data_3EH3 # _model_server_result.job_id v0rXinaXiFIhpTXrev4ydQ _model_server_result.datetime_utc '2025-07-13 01:40:27' _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 3eh3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":800}' # _entry.id 3EH3 # _exptl.entry_id 3EH3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _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 3EH3 _cell.length_a 119.75 _cell.length_b 119.75 _cell.length_c 150.814 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EH3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # 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 trimeric 3 software_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G 1 1 A,D,E,F 2 1 B,G 3 1 C 4 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 5 _struct_asym.id E _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 metalc ? metalc1 A NE2 HIS 128 A HIS 72 1_555 E FE HEM . A HEM 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.834 ? metalc ? metalc2 A ND1 HIS 289 A HIS 233 1_555 D CU CU1 . A CU1 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.925 ? metalc ? metalc3 A NE2 HIS 338 A HIS 282 1_555 D CU CU1 . A CU1 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc4 A NE2 HIS 339 A HIS 283 1_555 D CU CU1 . A CU1 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc5 A NE2 HIS 440 A HIS 384 1_555 F FE HAS . A HAS 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc6 A NE2 HIS 442 A HIS 386 1_555 E FE HEM . A HEM 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc7 B ND1 HIS 112 B HIS 114 1_555 G CU2 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc8 B ND1 HIS 155 B HIS 157 1_555 G CU1 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? # _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 266 n n CHA C4D HEM doub 267 n n CHA HHA HEM sing 268 n n CHB C4A HEM sing 269 n n CHB C1B HEM doub 270 n n CHB HHB HEM sing 271 n n CHC C4B HEM sing 272 n n CHC C1C HEM doub 273 n n CHC HHC HEM sing 274 n n CHD C4C HEM doub 275 n n CHD C1D HEM sing 276 n n CHD HHD HEM sing 277 n n C1A C2A HEM doub 278 n y C1A NA HEM sing 279 n y C2A C3A HEM sing 280 n y C2A CAA HEM sing 281 n n C3A C4A HEM doub 282 n y C3A CMA HEM sing 283 n n C4A NA HEM sing 284 n y CMA HMA HEM sing 285 n n CMA HMAA HEM sing 286 n n CMA HMAB HEM sing 287 n n CAA CBA HEM sing 288 n n CAA HAA HEM sing 289 n n CAA HAAA HEM sing 290 n n CBA CGA HEM sing 291 n n CBA HBA HEM sing 292 n n CBA HBAA HEM sing 293 n n CGA O1A HEM doub 294 n n CGA O2A HEM sing 295 n n C1B C2B HEM sing 296 n n C1B NB HEM sing 297 n n C2B C3B HEM doub 298 n n C2B CMB HEM sing 299 n n C3B C4B HEM sing 300 n n C3B CAB HEM sing 301 n n C4B NB HEM doub 302 n n CMB HMB HEM sing 303 n n CMB HMBA HEM sing 304 n n CMB HMBB HEM sing 305 n n CAB CBB HEM doub 306 n n CAB HAB HEM sing 307 n n CBB HBB HEM sing 308 n n CBB HBBA HEM sing 309 n n C1C C2C HEM sing 310 n y C1C NC HEM sing 311 n y C2C C3C HEM doub 312 n y C2C CMC HEM sing 313 n n C3C C4C HEM sing 314 n y C3C CAC HEM sing 315 n n C4C NC HEM sing 316 n y CMC HMC HEM sing 317 n n CMC HMCA HEM sing 318 n n CMC HMCB HEM sing 319 n n CAC CBC HEM doub 320 n n CAC HAC HEM sing 321 n n CBC HBC HEM sing 322 n n CBC HBCA HEM sing 323 n n C1D C2D HEM sing 324 n n C1D ND HEM doub 325 n n C2D C3D HEM doub 326 n n C2D CMD HEM sing 327 n n C3D C4D HEM sing 328 n n C3D CAD HEM sing 329 n n C4D ND HEM sing 330 n n CMD HMD HEM sing 331 n n CMD HMDA HEM sing 332 n n CMD HMDB HEM sing 333 n n CAD CBD HEM sing 334 n n CAD HAD HEM sing 335 n n CAD HADA HEM sing 336 n n CBD CGD HEM sing 337 n n CBD HBD HEM sing 338 n n CBD HBDA HEM sing 339 n n CGD O1D HEM doub 340 n n CGD O2D HEM sing 341 n n O2A H2A HEM sing 342 n n O2D H2D HEM sing 343 n n FE NA HEM sing 344 n n FE NB HEM sing 345 n n FE NC HEM sing 346 n n FE ND HEM sing 347 n n # _atom_sites.entry_id 3EH3 _atom_sites.fract_transf_matrix[1][1] 0.008351 _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] 0.008351 _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] 0.006631 _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 CU1 A 1 803 803 CU1 CU1 . E 5 HEM A 1 800 800 HEM HEM . F 6 HAS A 1 801 801 HAS HAS . G 7 CUA B 1 802 802 CUA CUA . # 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 5 -39.981 19.778 -5.221 1 83.32 ? CHA HEM 800 A 1 HETATM 2 C CHB HEM . . . E 5 -43.775 17.654 -3.325 1 71.09 ? CHB HEM 800 A 1 HETATM 3 C CHC HEM . . . E 5 -45.978 22.045 -3.25 1 72.73 ? CHC HEM 800 A 1 HETATM 4 C CHD HEM . . . E 5 -41.577 24.252 -3.998 1 69.35 ? CHD HEM 800 A 1 HETATM 5 C C1A HEM . . . E 5 -40.734 18.726 -4.672 1 74.34 ? C1A HEM 800 A 1 HETATM 6 C C2A HEM . . . E 5 -40.43 17.301 -4.43 1 71.11 ? C2A HEM 800 A 1 HETATM 7 C C3A HEM . . . E 5 -41.525 16.764 -3.891 1 71.78 ? C3A HEM 800 A 1 HETATM 8 C C4A HEM . . . E 5 -42.52 17.788 -3.804 1 75.25 ? C4A HEM 800 A 1 HETATM 9 C CMA HEM . . . E 5 -41.744 15.312 -3.43 1 73.51 ? CMA HEM 800 A 1 HETATM 10 C CAA HEM . . . E 5 -39.116 16.548 -4.689 1 70.93 ? CAA HEM 800 A 1 HETATM 11 C CBA HEM . . . E 5 -38.83 16.585 -6.176 1 82.43 ? CBA HEM 800 A 1 HETATM 12 C CGA HEM . . . E 5 -37.604 15.734 -6.229 1 103.78 ? CGA HEM 800 A 1 HETATM 13 O O1A HEM . . . E 5 -37.752 14.806 -7.077 1 93.98 ? O1A HEM 800 A 1 HETATM 14 O O2A HEM . . . E 5 -36.574 15.993 -5.455 1 118.08 ? O2A HEM 800 A 1 HETATM 15 C C1B HEM . . . E 5 -44.637 18.7 -3.277 1 81.48 ? C1B HEM 800 A 1 HETATM 16 C C2B HEM . . . E 5 -46.081 18.503 -3.059 1 102.52 ? C2B HEM 800 A 1 HETATM 17 C C3B HEM . . . E 5 -46.678 19.711 -3.058 1 96.43 ? C3B HEM 800 A 1 HETATM 18 C C4B HEM . . . E 5 -45.64 20.683 -3.277 1 80.87 ? C4B HEM 800 A 1 HETATM 19 C CMB HEM . . . E 5 -46.789 17.093 -2.86 1 84.93 ? CMB HEM 800 A 1 HETATM 20 C CAB HEM . . . E 5 -48.211 19.956 -2.825 1 100.18 ? CAB HEM 800 A 1 HETATM 21 C CBB HEM . . . E 5 -49.023 18.919 -2.485 1 97.35 ? CBB HEM 800 A 1 HETATM 22 C C1C HEM . . . E 5 -44.934 22.993 -3.339 1 79.89 ? C1C HEM 800 A 1 HETATM 23 C C2C HEM . . . E 5 -45.094 24.432 -3.106 1 77.73 ? C2C HEM 800 A 1 HETATM 24 C C3C HEM . . . E 5 -43.916 24.998 -3.335 1 80.27 ? C3C HEM 800 A 1 HETATM 25 C C4C HEM . . . E 5 -42.904 23.984 -3.683 1 76.9 ? C4C HEM 800 A 1 HETATM 26 C CMC HEM . . . E 5 -46.361 25.25 -2.71 1 71.28 ? CMC HEM 800 A 1 HETATM 27 C CAC HEM . . . E 5 -43.63 26.533 -3.25 1 79.52 ? CAC HEM 800 A 1 HETATM 28 C CBC HEM . . . E 5 -43.933 27.293 -2.195 1 74.52 ? CBC HEM 800 A 1 HETATM 29 C C1D HEM . . . E 5 -40.722 23.284 -4.491 1 77.06 ? C1D HEM 800 A 1 HETATM 30 C C2D HEM . . . E 5 -39.397 23.555 -5.064 1 90.32 ? C2D HEM 800 A 1 HETATM 31 C C3D HEM . . . E 5 -38.849 22.122 -5.461 1 81.98 ? C3D HEM 800 A 1 HETATM 32 C C4D HEM . . . E 5 -39.944 21.176 -5.075 1 73.54 ? C4D HEM 800 A 1 HETATM 33 C CMD HEM . . . E 5 -38.716 24.964 -5.251 1 78.47 ? CMD HEM 800 A 1 HETATM 34 C CAD HEM . . . E 5 -37.459 21.791 -6.09 1 73.67 ? CAD HEM 800 A 1 HETATM 35 C CBD HEM . . . E 5 -37.425 20.765 -7.222 1 85.7 ? CBD HEM 800 A 1 HETATM 36 C CGD HEM . . . E 5 -36.165 21.055 -8.027 1 100.75 ? CGD HEM 800 A 1 HETATM 37 O O1D HEM . . . E 5 -36.152 21.905 -9.042 1 89.84 ? O1D HEM 800 A 1 HETATM 38 O O2D HEM . . . E 5 -35.207 20.351 -7.531 1 89.4 ? O2D HEM 800 A 1 HETATM 39 N NA HEM . . . E 5 -42.005 18.9 -4.325 1 71.59 ? NA HEM 800 A 1 HETATM 40 N NB HEM . . . E 5 -44.332 20.052 -3.432 1 66.24 ? NB HEM 800 A 1 HETATM 41 N NC HEM . . . E 5 -43.529 22.683 -3.682 1 80.31 ? NC HEM 800 A 1 HETATM 42 N ND HEM . . . E 5 -40.972 21.921 -4.559 1 68.83 ? ND HEM 800 A 1 HETATM 43 FE FE HEM . . . E 5 -42.722 20.853 -4.013 1 84.49 ? FE HEM 800 A 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 449 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 43 #