data_3EH4 # _model_server_result.job_id udniDc-U2cjPN62yD1Vp-A _model_server_result.datetime_utc '2025-07-15 19:05:40' _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 3eh4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":800}' # _entry.id 3EH4 # _exptl.entry_id 3EH4 _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 3EH4 _cell.length_a 120.851 _cell.length_b 120.851 _cell.length_c 150.397 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EH4 _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,H,I,J,K 1 1 A,D,E,F,I 2 1 B,G,J 3 1 C,H,K 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc2 A ND1 HIS 289 A HIS 233 1_555 D CU CU1 . A CU1 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? metalc ? metalc3 A NE2 HIS 338 A HIS 282 1_555 D CU CU1 . A CU1 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc4 A NE2 HIS 339 A HIS 283 1_555 D CU CU1 . A CU1 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? metalc ? metalc5 A NE2 HIS 440 A HIS 384 1_555 F FE HAS . A HAS 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc6 A NE2 HIS 442 A HIS 386 1_555 E FE HEM . A HEM 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc7 I O HOH . A HOH 596 1_555 D CU CU1 . A CU1 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc8 B ND1 HIS 112 B HIS 114 1_555 G CU2 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc9 B ND1 HIS 155 B HIS 157 1_555 G CU1 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? # _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 317 n n CHA C4D HEM doub 318 n n CHA HHA HEM sing 319 n n CHB C4A HEM sing 320 n n CHB C1B HEM doub 321 n n CHB HHB HEM sing 322 n n CHC C4B HEM sing 323 n n CHC C1C HEM doub 324 n n CHC HHC HEM sing 325 n n CHD C4C HEM doub 326 n n CHD C1D HEM sing 327 n n CHD HHD HEM sing 328 n n C1A C2A HEM doub 329 n y C1A NA HEM sing 330 n y C2A C3A HEM sing 331 n y C2A CAA HEM sing 332 n n C3A C4A HEM doub 333 n y C3A CMA HEM sing 334 n n C4A NA HEM sing 335 n y CMA HMA HEM sing 336 n n CMA HMAA HEM sing 337 n n CMA HMAB HEM sing 338 n n CAA CBA HEM sing 339 n n CAA HAA HEM sing 340 n n CAA HAAA HEM sing 341 n n CBA CGA HEM sing 342 n n CBA HBA HEM sing 343 n n CBA HBAA HEM sing 344 n n CGA O1A HEM doub 345 n n CGA O2A HEM sing 346 n n C1B C2B HEM sing 347 n n C1B NB HEM sing 348 n n C2B C3B HEM doub 349 n n C2B CMB HEM sing 350 n n C3B C4B HEM sing 351 n n C3B CAB HEM sing 352 n n C4B NB HEM doub 353 n n CMB HMB HEM sing 354 n n CMB HMBA HEM sing 355 n n CMB HMBB HEM sing 356 n n CAB CBB HEM doub 357 n n CAB HAB HEM sing 358 n n CBB HBB HEM sing 359 n n CBB HBBA HEM sing 360 n n C1C C2C HEM sing 361 n y C1C NC HEM sing 362 n y C2C C3C HEM doub 363 n y C2C CMC HEM sing 364 n n C3C C4C HEM sing 365 n y C3C CAC HEM sing 366 n n C4C NC HEM sing 367 n y CMC HMC HEM sing 368 n n CMC HMCA HEM sing 369 n n CMC HMCB HEM sing 370 n n CAC CBC HEM doub 371 n n CAC HAC HEM sing 372 n n CBC HBC HEM sing 373 n n CBC HBCA HEM sing 374 n n C1D C2D HEM sing 375 n n C1D ND HEM doub 376 n n C2D C3D HEM doub 377 n n C2D CMD HEM sing 378 n n C3D C4D HEM sing 379 n n C3D CAD HEM sing 380 n n C4D ND HEM sing 381 n n CMD HMD HEM sing 382 n n CMD HMDA HEM sing 383 n n CMD HMDB HEM sing 384 n n CAD CBD HEM sing 385 n n CAD HAD HEM sing 386 n n CAD HADA HEM sing 387 n n CBD CGD HEM sing 388 n n CBD HBD HEM sing 389 n n CBD HBDA HEM sing 390 n n CGD O1D HEM doub 391 n n CGD O2D HEM sing 392 n n O2A H2A HEM sing 393 n n O2D H2D HEM sing 394 n n FE NA HEM sing 395 n n FE NB HEM sing 396 n n FE NC HEM sing 397 n n FE ND HEM sing 398 n n # _atom_sites.entry_id 3EH4 _atom_sites.fract_transf_matrix[1][1] 0.008275 _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] 0.008275 _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] 0.006649 _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 . H 8 BNG C 1 804 804 BNG BNG . I 9 HOH A 1 563 1 HOH HOH . I 9 HOH A 2 564 2 HOH HOH . I 9 HOH A 3 565 3 HOH HOH . I 9 HOH A 4 566 4 HOH HOH . I 9 HOH A 5 567 5 HOH HOH . I 9 HOH A 6 568 7 HOH HOH . I 9 HOH A 7 569 8 HOH HOH . I 9 HOH A 8 570 11 HOH HOH . I 9 HOH A 9 571 12 HOH HOH . I 9 HOH A 10 572 13 HOH HOH . I 9 HOH A 11 573 15 HOH HOH . I 9 HOH A 12 574 16 HOH HOH . I 9 HOH A 13 575 17 HOH HOH . I 9 HOH A 14 576 18 HOH HOH . I 9 HOH A 15 577 19 HOH HOH . I 9 HOH A 16 578 20 HOH HOH . I 9 HOH A 17 579 22 HOH HOH . I 9 HOH A 18 580 23 HOH HOH . I 9 HOH A 19 581 24 HOH HOH . I 9 HOH A 20 582 25 HOH HOH . I 9 HOH A 21 583 26 HOH HOH . I 9 HOH A 22 584 27 HOH HOH . I 9 HOH A 23 585 28 HOH HOH . I 9 HOH A 24 586 29 HOH HOH . I 9 HOH A 25 587 30 HOH HOH . I 9 HOH A 26 588 31 HOH HOH . I 9 HOH A 27 589 35 HOH HOH . I 9 HOH A 28 590 36 HOH HOH . I 9 HOH A 29 591 38 HOH HOH . I 9 HOH A 30 592 39 HOH HOH . I 9 HOH A 31 593 40 HOH HOH . I 9 HOH A 32 594 41 HOH HOH . I 9 HOH A 33 595 44 HOH HOH . I 9 HOH A 34 596 45 HOH HOH . J 9 HOH B 1 169 6 HOH HOH . J 9 HOH B 2 170 9 HOH HOH . J 9 HOH B 3 171 10 HOH HOH . J 9 HOH B 4 172 21 HOH HOH . J 9 HOH B 5 173 32 HOH HOH . J 9 HOH B 6 174 33 HOH HOH . J 9 HOH B 7 175 34 HOH HOH . J 9 HOH B 8 176 37 HOH HOH . J 9 HOH B 9 177 42 HOH HOH . J 9 HOH B 10 178 43 HOH HOH . K 9 HOH C 1 35 14 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 5 -40.848 19.878 4.626 1 85.57 ? CHA HEM 800 A 1 HETATM 2 C CHB HEM . . . E 5 -42.807 15.906 2.943 1 84.51 ? CHB HEM 800 A 1 HETATM 3 C CHC HEM . . . E 5 -38.413 13.846 2.767 1 78.56 ? CHC HEM 800 A 1 HETATM 4 C CHD HEM . . . E 5 -36.27 18.16 3.721 1 89.16 ? CHD HEM 800 A 1 HETATM 5 C C1A HEM . . . E 5 -41.772 18.987 4.132 1 85.05 ? C1A HEM 800 A 1 HETATM 6 C C2A HEM . . . E 5 -43.171 19.274 3.894 1 79.59 ? C2A HEM 800 A 1 HETATM 7 C C3A HEM . . . E 5 -43.721 18.176 3.421 1 80.78 ? C3A HEM 800 A 1 HETATM 8 C C4A HEM . . . E 5 -42.667 17.163 3.369 1 82.4 ? C4A HEM 800 A 1 HETATM 9 C CMA HEM . . . E 5 -45.209 17.998 2.968 1 81.49 ? CMA HEM 800 A 1 HETATM 10 C CAA HEM . . . E 5 -43.905 20.59 4.09 1 89.96 ? CAA HEM 800 A 1 HETATM 11 C CBA HEM . . . E 5 -44.543 20.716 5.489 1 100.18 ? CBA HEM 800 A 1 HETATM 12 C CGA HEM . . . E 5 -44.896 22.164 5.833 1 103.14 ? CGA HEM 800 A 1 HETATM 13 O O1A HEM . . . E 5 -45.764 22.294 6.781 1 99.6 ? O1A HEM 800 A 1 HETATM 14 O O2A HEM . . . E 5 -44.351 23.148 5.167 1 98.49 ? O2A HEM 800 A 1 HETATM 15 C C1B HEM . . . E 5 -41.77 15.045 2.851 1 85.73 ? C1B HEM 800 A 1 HETATM 16 C C2B HEM . . . E 5 -41.972 13.617 2.565 1 90.86 ? C2B HEM 800 A 1 HETATM 17 C C3B HEM . . . E 5 -40.723 13.02 2.534 1 92.58 ? C3B HEM 800 A 1 HETATM 18 C C4B HEM . . . E 5 -39.748 14.059 2.776 1 83.35 ? C4B HEM 800 A 1 HETATM 19 C CMB HEM . . . E 5 -43.411 13.002 2.385 1 84.38 ? CMB HEM 800 A 1 HETATM 20 C CAB HEM . . . E 5 -40.353 11.514 2.315 1 99.85 ? CAB HEM 800 A 1 HETATM 21 C CBB HEM . . . E 5 -41.268 10.482 2.582 1 100.69 ? CBB HEM 800 A 1 HETATM 22 C C1C HEM . . . E 5 -37.525 14.909 2.949 1 85.1 ? C1C HEM 800 A 1 HETATM 23 C C2C HEM . . . E 5 -36.062 14.719 2.815 1 85.4 ? C2C HEM 800 A 1 HETATM 24 C C3C HEM . . . E 5 -35.392 15.844 3.068 1 82.48 ? C3C HEM 800 A 1 HETATM 25 C C4C HEM . . . E 5 -36.446 16.847 3.375 1 84.82 ? C4C HEM 800 A 1 HETATM 26 C CMC HEM . . . E 5 -35.342 13.429 2.394 1 84.35 ? CMC HEM 800 A 1 HETATM 27 C CAC HEM . . . E 5 -33.847 15.708 2.96 1 87.41 ? CAC HEM 800 A 1 HETATM 28 C CBC HEM . . . E 5 -32.843 16.54 2.617 1 98.63 ? CBC HEM 800 A 1 HETATM 29 C C1D HEM . . . E 5 -37.357 18.949 4.117 1 90.98 ? C1D HEM 800 A 1 HETATM 30 C C2D HEM . . . E 5 -37.189 20.3 4.669 1 91.65 ? C2D HEM 800 A 1 HETATM 31 C C3D HEM . . . E 5 -38.592 20.817 4.948 1 91.61 ? C3D HEM 800 A 1 HETATM 32 C C4D HEM . . . E 5 -39.48 19.738 4.54 1 89.14 ? C4D HEM 800 A 1 HETATM 33 C CMD HEM . . . E 5 -35.931 21.161 4.951 1 94.55 ? CMD HEM 800 A 1 HETATM 34 C CAD HEM . . . E 5 -38.852 22.233 5.523 1 94.58 ? CAD HEM 800 A 1 HETATM 35 C CBD HEM . . . E 5 -39.537 22.208 6.905 1 98.4 ? CBD HEM 800 A 1 HETATM 36 C CGD HEM . . . E 5 -39.577 23.638 7.371 1 100.44 ? CGD HEM 800 A 1 HETATM 37 O O1D HEM . . . E 5 -39.086 23.903 8.513 1 103.57 ? O1D HEM 800 A 1 HETATM 38 O O2D HEM . . . E 5 -40.073 24.5 6.573 1 97.43 ? O2D HEM 800 A 1 HETATM 39 N NA HEM . . . E 5 -41.482 17.651 3.806 1 79.61 ? NA HEM 800 A 1 HETATM 40 N NB HEM . . . E 5 -40.438 15.3 2.986 1 84.46 ? NB HEM 800 A 1 HETATM 41 N NC HEM . . . E 5 -37.743 16.281 3.304 1 78 ? NC HEM 800 A 1 HETATM 42 N ND HEM . . . E 5 -38.735 18.626 4.049 1 83.95 ? ND HEM 800 A 1 HETATM 43 FE FE HEM . . . E 5 -39.796 17.043 3.484 1 94.41 ? FE HEM 800 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 350 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 43 #