data_5C3J
#
_model_server_result.job_id            IkJXTCcjcuof-97rG8JR8Q 
_model_server_result.datetime_utc      '2024-11-06 01:33:56' 
_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          5c3j 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"V","auth_seq_id":201}' 
#
_entry.id    5C3J 
#
_exptl.entry_id    5C3J 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          10 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PROTOPORPHYRIN IX CONTAINING FE' 
_entity.pdbx_number_of_molecules    2 
_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            5C3J 
_cell.length_a            123.75 
_cell.length_b            126.827 
_cell.length_c            220.449 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5C3J 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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 tetrameric 4 author_and_software_defined_assembly 1 
PISA tetrameric 4 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,I,J,K,L,M,N,O,P 1 1 
E,F,G,H,Q,R,S,T,U,V,W,X 2 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
? 10 N N N 
? 10 V 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 B SG CYS 89 B CYS 89 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? 
metalc ? metalc2 B SG CYS 94 B CYS 94 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? 
metalc ? metalc3 B SG CYS 97 B CYS 97 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? 
metalc ? metalc4 B SG CYS 109 B CYS 109 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? 
metalc ? metalc5 B SG CYS 182 B CYS 182 1_555 L FE3 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? 
metalc ? metalc6 B SG CYS 185 B CYS 185 1_555 L FE1 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? 
metalc ? metalc7 B SG CYS 188 B CYS 188 1_555 L FE2 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? 
metalc ? metalc8 B SG CYS 192 B CYS 192 1_555 M FE4 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? 
metalc ? metalc9 B SG CYS 239 B CYS 239 1_555 M FE1 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? 
metalc ? metalc10 B SG CYS 245 B CYS 245 1_555 M FE3 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? 
metalc ? metalc11 B SG CYS 249 B CYS 249 1_555 L FE4 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? 
metalc ? metalc12 C NE2 HIS 131 C HIS 131 1_555 N FE HEM . C HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? 
metalc ? metalc13 N FE HEM . C HEM 201 1_555 D NE2 HIS 95 D HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? 
metalc ? metalc14 F SG CYS 89 F CYS 89 1_555 S FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? 
metalc ? metalc15 F SG CYS 94 F CYS 94 1_555 S FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? 
metalc ? metalc16 F SG CYS 97 F CYS 97 1_555 S FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? 
metalc ? metalc17 F SG CYS 109 F CYS 109 1_555 S FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? 
metalc ? metalc18 F SG CYS 182 F CYS 182 1_555 T FE3 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? 
metalc ? metalc19 F SG CYS 185 F CYS 185 1_555 T FE1 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? 
metalc ? metalc20 F SG CYS 188 F CYS 188 1_555 T FE2 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? 
metalc ? metalc21 F SG CYS 192 F CYS 192 1_555 U FE4 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? 
metalc ? metalc22 F SG CYS 239 F CYS 239 1_555 U FE1 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
metalc ? metalc23 F SG CYS 245 F CYS 245 1_555 U FE3 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? 
metalc ? metalc24 F SG CYS 249 F CYS 249 1_555 T FE4 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? 
metalc ? metalc25 G NE2 HIS 131 G HIS 131 1_555 V FE HEM . G HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? 
metalc ? metalc26 V FE HEM . G HEM 201 1_555 H NE2 HIS 95 H HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? 
#
_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 349 n n 
CHA C4D HEM doub 350 n n 
CHA HHA HEM sing 351 n n 
CHB C4A HEM sing 352 n n 
CHB C1B HEM doub 353 n n 
CHB HHB HEM sing 354 n n 
CHC C4B HEM sing 355 n n 
CHC C1C HEM doub 356 n n 
CHC HHC HEM sing 357 n n 
CHD C4C HEM doub 358 n n 
CHD C1D HEM sing 359 n n 
CHD HHD HEM sing 360 n n 
C1A C2A HEM doub 361 n y 
C1A NA HEM sing 362 n y 
C2A C3A HEM sing 363 n y 
C2A CAA HEM sing 364 n n 
C3A C4A HEM doub 365 n y 
C3A CMA HEM sing 366 n n 
C4A NA HEM sing 367 n y 
CMA HMA HEM sing 368 n n 
CMA HMAA HEM sing 369 n n 
CMA HMAB HEM sing 370 n n 
CAA CBA HEM sing 371 n n 
CAA HAA HEM sing 372 n n 
CAA HAAA HEM sing 373 n n 
CBA CGA HEM sing 374 n n 
CBA HBA HEM sing 375 n n 
CBA HBAA HEM sing 376 n n 
CGA O1A HEM doub 377 n n 
CGA O2A HEM sing 378 n n 
C1B C2B HEM sing 379 n n 
C1B NB HEM sing 380 n n 
C2B C3B HEM doub 381 n n 
C2B CMB HEM sing 382 n n 
C3B C4B HEM sing 383 n n 
C3B CAB HEM sing 384 n n 
C4B NB HEM doub 385 n n 
CMB HMB HEM sing 386 n n 
CMB HMBA HEM sing 387 n n 
CMB HMBB HEM sing 388 n n 
CAB CBB HEM doub 389 n n 
CAB HAB HEM sing 390 n n 
CBB HBB HEM sing 391 n n 
CBB HBBA HEM sing 392 n n 
C1C C2C HEM sing 393 n y 
C1C NC HEM sing 394 n y 
C2C C3C HEM doub 395 n y 
C2C CMC HEM sing 396 n n 
C3C C4C HEM sing 397 n y 
C3C CAC HEM sing 398 n n 
C4C NC HEM sing 399 n y 
CMC HMC HEM sing 400 n n 
CMC HMCA HEM sing 401 n n 
CMC HMCB HEM sing 402 n n 
CAC CBC HEM doub 403 n n 
CAC HAC HEM sing 404 n n 
CBC HBC HEM sing 405 n n 
CBC HBCA HEM sing 406 n n 
C1D C2D HEM sing 407 n n 
C1D ND HEM doub 408 n n 
C2D C3D HEM doub 409 n n 
C2D CMD HEM sing 410 n n 
C3D C4D HEM sing 411 n n 
C3D CAD HEM sing 412 n n 
C4D ND HEM sing 413 n n 
CMD HMD HEM sing 414 n n 
CMD HMDA HEM sing 415 n n 
CMD HMDB HEM sing 416 n n 
CAD CBD HEM sing 417 n n 
CAD HAD HEM sing 418 n n 
CAD HADA HEM sing 419 n n 
CBD CGD HEM sing 420 n n 
CBD HBD HEM sing 421 n n 
CBD HBDA HEM sing 422 n n 
CGD O1D HEM doub 423 n n 
CGD O2D HEM sing 424 n n 
O2A H2A HEM sing 425 n n 
O2D H2D HEM sing 426 n n 
FE NA HEM sing 427 n n 
FE NB HEM sing 428 n n 
FE NC HEM sing 429 n n 
FE ND HEM sing 430 n n 
#
_atom_sites.entry_id                     5C3J 
_atom_sites.fract_transf_matrix[1][1]    0.008081 
_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]    0.007885 
_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]    0.004536 
_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
I 5 MLI A 1 701 701 MLI MLI . 
J 6 FAD A 1 702 702 FAD FAD . 
K 7 FES B 1 301 301 FES FES . 
L 8 SF4 B 1 302 302 SF4 SF4 . 
M 9 F3S B 1 303 303 F3S F3S . 
N 10 HEM C 1 201 201 HEM HEM . 
O 11 UQ1 C 1 202 301 UQ1 DRG . 
P 12 EPH D 1 201 201 EPH EPH . 
Q 5 MLI E 1 701 701 MLI MLI . 
R 6 FAD E 1 702 702 FAD FAD . 
S 7 FES F 1 301 301 FES FES . 
T 8 SF4 F 1 302 302 SF4 SF4 . 
U 9 F3S F 1 303 303 F3S F3S . 
V 10 HEM G 1 201 201 HEM HEM . 
W 11 UQ1 G 1 202 301 UQ1 DRG . 
X 12 EPH H 1 201 201 EPH EPH . 
#
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 . . . V 10 67.422 -53.919 81.557 1 66.77 ? CHA HEM 201 G 1 
HETATM 2 C CHB HEM . . . V 10 68.87 -58.497 81.287 1 71.75 ? CHB HEM 201 G 1 
HETATM 3 C CHC HEM . . . V 10 73.495 -57.048 81.671 1 73.28 ? CHC HEM 201 G 1 
HETATM 4 C CHD HEM . . . V 10 72.013 -52.434 81.933 1 67.93 ? CHD HEM 201 G 1 
HETATM 5 C C1A HEM . . . V 10 67.438 -55.279 81.439 1 65.83 ? C1A HEM 201 G 1 
HETATM 6 C C2A HEM . . . V 10 66.285 -56.074 81.227 1 64.54 ? C2A HEM 201 G 1 
HETATM 7 C C3A HEM . . . V 10 66.686 -57.365 81.149 1 63.89 ? C3A HEM 201 G 1 
HETATM 8 C C4A HEM . . . V 10 68.089 -57.364 81.316 1 68.44 ? C4A HEM 201 G 1 
HETATM 9 C CMA HEM . . . V 10 65.803 -58.568 80.929 1 61.98 ? CMA HEM 201 G 1 
HETATM 10 C CAA HEM . . . V 10 64.867 -55.564 81.1 1 61.95 ? CAA HEM 201 G 1 
HETATM 11 C CBA HEM . . . V 10 64.336 -55.171 82.479 1 58.96 ? CBA HEM 201 G 1 
HETATM 12 C CGA HEM . . . V 10 63.111 -54.309 82.375 1 57.17 ? CGA HEM 201 G 1 
HETATM 13 O O1A HEM . . . V 10 62.507 -54.143 81.281 1 51.59 ? O1A HEM 201 G 1 
HETATM 14 O O2A HEM . . . V 10 62.71 -53.757 83.429 1 59.8 ? O2A HEM 201 G 1 
HETATM 15 C C1B HEM . . . V 10 70.266 -58.483 81.372 1 72.63 ? C1B HEM 201 G 1 
HETATM 16 C C2B HEM . . . V 10 71.028 -59.683 81.338 1 73.39 ? C2B HEM 201 G 1 
HETATM 17 C C3B HEM . . . V 10 72.344 -59.337 81.444 1 73.98 ? C3B HEM 201 G 1 
HETATM 18 C C4B HEM . . . V 10 72.354 -57.841 81.545 1 73.24 ? C4B HEM 201 G 1 
HETATM 19 C CMB HEM . . . V 10 70.511 -61.1 81.207 1 70.93 ? CMB HEM 201 G 1 
HETATM 20 C CAB HEM . . . V 10 73.422 -60.359 81.432 1 74.4 ? CAB HEM 201 G 1 
HETATM 21 C CBB HEM . . . V 10 74.726 -60.126 81.506 1 74.52 ? CBB HEM 201 G 1 
HETATM 22 C C1C HEM . . . V 10 73.502 -55.655 81.763 1 74.79 ? C1C HEM 201 G 1 
HETATM 23 C C2C HEM . . . V 10 74.664 -54.873 81.87 1 75.75 ? C2C HEM 201 G 1 
HETATM 24 C C3C HEM . . . V 10 74.279 -53.553 81.952 1 75.63 ? C3C HEM 201 G 1 
HETATM 25 C C4C HEM . . . V 10 72.838 -53.527 81.884 1 71.8 ? C4C HEM 201 G 1 
HETATM 26 C CMC HEM . . . V 10 76.104 -55.335 81.893 1 75.1 ? CMC HEM 201 G 1 
HETATM 27 C CAC HEM . . . V 10 75.328 -52.508 82.04 1 81 ? CAC HEM 201 G 1 
HETATM 28 C CBC HEM . . . V 10 75.137 -51.2 82.002 1 84.81 ? CBC HEM 201 G 1 
HETATM 29 C C1D HEM . . . V 10 70.625 -52.513 81.852 1 64.16 ? C1D HEM 201 G 1 
HETATM 30 C C2D HEM . . . V 10 69.786 -51.3 81.91 1 63.74 ? C2D HEM 201 G 1 
HETATM 31 C C3D HEM . . . V 10 68.493 -51.689 81.815 1 64.62 ? C3D HEM 201 G 1 
HETATM 32 C C4D HEM . . . V 10 68.569 -53.16 81.679 1 66.87 ? C4D HEM 201 G 1 
HETATM 33 C CMD HEM . . . V 10 70.236 -49.861 82.057 1 59.85 ? CMD HEM 201 G 1 
HETATM 34 C CAD HEM . . . V 10 67.333 -50.681 81.848 1 62.7 ? CAD HEM 201 G 1 
HETATM 35 C CBD HEM . . . V 10 65.861 -51.044 82.173 1 59.84 ? CBD HEM 201 G 1 
HETATM 36 C CGD HEM . . . V 10 65.602 -51.057 83.669 1 58.92 ? CGD HEM 201 G 1 
HETATM 37 O O1D HEM . . . V 10 64.453 -50.886 84.155 1 50.96 ? O1D HEM 201 G 1 
HETATM 38 O O2D HEM . . . V 10 66.56 -51.252 84.448 1 60.27 ? O2D HEM 201 G 1 
HETATM 39 N NA HEM . . . V 10 68.54 -56.079 81.5 1 67.06 ? NA HEM 201 G 1 
HETATM 40 N NB HEM . . . V 10 71.075 -57.419 81.488 1 73.37 ? NB HEM 201 G 1 
HETATM 41 N NC HEM . . . V 10 72.412 -54.825 81.796 1 70.63 ? NC HEM 201 G 1 
HETATM 42 N ND HEM . . . V 10 69.855 -53.604 81.706 1 66.23 ? ND HEM 201 G 1 
HETATM 43 FE FE HEM . . . V 10 70.422 -55.409 81.594 1 61.41 ? FE HEM 201 G 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           313 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           43 
#