data_1ZRT
#
_model_server_result.job_id            mxGqtB46-JfncysZdbv7Lw 
_model_server_result.datetime_utc      '2025-04-24 11:24:09' 
_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          1zrt 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":502}' 
#
_entry.id    1ZRT 
#
_exptl.entry_id    1ZRT 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          4 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            'PROTOPORPHYRIN IX CONTAINING FE' 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          113.57 
_cell.angle_gamma         90 
_cell.entry_id            1ZRT 
_cell.length_a            95.633 
_cell.length_b            154.36 
_cell.length_c            103.057 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1ZRT 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    'P 2yb' 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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
? 4 G N N 
? 4 H N N 
? 4 N N N 
? 4 O 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
disulf ? disulf1 B SG CYS 144 D CYS 144 1_555 B SG CYS 167 D CYS 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
disulf ? disulf2 C SG CYS 138 E CYS 138 1_555 C SG CYS 155 E CYS 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf3 E SG CYS 144 Q CYS 144 1_555 E SG CYS 167 Q CYS 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? 
disulf ? disulf4 F SG CYS 138 R CYS 138 1_555 F SG CYS 155 R CYS 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
covale ? covale1 B SG CYS 34 D CYS 34 1_555 L CAB HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.796 ? 
covale ? covale2 B SG CYS 37 D CYS 37 1_555 L CAC HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.804 ? 
covale ? covale3 E SG CYS 34 Q CYS 34 1_555 S CAB HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.896 ? 
covale ? covale4 E SG CYS 37 Q CYS 37 1_555 S CAC HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
metalc ? metalc1 A NE2 HIS 97 C HIS 97 1_555 G FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? 
metalc ? metalc2 A NE2 HIS 111 C HIS 111 1_555 H FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? 
metalc ? metalc3 A NE2 HIS 198 C HIS 198 1_555 G FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
metalc ? metalc4 A NE2 HIS 212 C HIS 212 1_555 H FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? 
metalc ? metalc5 B NE2 HIS 38 D HIS 38 1_555 L FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? 
metalc ? metalc6 B SD MET 183 D MET 183 1_555 L FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? 
metalc ? metalc7 C SG CYS 133 E CYS 133 1_555 M FE1 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? 
metalc ? metalc8 C ND1 HIS 135 E HIS 135 1_555 M FE2 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? 
metalc ? metalc9 C SG CYS 153 E CYS 153 1_555 M FE1 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? 
metalc ? metalc10 C N HIS 156 E HIS 156 1_555 M FE2 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? 
metalc ? metalc11 C ND1 HIS 156 E HIS 156 1_555 M FE2 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? 
metalc ? metalc12 D NE2 HIS 97 P HIS 97 1_555 N FE HEM . P HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
metalc ? metalc13 D NE2 HIS 111 P HIS 111 1_555 O FE HEM . P HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? 
metalc ? metalc14 D NE2 HIS 198 P HIS 198 1_555 N FE HEM . P HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? 
metalc ? metalc15 D NE2 HIS 212 P HIS 212 1_555 O FE HEM . P HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? 
metalc ? metalc16 E NE2 HIS 38 Q HIS 38 1_555 S FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? 
metalc ? metalc17 E SD MET 183 Q MET 183 1_555 S FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? 
metalc ? metalc18 F SG CYS 133 R CYS 133 1_555 U FE1 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? 
metalc ? metalc19 F ND1 HIS 135 R HIS 135 1_555 U FE2 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? 
metalc ? metalc20 F SG CYS 153 R CYS 153 1_555 U FE1 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? 
metalc ? metalc21 F N HIS 156 R HIS 156 1_555 U FE2 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? 
metalc ? metalc22 F ND1 HIS 156 R HIS 156 1_555 U FE2 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? 
#
_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 217 n n 
CHA C4D HEM doub 218 n n 
CHA HHA HEM sing 219 n n 
CHB C4A HEM sing 220 n n 
CHB C1B HEM doub 221 n n 
CHB HHB HEM sing 222 n n 
CHC C4B HEM sing 223 n n 
CHC C1C HEM doub 224 n n 
CHC HHC HEM sing 225 n n 
CHD C4C HEM doub 226 n n 
CHD C1D HEM sing 227 n n 
CHD HHD HEM sing 228 n n 
C1A C2A HEM doub 229 n y 
C1A NA HEM sing 230 n y 
C2A C3A HEM sing 231 n y 
C2A CAA HEM sing 232 n n 
C3A C4A HEM doub 233 n y 
C3A CMA HEM sing 234 n n 
C4A NA HEM sing 235 n y 
CMA HMA HEM sing 236 n n 
CMA HMAA HEM sing 237 n n 
CMA HMAB HEM sing 238 n n 
CAA CBA HEM sing 239 n n 
CAA HAA HEM sing 240 n n 
CAA HAAA HEM sing 241 n n 
CBA CGA HEM sing 242 n n 
CBA HBA HEM sing 243 n n 
CBA HBAA HEM sing 244 n n 
CGA O1A HEM doub 245 n n 
CGA O2A HEM sing 246 n n 
C1B C2B HEM sing 247 n n 
C1B NB HEM sing 248 n n 
C2B C3B HEM doub 249 n n 
C2B CMB HEM sing 250 n n 
C3B C4B HEM sing 251 n n 
C3B CAB HEM sing 252 n n 
C4B NB HEM doub 253 n n 
CMB HMB HEM sing 254 n n 
CMB HMBA HEM sing 255 n n 
CMB HMBB HEM sing 256 n n 
CAB CBB HEM doub 257 n n 
CAB HAB HEM sing 258 n n 
CBB HBB HEM sing 259 n n 
CBB HBBA HEM sing 260 n n 
C1C C2C HEM sing 261 n y 
C1C NC HEM sing 262 n y 
C2C C3C HEM doub 263 n y 
C2C CMC HEM sing 264 n n 
C3C C4C HEM sing 265 n y 
C3C CAC HEM sing 266 n n 
C4C NC HEM sing 267 n y 
CMC HMC HEM sing 268 n n 
CMC HMCA HEM sing 269 n n 
CMC HMCB HEM sing 270 n n 
CAC CBC HEM doub 271 n n 
CAC HAC HEM sing 272 n n 
CBC HBC HEM sing 273 n n 
CBC HBCA HEM sing 274 n n 
C1D C2D HEM sing 275 n n 
C1D ND HEM doub 276 n n 
C2D C3D HEM doub 277 n n 
C2D CMD HEM sing 278 n n 
C3D C4D HEM sing 279 n n 
C3D CAD HEM sing 280 n n 
C4D ND HEM sing 281 n n 
CMD HMD HEM sing 282 n n 
CMD HMDA HEM sing 283 n n 
CMD HMDB HEM sing 284 n n 
CAD CBD HEM sing 285 n n 
CAD HAD HEM sing 286 n n 
CAD HADA HEM sing 287 n n 
CBD CGD HEM sing 288 n n 
CBD HBD HEM sing 289 n n 
CBD HBDA HEM sing 290 n n 
CGD O1D HEM doub 291 n n 
CGD O2D HEM sing 292 n n 
O2A H2A HEM sing 293 n n 
O2D H2D HEM sing 294 n n 
FE NA HEM sing 295 n n 
FE NB HEM sing 296 n n 
FE NC HEM sing 297 n n 
FE ND HEM sing 298 n n 
#
_atom_sites.entry_id                     1ZRT 
_atom_sites.fract_transf_matrix[1][1]    0.010457 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.004562 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006478 
_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]    0.010587 
_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
G 4 HEM C 1 501 501 HEM HEM . 
H 4 HEM C 1 502 502 HEM HEM . 
I 5 SMA C 1 503 503 SMA SMA . 
J 6 UNL C 1 504 504 UNL UNK . 
K 6 UNL C 1 505 505 UNL UNK . 
L 7 HEC D 1 501 501 HEC HEC . 
M 8 FES E 1 501 501 FES FES . 
N 4 HEM P 1 501 501 HEM HEM . 
O 4 HEM P 1 502 502 HEM HEM . 
P 5 SMA P 1 503 503 SMA SMA . 
Q 6 UNL P 1 504 504 UNL UNK . 
R 6 UNL P 1 505 505 UNL UNK . 
S 7 HEC Q 1 501 501 HEC HEC . 
T 9 PG6 Q 1 502 502 PG6 PG6 . 
U 8 FES R 1 501 501 FES FES . 
#
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 . . . H 4 21.101 13.115 17.411 1 113.8 ? CHA HEM 502 C 1 
HETATM 2 C CHB HEM . . . H 4 16.64 12.668 19.282 1 98.64 ? CHB HEM 502 C 1 
HETATM 3 C CHC HEM . . . H 4 15.955 9.943 15.334 1 109.26 ? CHC HEM 502 C 1 
HETATM 4 C CHD HEM . . . H 4 20.632 9.279 14.471 1 105.91 ? CHD HEM 502 C 1 
HETATM 5 C C1A HEM . . . H 4 19.981 13.273 18.207 1 116.11 ? C1A HEM 502 C 1 
HETATM 6 C C2A HEM . . . H 4 19.894 14.187 19.323 1 117.93 ? C2A HEM 502 C 1 
HETATM 7 C C3A HEM . . . H 4 18.661 14.083 19.852 1 110.9 ? C3A HEM 502 C 1 
HETATM 8 C C4A HEM . . . H 4 17.927 13.09 19.089 1 105.7 ? C4A HEM 502 C 1 
HETATM 9 C CMA HEM . . . H 4 18.118 14.87 21.062 1 110.4 ? CMA HEM 502 C 1 
HETATM 10 C CAA HEM . . . H 4 21.045 15.121 19.768 1 114.96 ? CAA HEM 502 C 1 
HETATM 11 C CBA HEM . . . H 4 21.323 16.288 18.808 1 115.41 ? CBA HEM 502 C 1 
HETATM 12 C CGA HEM . . . H 4 20.233 16.683 17.818 1 117.01 ? CGA HEM 502 C 1 
HETATM 13 O O1A HEM . . . H 4 19.091 16.963 18.275 1 115.11 ? O1A HEM 502 C 1 
HETATM 14 O O2A HEM . . . H 4 20.494 16.785 16.581 1 111.95 ? O2A HEM 502 C 1 
HETATM 15 C C1B HEM . . . H 4 16.02 11.86 18.358 1 106.47 ? C1B HEM 502 C 1 
HETATM 16 C C2B HEM . . . H 4 14.671 11.296 18.369 1 108.95 ? C2B HEM 502 C 1 
HETATM 17 C C3B HEM . . . H 4 14.477 10.551 17.303 1 102.81 ? C3B HEM 502 C 1 
HETATM 18 C C4B HEM . . . H 4 15.724 10.577 16.542 1 108.84 ? C4B HEM 502 C 1 
HETATM 19 C CMB HEM . . . H 4 13.558 11.448 19.389 1 91.41 ? CMB HEM 502 C 1 
HETATM 20 C CAB HEM . . . H 4 13.139 9.831 17.059 1 94.64 ? CAB HEM 502 C 1 
HETATM 21 C CBB HEM . . . H 4 12.594 9.708 15.861 1 98.82 ? CBB HEM 502 C 1 
HETATM 22 C C1C HEM . . . H 4 17.111 9.497 14.765 1 96.11 ? C1C HEM 502 C 1 
HETATM 23 C C2C HEM . . . H 4 17.165 8.642 13.618 1 85.31 ? C2C HEM 502 C 1 
HETATM 24 C C3C HEM . . . H 4 18.462 8.405 13.339 1 97.32 ? C3C HEM 502 C 1 
HETATM 25 C C4C HEM . . . H 4 19.241 9.17 14.336 1 107.3 ? C4C HEM 502 C 1 
HETATM 26 C CMC HEM . . . H 4 15.88 8.127 12.927 1 80.37 ? CMC HEM 502 C 1 
HETATM 27 C CAC HEM . . . H 4 19.125 7.528 12.189 1 99.05 ? CAC HEM 502 C 1 
HETATM 28 C CBC HEM . . . H 4 18.672 7.194 10.946 1 85.37 ? CBC HEM 502 C 1 
HETATM 29 C C1D HEM . . . H 4 21.166 10.333 15.186 1 104.2 ? C1D HEM 502 C 1 
HETATM 30 C C2D HEM . . . H 4 22.517 10.772 15.174 1 96.43 ? C2D HEM 502 C 1 
HETATM 31 C C3D HEM . . . H 4 22.701 11.839 15.979 1 107.33 ? C3D HEM 502 C 1 
HETATM 32 C C4D HEM . . . H 4 21.389 12.106 16.53 1 113.52 ? C4D HEM 502 C 1 
HETATM 33 C CMD HEM . . . H 4 23.502 10.011 14.341 1 97.22 ? CMD HEM 502 C 1 
HETATM 34 C CAD HEM . . . H 4 23.969 12.699 16.292 1 101.82 ? CAD HEM 502 C 1 
HETATM 35 C CBD HEM . . . H 4 24.833 12.171 17.435 1 111.51 ? CBD HEM 502 C 1 
HETATM 36 C CGD HEM . . . H 4 25.622 13.279 18.063 1 126.36 ? CGD HEM 502 C 1 
HETATM 37 O O1D HEM . . . H 4 26.568 12.931 18.862 1 118.33 ? O1D HEM 502 C 1 
HETATM 38 O O2D HEM . . . H 4 25.254 14.461 17.73 1 125.79 ? O2D HEM 502 C 1 
HETATM 39 N NA HEM . . . H 4 18.761 12.621 18.084 1 114.14 ? NA HEM 502 C 1 
HETATM 40 N NB HEM . . . H 4 16.634 11.393 17.208 1 110.02 ? NB HEM 502 C 1 
HETATM 41 N NC HEM . . . H 4 18.357 9.82 15.181 1 97.79 ? NC HEM 502 C 1 
HETATM 42 N ND HEM . . . H 4 20.484 11.177 16.039 1 110.42 ? ND HEM 502 C 1 
HETATM 43 FE FE HEM . . . H 4 18.534 11.199 16.523 1 94.72 ? FE HEM 502 C 1 
#
_model_server_stats.io_time_ms              84 
_model_server_stats.parse_time_ms           40 
_model_server_stats.create_model_time_ms    30 
_model_server_stats.query_time_ms           536 
_model_server_stats.encode_time_ms          16 
_model_server_stats.element_count           43 
#