data_3EH5
#
_model_server_result.job_id            eIQfDWot1PavZDH3j5ZjjA 
_model_server_result.datetime_utc      '2025-07-13 15:11:48' 
_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          3eh5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":800}' 
#
_entry.id    3EH5 
#
_exptl.entry_id    3EH5 
_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            3EH5 
_cell.length_a            115.631 
_cell.length_b            115.631 
_cell.length_c            149.169 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3EH5 
_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,L,M,N 1 1 
A,D,E,F,G,H,I,L 2 1 
B,J,M 3 1 
C,K,N 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? 
metalc ? metalc2 A ND1 HIS 289 A HIS 233 1_555 D CU CU1 . A CU1 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? 
metalc ? metalc3 A NE2 HIS 338 A HIS 282 1_555 D CU CU1 . A CU1 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? 
metalc ? metalc4 A NE2 HIS 339 A HIS 283 1_555 D CU CU1 . A CU1 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc5 A NE2 HIS 440 A HIS 384 1_555 F FE HAS . A HAS 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? 
metalc ? metalc6 A NE2 HIS 442 A HIS 386 1_555 E FE HEM . A HEM 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
metalc ? metalc7 B ND1 HIS 112 B HIS 114 1_555 J CU2 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? 
metalc ? metalc8 B ND1 HIS 155 B HIS 157 1_555 J CU1 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
#
_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                     3EH5 
_atom_sites.fract_transf_matrix[1][1]    0.008648 
_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]    0.008648 
_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]    0.006704 
_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 BNG A 1 805 805 BNG BNG . 
H 7 BNG A 1 806 806 BNG BNG . 
I 7 BNG A 1 807 807 BNG BNG . 
J 8 CUA B 1 802 802 CUA CUA . 
K 7 BNG C 1 804 804 BNG BNG . 
L 9 HOH A 1 563 1 HOH HOH . 
L 9 HOH A 2 564 2 HOH HOH . 
L 9 HOH A 3 565 3 HOH HOH . 
L 9 HOH A 4 566 4 HOH HOH . 
L 9 HOH A 5 567 5 HOH HOH . 
L 9 HOH A 6 568 6 HOH HOH . 
L 9 HOH A 7 569 7 HOH HOH . 
L 9 HOH A 8 570 8 HOH HOH . 
L 9 HOH A 9 571 9 HOH HOH . 
L 9 HOH A 10 572 10 HOH HOH . 
L 9 HOH A 11 573 11 HOH HOH . 
L 9 HOH A 12 574 13 HOH HOH . 
L 9 HOH A 13 575 15 HOH HOH . 
L 9 HOH A 14 576 16 HOH HOH . 
L 9 HOH A 15 577 17 HOH HOH . 
L 9 HOH A 16 578 19 HOH HOH . 
L 9 HOH A 17 579 20 HOH HOH . 
L 9 HOH A 18 580 21 HOH HOH . 
L 9 HOH A 19 581 22 HOH HOH . 
L 9 HOH A 20 582 23 HOH HOH . 
L 9 HOH A 21 583 24 HOH HOH . 
L 9 HOH A 22 584 25 HOH HOH . 
L 9 HOH A 23 585 27 HOH HOH . 
L 9 HOH A 24 586 28 HOH HOH . 
L 9 HOH A 25 587 30 HOH HOH . 
L 9 HOH A 26 588 31 HOH HOH . 
L 9 HOH A 27 589 32 HOH HOH . 
L 9 HOH A 28 590 33 HOH HOH . 
L 9 HOH A 29 591 34 HOH HOH . 
L 9 HOH A 30 592 35 HOH HOH . 
L 9 HOH A 31 593 36 HOH HOH . 
L 9 HOH A 32 594 37 HOH HOH . 
L 9 HOH A 33 595 38 HOH HOH . 
L 9 HOH A 34 596 39 HOH HOH . 
L 9 HOH A 35 597 40 HOH HOH . 
L 9 HOH A 36 598 41 HOH HOH . 
L 9 HOH A 37 599 42 HOH HOH . 
L 9 HOH A 38 600 44 HOH HOH . 
L 9 HOH A 39 601 45 HOH HOH . 
L 9 HOH A 40 602 46 HOH HOH . 
L 9 HOH A 41 603 47 HOH HOH . 
L 9 HOH A 42 604 51 HOH HOH . 
L 9 HOH A 43 605 52 HOH HOH . 
L 9 HOH A 44 606 57 HOH HOH . 
L 9 HOH A 45 607 58 HOH HOH . 
L 9 HOH A 46 608 59 HOH HOH . 
L 9 HOH A 47 609 60 HOH HOH . 
L 9 HOH A 48 610 61 HOH HOH . 
L 9 HOH A 49 611 62 HOH HOH . 
L 9 HOH A 50 612 63 HOH HOH . 
L 9 HOH A 51 613 64 HOH HOH . 
L 9 HOH A 52 614 66 HOH HOH . 
L 9 HOH A 53 615 67 HOH HOH . 
L 9 HOH A 54 616 72 HOH HOH . 
L 9 HOH A 55 617 75 HOH HOH . 
L 9 HOH A 56 618 76 HOH HOH . 
L 9 HOH A 57 619 77 HOH HOH . 
L 9 HOH A 58 620 78 HOH HOH . 
L 9 HOH A 59 621 79 HOH HOH . 
L 9 HOH A 60 622 80 HOH HOH . 
L 9 HOH A 61 623 81 HOH HOH . 
L 9 HOH A 62 624 82 HOH HOH . 
L 9 HOH A 63 625 83 HOH HOH . 
M 9 HOH B 1 169 12 HOH HOH . 
M 9 HOH B 2 170 14 HOH HOH . 
M 9 HOH B 3 171 26 HOH HOH . 
M 9 HOH B 4 172 29 HOH HOH . 
M 9 HOH B 5 173 43 HOH HOH . 
M 9 HOH B 6 174 48 HOH HOH . 
M 9 HOH B 7 175 49 HOH HOH . 
M 9 HOH B 8 176 50 HOH HOH . 
M 9 HOH B 9 177 53 HOH HOH . 
M 9 HOH B 10 178 54 HOH HOH . 
M 9 HOH B 11 179 55 HOH HOH . 
M 9 HOH B 12 180 56 HOH HOH . 
M 9 HOH B 13 181 65 HOH HOH . 
M 9 HOH B 14 182 68 HOH HOH . 
M 9 HOH B 15 183 69 HOH HOH . 
M 9 HOH B 16 184 70 HOH HOH . 
M 9 HOH B 17 185 71 HOH HOH . 
M 9 HOH B 18 186 73 HOH HOH . 
M 9 HOH B 19 187 74 HOH HOH . 
N 9 HOH C 1 35 18 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 -37.941 18.909 3.983 1 56.09 ? CHA HEM 800 A 1 
HETATM 2 C CHB HEM . . . E 5 -40.208 14.945 2.183 1 66.54 ? CHB HEM 800 A 1 
HETATM 3 C CHC HEM . . . E 5 -35.931 12.59 1.962 1 58.28 ? CHC HEM 800 A 1 
HETATM 4 C CHD HEM . . . E 5 -33.57 16.769 3.016 1 63.08 ? CHD HEM 800 A 1 
HETATM 5 C C1A HEM . . . E 5 -38.912 18.065 3.433 1 61.35 ? C1A HEM 800 A 1 
HETATM 6 C C2A HEM . . . E 5 -40.303 18.433 3.124 1 62.97 ? C2A HEM 800 A 1 
HETATM 7 C C3A HEM . . . E 5 -40.899 17.31 2.629 1 60.99 ? C3A HEM 800 A 1 
HETATM 8 C C4A HEM . . . E 5 -39.935 16.252 2.611 1 61.89 ? C4A HEM 800 A 1 
HETATM 9 C CMA HEM . . . E 5 -42.31 17.012 2.101 1 63.34 ? CMA HEM 800 A 1 
HETATM 10 C CAA HEM . . . E 5 -40.84 19.888 3.355 1 65.13 ? CAA HEM 800 A 1 
HETATM 11 C CBA HEM . . . E 5 -41.476 20.069 4.741 1 73.11 ? CBA HEM 800 A 1 
HETATM 12 C CGA HEM . . . E 5 -41.452 21.507 5.269 1 75.62 ? CGA HEM 800 A 1 
HETATM 13 O O1A HEM . . . E 5 -42.128 21.821 6.308 1 74.02 ? O1A HEM 800 A 1 
HETATM 14 O O2A HEM . . . E 5 -40.726 22.327 4.642 1 79.08 ? O2A HEM 800 A 1 
HETATM 15 C C1B HEM . . . E 5 -39.263 13.909 2.069 1 62.36 ? C1B HEM 800 A 1 
HETATM 16 C C2B HEM . . . E 5 -39.548 12.511 1.786 1 58.66 ? C2B HEM 800 A 1 
HETATM 17 C C3B HEM . . . E 5 -38.33 11.91 1.717 1 65.72 ? C3B HEM 800 A 1 
HETATM 18 C C4B HEM . . . E 5 -37.267 12.864 1.992 1 56.81 ? C4B HEM 800 A 1 
HETATM 19 C CMB HEM . . . E 5 -40.966 11.811 1.54 1 60.28 ? CMB HEM 800 A 1 
HETATM 20 C CAB HEM . . . E 5 -38.047 10.414 1.408 1 68.87 ? CAB HEM 800 A 1 
HETATM 21 C CBB HEM . . . E 5 -37.28 9.671 2.227 1 77.41 ? CBB HEM 800 A 1 
HETATM 22 C C1C HEM . . . E 5 -34.967 13.581 2.175 1 62.38 ? C1C HEM 800 A 1 
HETATM 23 C C2C HEM . . . E 5 -33.533 13.336 2.068 1 60.63 ? C2C HEM 800 A 1 
HETATM 24 C C3C HEM . . . E 5 -32.911 14.491 2.341 1 61.04 ? C3C HEM 800 A 1 
HETATM 25 C C4C HEM . . . E 5 -33.908 15.501 2.629 1 62.6 ? C4C HEM 800 A 1 
HETATM 26 C CMC HEM . . . E 5 -32.929 11.944 1.656 1 63.38 ? CMC HEM 800 A 1 
HETATM 27 C CAC HEM . . . E 5 -31.415 14.866 2.372 1 66.47 ? CAC HEM 800 A 1 
HETATM 28 C CBC HEM . . . E 5 -30.393 13.982 2.349 1 69.94 ? CBC HEM 800 A 1 
HETATM 29 C C1D HEM . . . E 5 -34.522 17.646 3.48 1 61.99 ? C1D HEM 800 A 1 
HETATM 30 C C2D HEM . . . E 5 -34.236 18.943 4.084 1 63.93 ? C2D HEM 800 A 1 
HETATM 31 C C3D HEM . . . E 5 -35.615 19.609 4.369 1 62.31 ? C3D HEM 800 A 1 
HETATM 32 C C4D HEM . . . E 5 -36.578 18.647 3.922 1 62.1 ? C4D HEM 800 A 1 
HETATM 33 C CMD HEM . . . E 5 -32.847 19.54 4.374 1 62.25 ? CMD HEM 800 A 1 
HETATM 34 C CAD HEM . . . E 5 -36 20.963 4.966 1 63.97 ? CAD HEM 800 A 1 
HETATM 35 C CBD HEM . . . E 5 -35.516 21.175 6.396 1 69.47 ? CBD HEM 800 A 1 
HETATM 36 C CGD HEM . . . E 5 -36.001 22.504 6.915 1 70.01 ? CGD HEM 800 A 1 
HETATM 37 O O1D HEM . . . E 5 -35.606 22.86 8.03 1 74.4 ? O1D HEM 800 A 1 
HETATM 38 O O2D HEM . . . E 5 -36.749 23.236 6.244 1 71.74 ? O2D HEM 800 A 1 
HETATM 39 N NA HEM . . . E 5 -38.724 16.705 3.109 1 57.94 ? NA HEM 800 A 1 
HETATM 40 N NB HEM . . . E 5 -37.864 14.118 2.228 1 58.51 ? NB HEM 800 A 1 
HETATM 41 N NC HEM . . . E 5 -35.186 14.911 2.537 1 62.04 ? NC HEM 800 A 1 
HETATM 42 N ND HEM . . . E 5 -35.886 17.496 3.412 1 57.69 ? ND HEM 800 A 1 
HETATM 43 FE FE HEM . . . E 5 -36.819 15.821 2.968 1 71.56 ? FE HEM 800 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           231 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           43 
#