data_3D1A # _model_server_result.job_id xgZpQCdTUjjgnT5ec83A_Q _model_server_result.datetime_utc '2025-04-26 04:03:41' _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 3d1a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":142}' # _entry.id 3D1A # _exptl.entry_id 3D1A _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _entity.pdbx_number_of_molecules 4 _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 3D1A _cell.length_a 53.402 _cell.length_b 67.138 _cell.length_c 153.454 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3D1A _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,E,F,G,H,I,J,K,L _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 F N N ? 3 G N N ? 3 H 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 metalc ? metalc1 E FE HEM . A HEM 142 1_555 I O HOH . A HOH 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.837 ? metalc ? metalc2 B NE2 HIS 91 B HIS 92 1_555 F FE HEM . B HEM 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc3 F FE HEM . B HEM 147 1_555 J O HOH . B HOH 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? metalc ? metalc4 G FE HEM . C HEM 142 1_555 K O HOH . C HOH 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc5 H FE HEM . D HEM 147 1_555 L O HOH . D HOH 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? # _chem_comp.formula 'C34 H32 Fe N4 O4' _chem_comp.formula_weight 616.487 _chem_comp.id HEM _chem_comp.mon_nstd_flag . _chem_comp.name 'PROTOPORPHYRIN IX CONTAINING FE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms HEME # 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 CHA C1A HEM sing 129 n n CHA C4D HEM doub 130 n n CHA HHA HEM sing 131 n n CHB C4A HEM sing 132 n n CHB C1B HEM doub 133 n n CHB HHB HEM sing 134 n n CHC C4B HEM sing 135 n n CHC C1C HEM doub 136 n n CHC HHC HEM sing 137 n n CHD C4C HEM doub 138 n n CHD C1D HEM sing 139 n n CHD HHD HEM sing 140 n n C1A C2A HEM doub 141 n y C1A NA HEM sing 142 n y C2A C3A HEM sing 143 n y C2A CAA HEM sing 144 n n C3A C4A HEM doub 145 n y C3A CMA HEM sing 146 n n C4A NA HEM sing 147 n y CMA HMA HEM sing 148 n n CMA HMAA HEM sing 149 n n CMA HMAB HEM sing 150 n n CAA CBA HEM sing 151 n n CAA HAA HEM sing 152 n n CAA HAAA HEM sing 153 n n CBA CGA HEM sing 154 n n CBA HBA HEM sing 155 n n CBA HBAA HEM sing 156 n n CGA O1A HEM doub 157 n n CGA O2A HEM sing 158 n n C1B C2B HEM sing 159 n n C1B NB HEM sing 160 n n C2B C3B HEM doub 161 n n C2B CMB HEM sing 162 n n C3B C4B HEM sing 163 n n C3B CAB HEM sing 164 n n C4B NB HEM doub 165 n n CMB HMB HEM sing 166 n n CMB HMBA HEM sing 167 n n CMB HMBB HEM sing 168 n n CAB CBB HEM doub 169 n n CAB HAB HEM sing 170 n n CBB HBB HEM sing 171 n n CBB HBBA HEM sing 172 n n C1C C2C HEM sing 173 n y C1C NC HEM sing 174 n y C2C C3C HEM doub 175 n y C2C CMC HEM sing 176 n n C3C C4C HEM sing 177 n y C3C CAC HEM sing 178 n n C4C NC HEM sing 179 n y CMC HMC HEM sing 180 n n CMC HMCA HEM sing 181 n n CMC HMCB HEM sing 182 n n CAC CBC HEM doub 183 n n CAC HAC HEM sing 184 n n CBC HBC HEM sing 185 n n CBC HBCA HEM sing 186 n n C1D C2D HEM sing 187 n n C1D ND HEM doub 188 n n C2D C3D HEM doub 189 n n C2D CMD HEM sing 190 n n C3D C4D HEM sing 191 n n C3D CAD HEM sing 192 n n C4D ND HEM sing 193 n n CMD HMD HEM sing 194 n n CMD HMDA HEM sing 195 n n CMD HMDB HEM sing 196 n n CAD CBD HEM sing 197 n n CAD HAD HEM sing 198 n n CAD HADA HEM sing 199 n n CBD CGD HEM sing 200 n n CBD HBD HEM sing 201 n n CBD HBDA HEM sing 202 n n CGD O1D HEM doub 203 n n CGD O2D HEM sing 204 n n O2A H2A HEM sing 205 n n O2D H2D HEM sing 206 n n FE NA HEM sing 207 n n FE NB HEM sing 208 n n FE NC HEM sing 209 n n FE ND HEM sing 210 n n # _atom_sites.entry_id 3D1A _atom_sites.fract_transf_matrix[1][1] 0.018726 _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] 0.014895 _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] 0.006517 _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 E 3 HEM A 1 142 142 HEM HEM . F 3 HEM B 1 147 147 HEM HEM . G 3 HEM C 1 142 142 HEM HEM . H 3 HEM D 1 147 147 HEM HEM . I 4 HOH A 1 143 7 HOH HOH . I 4 HOH A 2 144 16 HOH HOH . I 4 HOH A 3 145 18 HOH HOH . I 4 HOH A 4 146 46 HOH HOH . I 4 HOH A 5 147 54 HOH HOH . I 4 HOH A 6 148 56 HOH HOH . I 4 HOH A 7 149 72 HOH HOH . I 4 HOH A 8 150 76 HOH HOH . I 4 HOH A 9 151 85 HOH HOH . I 4 HOH A 10 152 103 HOH HOH . I 4 HOH A 11 153 127 HOH HOH . I 4 HOH A 12 154 151 HOH HOH . I 4 HOH A 13 155 153 HOH HOH . I 4 HOH A 14 156 227 HOH HOH . I 4 HOH A 15 157 233 HOH HOH . I 4 HOH A 16 158 244 HOH HOH . I 4 HOH A 17 159 249 HOH HOH . I 4 HOH A 18 160 254 HOH HOH . I 4 HOH A 19 161 257 HOH HOH . I 4 HOH A 20 162 262 HOH HOH . I 4 HOH A 21 163 267 HOH HOH . I 4 HOH A 22 164 269 HOH HOH . I 4 HOH A 23 165 274 HOH HOH . I 4 HOH A 24 166 276 HOH HOH . I 4 HOH A 25 167 279 HOH HOH . I 4 HOH A 26 168 280 HOH HOH . I 4 HOH A 27 169 285 HOH HOH . I 4 HOH A 28 170 293 HOH HOH . I 4 HOH A 29 171 314 HOH HOH . I 4 HOH A 30 172 316 HOH HOH . I 4 HOH A 31 173 322 HOH HOH . I 4 HOH A 32 174 324 HOH HOH . I 4 HOH A 33 175 325 HOH HOH . I 4 HOH A 34 176 25 HOH HOH . I 4 HOH A 35 177 9 HOH HOH . I 4 HOH A 36 178 25 HOH HOH . J 4 HOH B 1 148 4 HOH HOH . J 4 HOH B 2 149 37 HOH HOH . J 4 HOH B 3 150 92 HOH HOH . J 4 HOH B 4 151 101 HOH HOH . J 4 HOH B 5 152 231 HOH HOH . J 4 HOH B 6 153 239 HOH HOH . J 4 HOH B 7 154 245 HOH HOH . J 4 HOH B 8 155 246 HOH HOH . J 4 HOH B 9 156 259 HOH HOH . J 4 HOH B 10 157 261 HOH HOH . J 4 HOH B 11 158 266 HOH HOH . J 4 HOH B 12 159 275 HOH HOH . J 4 HOH B 13 160 278 HOH HOH . J 4 HOH B 14 161 281 HOH HOH . J 4 HOH B 15 162 299 HOH HOH . J 4 HOH B 16 163 307 HOH HOH . J 4 HOH B 17 164 3 HOH HOH . J 4 HOH B 18 165 1 HOH HOH . K 4 HOH C 1 143 5 HOH HOH . K 4 HOH C 2 144 21 HOH HOH . K 4 HOH C 3 145 30 HOH HOH . K 4 HOH C 4 146 31 HOH HOH . K 4 HOH C 5 147 41 HOH HOH . K 4 HOH C 6 148 74 HOH HOH . K 4 HOH C 7 149 106 HOH HOH . K 4 HOH C 8 150 195 HOH HOH . K 4 HOH C 9 151 215 HOH HOH . K 4 HOH C 10 152 216 HOH HOH . K 4 HOH C 11 153 225 HOH HOH . K 4 HOH C 12 154 229 HOH HOH . K 4 HOH C 13 155 232 HOH HOH . K 4 HOH C 14 156 240 HOH HOH . K 4 HOH C 15 157 255 HOH HOH . K 4 HOH C 16 158 283 HOH HOH . K 4 HOH C 17 159 311 HOH HOH . K 4 HOH C 18 160 326 HOH HOH . K 4 HOH C 19 161 12 HOH HOH . K 4 HOH C 20 162 37 HOH HOH . L 4 HOH D 1 148 17 HOH HOH . L 4 HOH D 2 149 35 HOH HOH . L 4 HOH D 3 150 50 HOH HOH . L 4 HOH D 4 151 70 HOH HOH . L 4 HOH D 5 152 171 HOH HOH . L 4 HOH D 6 153 212 HOH HOH . L 4 HOH D 7 154 226 HOH HOH . L 4 HOH D 8 155 234 HOH HOH . L 4 HOH D 9 156 236 HOH HOH . L 4 HOH D 10 157 248 HOH HOH . L 4 HOH D 11 158 264 HOH HOH . L 4 HOH D 12 159 268 HOH HOH . L 4 HOH D 13 160 272 HOH HOH . L 4 HOH D 14 161 277 HOH HOH . L 4 HOH D 15 162 294 HOH HOH . L 4 HOH D 16 163 296 HOH HOH . L 4 HOH D 17 164 301 HOH HOH . L 4 HOH D 18 165 323 HOH HOH . L 4 HOH D 19 166 7 HOH HOH . L 4 HOH D 20 167 14 HOH HOH . L 4 HOH D 21 168 29 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 C CHA HEM . . . E 3 30.21 29.803 4.406 1 19.96 ? CHA HEM 142 A 1 HETATM 2 C CHB HEM . . . E 3 25.886 29.256 2.341 1 21.13 ? CHB HEM 142 A 1 HETATM 3 C CHC HEM . . . E 3 23.941 30.242 6.625 1 20.35 ? CHC HEM 142 A 1 HETATM 4 C CHD HEM . . . E 3 28.262 30.907 8.719 1 21.41 ? CHD HEM 142 A 1 HETATM 5 C C1A HEM . . . E 3 29.209 29.668 3.48 1 20.96 ? C1A HEM 142 A 1 HETATM 6 C C2A HEM . . . E 3 29.413 29.648 2.049 1 23.15 ? C2A HEM 142 A 1 HETATM 7 C C3A HEM . . . E 3 28.215 29.503 1.454 1 22.09 ? C3A HEM 142 A 1 HETATM 8 C C4A HEM . . . E 3 27.233 29.415 2.511 1 20.75 ? C4A HEM 142 A 1 HETATM 9 C CMA HEM . . . E 3 27.915 29.414 -0.07 1 20.48 ? CMA HEM 142 A 1 HETATM 10 C CAA HEM . . . E 3 30.801 29.84 1.38 1 26.02 ? CAA HEM 142 A 1 HETATM 11 C CBA HEM . . . E 3 31.476 28.625 0.765 1 29.54 ? CBA HEM 142 A 1 HETATM 12 C CGA HEM . . . E 3 32.457 29.221 -0.221 1 32.17 ? CGA HEM 142 A 1 HETATM 13 O O1A HEM . . . E 3 32.278 28.942 -1.455 1 33.52 ? O1A HEM 142 A 1 HETATM 14 O O2A HEM . . . E 3 33.382 29.98 0.222 1 32.01 ? O2A HEM 142 A 1 HETATM 15 C C1B HEM . . . E 3 24.959 29.524 3.316 1 20.28 ? C1B HEM 142 A 1 HETATM 16 C C2B HEM . . . E 3 23.53 29.575 3.143 1 19.81 ? C2B HEM 142 A 1 HETATM 17 C C3B HEM . . . E 3 22.992 29.846 4.348 1 20.39 ? C3B HEM 142 A 1 HETATM 18 C C4B HEM . . . E 3 24.084 29.963 5.287 1 20.32 ? C4B HEM 142 A 1 HETATM 19 C CMB HEM . . . E 3 22.819 29.341 1.785 1 18.95 ? CMB HEM 142 A 1 HETATM 20 C CAB HEM . . . E 3 21.499 30.014 4.776 1 19.8 ? CAB HEM 142 A 1 HETATM 21 C CBB HEM . . . E 3 20.499 30.088 3.891 1 20.09 ? CBB HEM 142 A 1 HETATM 22 C C1C HEM . . . E 3 24.917 30.514 7.546 1 19.68 ? C1C HEM 142 A 1 HETATM 23 C C2C HEM . . . E 3 24.67 30.874 8.916 1 20.08 ? C2C HEM 142 A 1 HETATM 24 C C3C HEM . . . E 3 25.849 31.059 9.524 1 20.58 ? C3C HEM 142 A 1 HETATM 25 C C4C HEM . . . E 3 26.888 30.813 8.533 1 20.73 ? C4C HEM 142 A 1 HETATM 26 C CMC HEM . . . E 3 23.259 30.999 9.529 1 20.42 ? CMC HEM 142 A 1 HETATM 27 C CAC HEM . . . E 3 26.083 31.455 11.014 1 20.85 ? CAC HEM 142 A 1 HETATM 28 C CBC HEM . . . E 3 25.636 32.601 11.554 1 20.3 ? CBC HEM 142 A 1 HETATM 29 C C1D HEM . . . E 3 29.227 30.75 7.731 1 21.41 ? C1D HEM 142 A 1 HETATM 30 C C2D HEM . . . E 3 30.649 31.036 7.851 1 21.8 ? C2D HEM 142 A 1 HETATM 31 C C3D HEM . . . E 3 31.245 30.681 6.493 1 22.43 ? C3D HEM 142 A 1 HETATM 32 C C4D HEM . . . E 3 30.123 30.229 5.699 1 20.57 ? C4D HEM 142 A 1 HETATM 33 C CMD HEM . . . E 3 31.432 31.577 9.067 1 21.45 ? CMD HEM 142 A 1 HETATM 34 C CAD HEM . . . E 3 32.733 30.796 6.062 1 24.34 ? CAD HEM 142 A 1 HETATM 35 C CBD HEM . . . E 3 33.021 32.25 5.673 1 26.24 ? CBD HEM 142 A 1 HETATM 36 C CGD HEM . . . E 3 34.283 32.383 4.859 1 26.71 ? CGD HEM 142 A 1 HETATM 37 O O1D HEM . . . E 3 35.36 31.97 5.355 1 27.86 ? O1D HEM 142 A 1 HETATM 38 O O2D HEM . . . E 3 34.211 32.904 3.714 1 27.17 ? O2D HEM 142 A 1 HETATM 39 N NA HEM . . . E 3 27.868 29.517 3.725 1 20.53 ? NA HEM 142 A 1 HETATM 40 N NB HEM . . . E 3 25.265 29.772 4.626 1 20.06 ? NB HEM 142 A 1 HETATM 41 N NC HEM . . . E 3 26.27 30.484 7.339 1 19.69 ? NC HEM 142 A 1 HETATM 42 N ND HEM . . . E 3 28.972 30.28 6.448 1 20.26 ? ND HEM 142 A 1 HETATM 43 FE FE HEM . . . E 3 27.085 29.965 5.537 1 20.37 ? FE HEM 142 A 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 857 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 43 #