HOH . D 4 HOH A 21 167 167 HOH HOH . D 4 HOH A 22 168 168 HOH HOH . D 4 HOH A 23 169 169 HOH HOH . D 4 HOH A 24 170 170 HOH HOH . D 4 HOH A 25 171 171 HOH HOH . D 4 HOH A 26 172 172 HOH HOH . D 4 HOH A 27 173 173 HOH HOH . D 4 HOH A 28 174 174 HOH HOH . D 4 HOH A 29 175 175 HOH HOH . D 4 HOH A 30 176 176 HOH HOH . D 4 HOH A 31 177 177 HOH HOH . D 4 HOH A 32 178 178 HOH HOH . D 4 HOH A 33 179 179 HOH HOH . D 4 HOH A 34 180 180 HOH HOH . D 4 HOH A 35 181 181 HOH HOH . D 4 HOH A 36 182 182 HOH HOH . D 4 HOH A 37 183 183 HOH HOH . D 4 HOH A 38 184 184 HOH HOH . D 4 HOH A 39 185 185 HOH HOH . D 4 HOH A 40 186 186 HOH HOH . D 4 HOH A 41 187 187 HOH HOH . D 4 HOH A 42 188 188 HOH HOH . D 4 HOH A 43 189 189 HOH HOH . D 4 HOH A 44 190 190 HOH HOH . D 4 HOH A 45 191 191 HOH HOH . D 4 HOH A 46 192 192 HOH HOH . D 4 HOH A 47 193 193 HOH HOH . D 4 HOH A 48 194 194 HOH HOH . D 4 HOH A 49 195 195 HOH HOH . D 4 HOH A 50 196 196 HOH HOH . D 4 HOH A 51 197 197 HOH HOH . D 4 HOH A 52 198 198 HOH HOH . D 4 HOH A 53 199 199 HOH HOH . D 4 HOH A 54 200 200 HOH HOH . D 4 HOH A 55 201 201 HOH HOH . D 4 HOH A 56 202 202 HOH HOH . D 4 HOH A 57 203 203 HOH HOH . D 4 HOH A 58 204 204 HOH HOH . D 4 HOH A 59 205 205 HOH HOH . D 4 HOH A 60 206 206 HOH HOH . D 4 HOH A 61 207 207 HOH HOH . D 4 HOH A 62 208 208 HOH HOH . D 4 HOH A 63 209 209 HOH HOH . D 4 HOH A 64 210 210 HOH HOH . D 4 HOH A 65 211 211 HOH HOH . D 4 HOH A 66 212 212 HOH HOH . D 4 HOH A 67 213 213 HOH HOH . D 4 HOH A 68 214 214 HOH HOH . D 4 HOH A 69 215 215 HOH HOH . D 4 HOH A 70 216 216 HOH HOH . D 4 HOH A 71 217 217 HOH HOH . D 4 HOH A 72 218 218 HOH HOH . D 4 HOH A 73 219 219 HOH HOH . D 4 HOH A 74 220 220 HOH HOH . D 4 HOH A 75 221 221 HOH HOH . D 4 HOH A 76 222 222 HOH HOH . D 4 HOH A 77 223 223 HOH HOH . D 4 HOH A 78 224 224 HOH HOH . D 4 HOH A 79 225 225 HOH HOH . D 4 HOH A 80 226 226 HOH HOH . D 4 HOH A 81 227 227 HOH HOH . D 4 HOH A 82 228 228 HOH HOH . D 4 HOH A 83 229 229 HOH HOH . D 4 HOH A 84 230 230 HOH HOH . D 4 HOH A 85 231 231 HOH HOH . D 4 HOH A 86 232 232 HOH HOH . D 4 HOH A 87 233 233 HOH HOH . D 4 HOH A 88 234 234 HOH HOH . D 4 HOH A 89 235 235 HOH HOH . D 4 HOH A 90 236 236 HOH HOH . D 4 HOH A 91 237 237 HOH HOH . D 4 HOH A 92 238 238 HOH HOH . D 4 HOH A 93 239 239 HOH HOH . D 4 HOH A 94 240 240 HOH HOH . D 4 HOH A 95 241 241 HOH HOH . D 4 HOH A 96 242 242 HOH HOH . D 4 HOH A 97 243 243 HOH HOH . D 4 HOH A 98 244 244 HOH HOH . D 4 HOH A 99 245 245 HOH HOH . D 4 HOH A 100 246 246 HOH HOH . D 4 HOH A 101 247 247 HOH HOH . D 4 HOH A 102 248 248 HOH HOH . D 4 HOH A 103 249 249 HOH HOH . D 4 HOH A 104 250 250 HOH HOH . D 4 HOH A 105 251 251 HOH HOH . D 4 HOH A 106 252 252 HOH HOH . D 4 HOH A 107 253 253 HOH HOH . D 4 HOH A 108 254 254 HOH HOH . D 4 HOH A 109 255 255 HOH HOH . D 4 HOH A 110 256 256 HOH HOH . D 4 HOH A 111 257 257 HOH HOH . D 4 HOH A 112 258 258 HOH HOH . D 4 HOH A 113 259 259 HOH HOH . D 4 HOH A 114 260 260 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 . . . C 3 13.138 66.865 26.793 1 5.47 ? FE HEC 146 A 1 HETATM 2 C CHA HEC . . . C 3 11.96 64.478 28.88 1 6.39 ? CHA HEC 146 A 1 HETATM 3 C CHB HEC . . . C 3 11.307 69.226 28.411 1 6.24 ? CHB HEC 146 A 1 HETATM 4 C CHC HEC . . . C 3 14.806 69.308 25.062 1 6.36 ? CHC HEC 146 A 1 HETATM 5 C CHD HEC . . . C 3 14.564 64.485 24.768 1 6.45 ? CHD HEC 146 A 1 HETATM 6 N NA HEC . . . C 3 11.888 66.851 28.349 1 5.42 ? NA HEC 146 A 1 HETATM 7 C C1A HEC . . . C 3 11.48 65.744 29.051 1 5.67 ? C1A HEC 146 A 1 HETATM 8 C C2A HEC . . . C 3 10.502 66.131 30.038 1 5.93 ? C2A HEC 146 A 1 HETATM 9 C C3A HEC . . . C 3 10.328 67.457 29.928 1 5.75 ? C3A HEC 146 A 1 HETATM 10 C C4A HEC . . . C 3 11.198 67.935 28.87 1 5.76 ? C4A HEC 146 A 1 HETATM 11 C CMA HEC . . . C 3 9.37 68.353 30.753 1 7.66 ? CMA HEC 146 A 1 HETATM 12 C CAA HEC . . . C 3 9.786 65.133 30.986 1 6.48 ? CAA HEC 146 A 1 HETATM 13 C CBA HEC . . . C 3 8.754 64.373 30.117 1 7.65 ? CBA HEC 146 A 1 HETATM 14 C CGA HEC . . . C 3 8.191 63.122 30.763 1 7.55 ? CGA HEC 146 A 1 HETATM 15 O O1A HEC . . . C 3 8.84 62.572 31.686 1 9.3 ? O1A HEC 146 A 1 HETATM 16 O O2A HEC . . . C 3 7.083 62.661 30.357 1 6.7 ? O2A HEC 146 A 1 HETATM 17 N NB HEC . . . C 3 13.089 68.893 26.741 1 5.64 ? NB HEC 146 A 1 HETATM 18 C C1B HEC . . . C 3 12.198 69.676 27.455 1 5.91 ? C1B HEC 146 A 1 HETATM 19 C C2B HEC . . . C 3 12.379 71.052 27.043 1 6.31 ? C2B HEC 146 A 1 HETATM 20 C C3B HEC . . . C 3 13.352 71.094 26.113 1 6.02 ? C3B HEC 146 A 1 HETATM 21 C C4B HEC . . . C 3 13.815 69.734 25.919 1 4.87 ? C4B HEC 146 A 1 HETATM 22 C CMB HEC . . . C 3 11.556 72.236 27.592 1 5.89 ? CMB HEC 146 A 1 HETATM 23 C CAB HEC . . . C 3 13.885 72.364 25.399 1 6.09 ? CAB HEC 146 A 1 HETATM 24 C CBB HEC . . . C 3 14.641 73.186 26.178 1 8.42 ? CBB HEC 146 A 1 HETATM 25 N NC HEC . . . C 3 14.482 66.868 25.269 1 5.49 ? NC HEC 146 A 1 HETATM 26 C C1C HEC . . . C 3 14.959 68.007 24.64 1 5.96 ? C1C HEC 146 A 1 HETATM 27 C C2C HEC . . . C 3 15.637 67.609 23.429 1 6.86 ? C2C HEC 146 A 1 HETATM 28 C C3C HEC . . . C 3 15.581 66.272 23.311 1 6.98 ? C3C HEC 146 A 1 HETATM 29 C C4C HEC . . . C 3 14.847 65.788 24.469 1 6.17 ? C4C HEC 146 A 1 HETATM 30 C CMC HEC . . . C 3 16.316 68.582 22.437 1 7.88 ? CMC HEC 146 A 1 HETATM 31 C CAC HEC . . . C 3 16.142 65.444 22.106 1 7.14 ? CAC HEC 146 A 1 HETATM 32 C CBC HEC . . . C 3 17.489 65.264 22.009 1 6.5 ? CBC HEC 146 A 1 HETATM 33 N ND HEC . . . C 3 13.227 64.816 26.807 1 5.04 ? ND HEC 146 A 1 HETATM 34 C C1D HEC . . . C 3 13.972 64.035 25.923 1 5.32 ? C1D HEC 146 A 1 HETATM 35 C C2D HEC . . . C 3 14.011 62.675 26.422 1 6.02 ? C2D HEC 146 A 1 HETATM 36 C C3D HEC . . . C 3 13.203 62.687 27.701 1 6.14 ? C3D HEC 146 A 1 HETATM 37 C C4D HEC . . . C 3 12.751 64.048 27.862 1 5.52 ? C4D HEC 146 A 1 HETATM 38 C CMD HEC . . . C 3 14.723 61.451 25.8 1 7.59 ? CMD HEC 146 A 1 HETATM 39 C CAD HEC . . . C 3 12.965 61.493 28.64 1 7.11 ? CAD HEC 146 A 1 HETATM 40 C CBD HEC . . . C 3 14.102 61.5 29.671 1 8.32 ? CBD HEC 146 A 1 HETATM 41 C CGD HEC . . . C 3 14.024 60.263 30.528 1 10.08 ? CGD HEC 146 A 1 HETATM 42 O O1D HEC . . . C 3 13.251 60.249 31.511 1 10.57 ? O1D HEC 146 A 1 HETATM 43 O O2D HEC . . . C 3 14.742 59.285 30.19 1 12.98 ? O2D HEC 146 A 1 # _model_server_stats.io_time_ms 3 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 361 _model_server_stats.encode_time_ms 52 _model_server_stats.element_count 43 #