data_4YTM
#
_model_server_result.job_id            yY499A231vixQm85gdA0Xg 
_model_server_result.datetime_utc      '2024-11-24 18:30:39' 
_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          4ytm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":201}' 
#
_entry.id    4YTM 
#
_exptl.entry_id    4YTM 
_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            4YTM 
_cell.length_a            123.654 
_cell.length_b            126.426 
_cell.length_c            220.873 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4YTM 
_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 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? 
metalc ? metalc2 B SG CYS 94 B CYS 94 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? 
metalc ? metalc3 B SG CYS 97 B CYS 97 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? 
metalc ? metalc4 B SG CYS 109 B CYS 109 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
metalc ? metalc5 B SG CYS 182 B CYS 182 1_555 L FE3 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? 
metalc ? metalc6 B SG CYS 185 B CYS 185 1_555 L FE1 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? 
metalc ? metalc7 B SG CYS 188 B CYS 188 1_555 L FE2 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? 
metalc ? metalc8 B SG CYS 192 B CYS 192 1_555 M FE4 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? 
metalc ? metalc9 B SG CYS 239 B CYS 239 1_555 M FE1 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? 
metalc ? metalc10 B SG CYS 245 B CYS 245 1_555 M FE3 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? 
metalc ? metalc11 B SG CYS 249 B CYS 249 1_555 L FE4 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
metalc ? metalc12 C NE2 HIS 131 C HIS 131 1_555 N FE HEM . C HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? 
metalc ? metalc13 N FE HEM . C HEM 201 1_555 D NE2 HIS 95 D HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? 
metalc ? metalc14 F SG CYS 89 F CYS 89 1_555 S FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? 
metalc ? metalc15 F SG CYS 94 F CYS 94 1_555 S FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? 
metalc ? metalc16 F SG CYS 97 F CYS 97 1_555 S FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? 
metalc ? metalc17 F SG CYS 109 F CYS 109 1_555 S FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? 
metalc ? metalc18 F SG CYS 182 F CYS 182 1_555 T FE3 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? 
metalc ? metalc19 F SG CYS 185 F CYS 185 1_555 T FE1 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? 
metalc ? metalc20 F SG CYS 188 F CYS 188 1_555 T FE2 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? 
metalc ? metalc21 F SG CYS 192 F CYS 192 1_555 U FE4 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? 
metalc ? metalc22 F SG CYS 239 F CYS 239 1_555 U FE1 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? 
metalc ? metalc23 F SG CYS 245 F CYS 245 1_555 U FE3 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? 
metalc ? metalc24 F SG CYS 249 F CYS 249 1_555 T FE4 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? 
metalc ? metalc25 G NE2 HIS 131 G HIS 131 1_555 V FE HEM . G HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? 
metalc ? metalc26 V FE HEM . G HEM 201 1_555 H NE2 HIS 95 H HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? 
#
_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 390 n n 
CHA C4D HEM doub 391 n n 
CHA HHA HEM sing 392 n n 
CHB C4A HEM sing 393 n n 
CHB C1B HEM doub 394 n n 
CHB HHB HEM sing 395 n n 
CHC C4B HEM sing 396 n n 
CHC C1C HEM doub 397 n n 
CHC HHC HEM sing 398 n n 
CHD C4C HEM doub 399 n n 
CHD C1D HEM sing 400 n n 
CHD HHD HEM sing 401 n n 
C1A C2A HEM doub 402 n y 
C1A NA HEM sing 403 n y 
C2A C3A HEM sing 404 n y 
C2A CAA HEM sing 405 n n 
C3A C4A HEM doub 406 n y 
C3A CMA HEM sing 407 n n 
C4A NA HEM sing 408 n y 
CMA HMA HEM sing 409 n n 
CMA HMAA HEM sing 410 n n 
CMA HMAB HEM sing 411 n n 
CAA CBA HEM sing 412 n n 
CAA HAA HEM sing 413 n n 
CAA HAAA HEM sing 414 n n 
CBA CGA HEM sing 415 n n 
CBA HBA HEM sing 416 n n 
CBA HBAA HEM sing 417 n n 
CGA O1A HEM doub 418 n n 
CGA O2A HEM sing 419 n n 
C1B C2B HEM sing 420 n n 
C1B NB HEM sing 421 n n 
C2B C3B HEM doub 422 n n 
C2B CMB HEM sing 423 n n 
C3B C4B HEM sing 424 n n 
C3B CAB HEM sing 425 n n 
C4B NB HEM doub 426 n n 
CMB HMB HEM sing 427 n n 
CMB HMBA HEM sing 428 n n 
CMB HMBB HEM sing 429 n n 
CAB CBB HEM doub 430 n n 
CAB HAB HEM sing 431 n n 
CBB HBB HEM sing 432 n n 
CBB HBBA HEM sing 433 n n 
C1C C2C HEM sing 434 n y 
C1C NC HEM sing 435 n y 
C2C C3C HEM doub 436 n y 
C2C CMC HEM sing 437 n n 
C3C C4C HEM sing 438 n y 
C3C CAC HEM sing 439 n n 
C4C NC HEM sing 440 n y 
CMC HMC HEM sing 441 n n 
CMC HMCA HEM sing 442 n n 
CMC HMCB HEM sing 443 n n 
CAC CBC HEM doub 444 n n 
CAC HAC HEM sing 445 n n 
CBC HBC HEM sing 446 n n 
CBC HBCA HEM sing 447 n n 
C1D C2D HEM sing 448 n n 
C1D ND HEM doub 449 n n 
C2D C3D HEM doub 450 n n 
C2D CMD HEM sing 451 n n 
C3D C4D HEM sing 452 n n 
C3D CAD HEM sing 453 n n 
C4D ND HEM sing 454 n n 
CMD HMD HEM sing 455 n n 
CMD HMDA HEM sing 456 n n 
CMD HMDB HEM sing 457 n n 
CAD CBD HEM sing 458 n n 
CAD HAD HEM sing 459 n n 
CAD HADA HEM sing 460 n n 
CBD CGD HEM sing 461 n n 
CBD HBD HEM sing 462 n n 
CBD HBDA HEM sing 463 n n 
CGD O1D HEM doub 464 n n 
CGD O2D HEM sing 465 n n 
O2A H2A HEM sing 466 n n 
O2D H2D HEM sing 467 n n 
FE NA HEM sing 468 n n 
FE NB HEM sing 469 n n 
FE NC HEM sing 470 n n 
FE ND HEM sing 471 n n 
#
_atom_sites.entry_id                     4YTM 
_atom_sites.fract_transf_matrix[1][1]    0.008087 
_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]    0.00791 
_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]    0.004527 
_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 F6A C 1 202 202 F6A F6A . 
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 F6A G 1 202 202 F6A F6A . 
#
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 . . . N 10 36.935 -50.313 -53.674 1 86.66 ? CHA HEM 201 C 1 
HETATM 2 C CHB HEM . . . N 10 38.028 -54.969 -53.096 1 89.36 ? CHB HEM 201 C 1 
HETATM 3 C CHC HEM . . . N 10 42.751 -53.851 -53.297 1 95.07 ? CHC HEM 201 C 1 
HETATM 4 C CHD HEM . . . N 10 41.615 -49.216 -54.169 1 88.91 ? CHD HEM 201 C 1 
HETATM 5 C C1A HEM . . . N 10 36.849 -51.661 -53.494 1 89.01 ? C1A HEM 201 C 1 
HETATM 6 C C2A HEM . . . N 10 35.632 -52.38 -53.437 1 90.91 ? C2A HEM 201 C 1 
HETATM 7 C C3A HEM . . . N 10 35.945 -53.691 -53.277 1 87.92 ? C3A HEM 201 C 1 
HETATM 8 C C4A HEM . . . N 10 37.348 -53.781 -53.231 1 87.75 ? C4A HEM 201 C 1 
HETATM 9 C CMA HEM . . . N 10 34.978 -54.843 -53.167 1 87.04 ? CMA HEM 201 C 1 
HETATM 10 C CAA HEM . . . N 10 34.235 -51.8 -53.551 1 94.4 ? CAA HEM 201 C 1 
HETATM 11 C CBA HEM . . . N 10 33.601 -51.584 -52.17 1 96.76 ? CBA HEM 201 C 1 
HETATM 12 C CGA HEM . . . N 10 32.455 -50.607 -52.244 1 92.09 ? CGA HEM 201 C 1 
HETATM 13 O O1A HEM . . . N 10 31.75 -50.55 -53.291 1 79.2 ? O1A HEM 201 C 1 
HETATM 14 O O2A HEM . . . N 10 32.24 -49.863 -51.244 1 89.22 ? O2A HEM 201 C 1 
HETATM 15 C C1B HEM . . . N 10 39.423 -55.057 -53.106 1 92.77 ? C1B HEM 201 C 1 
HETATM 16 C C2B HEM . . . N 10 40.086 -56.302 -52.925 1 96.74 ? C2B HEM 201 C 1 
HETATM 17 C C3B HEM . . . N 10 41.432 -56.05 -52.96 1 98.39 ? C3B HEM 201 C 1 
HETATM 18 C C4B HEM . . . N 10 41.558 -54.569 -53.183 1 93.86 ? C4B HEM 201 C 1 
HETATM 19 C CMB HEM . . . N 10 39.426 -57.656 -52.713 1 93.77 ? CMB HEM 201 C 1 
HETATM 20 C CAB HEM . . . N 10 42.442 -57.136 -52.812 1 103.86 ? CAB HEM 201 C 1 
HETATM 21 C CBB HEM . . . N 10 43.761 -57.002 -52.926 1 107.86 ? CBB HEM 201 C 1 
HETATM 22 C C1C HEM . . . N 10 42.864 -52.482 -53.566 1 92.25 ? C1C HEM 201 C 1 
HETATM 23 C C2C HEM . . . N 10 44.078 -51.807 -53.765 1 91.61 ? C2C HEM 201 C 1 
HETATM 24 C C3C HEM . . . N 10 43.79 -50.48 -54.022 1 87.99 ? C3C HEM 201 C 1 
HETATM 25 C C4C HEM . . . N 10 42.36 -50.349 -53.98 1 87.68 ? C4C HEM 201 C 1 
HETATM 26 C CMC HEM . . . N 10 45.472 -52.395 -53.721 1 92.34 ? CMC HEM 201 C 1 
HETATM 27 C CAC HEM . . . N 10 44.879 -49.511 -54.282 1 86.58 ? CAC HEM 201 C 1 
HETATM 28 C CBC HEM . . . N 10 44.728 -48.221 -54.55 1 87.61 ? CBC HEM 201 C 1 
HETATM 29 C C1D HEM . . . N 10 40.224 -49.191 -54.094 1 86.23 ? C1D HEM 201 C 1 
HETATM 30 C C2D HEM . . . N 10 39.482 -47.931 -54.26 1 82.05 ? C2D HEM 201 C 1 
HETATM 31 C C3D HEM . . . N 10 38.185 -48.209 -54.129 1 84.24 ? C3D HEM 201 C 1 
HETATM 32 C C4D HEM . . . N 10 38.138 -49.663 -53.869 1 85.67 ? C4D HEM 201 C 1 
HETATM 33 C CMD HEM . . . N 10 40.006 -46.548 -54.537 1 81.97 ? CMD HEM 201 C 1 
HETATM 34 C CAD HEM . . . N 10 37.134 -47.108 -54.243 1 87.63 ? CAD HEM 201 C 1 
HETATM 35 C CBD HEM . . . N 10 35.624 -47.428 -54.153 1 86.53 ? CBD HEM 201 C 1 
HETATM 36 C CGD HEM . . . N 10 35.038 -47.223 -52.765 1 85.41 ? CGD HEM 201 C 1 
HETATM 37 O O1D HEM . . . N 10 33.802 -47.288 -52.588 1 82.82 ? O1D HEM 201 C 1 
HETATM 38 O O2D HEM . . . N 10 35.748 -46.972 -51.768 1 85.01 ? O2D HEM 201 C 1 
HETATM 39 N NA HEM . . . N 10 37.897 -52.522 -53.349 1 88.79 ? NA HEM 201 C 1 
HETATM 40 N NB HEM . . . N 10 40.318 -54.066 -53.241 1 91.26 ? NB HEM 201 C 1 
HETATM 41 N NC HEM . . . N 10 41.848 -51.572 -53.666 1 85.72 ? NC HEM 201 C 1 
HETATM 42 N ND HEM . . . N 10 39.383 -50.21 -53.845 1 85.58 ? ND HEM 201 C 1 
HETATM 43 FE FE HEM . . . N 10 39.827 -52.048 -53.598 1 78.13 ? FE HEM 201 C 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    40 
_model_server_stats.query_time_ms           310 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           43 
#