data_3ZJ4
#
_model_server_result.job_id            JDwanpsTa3tWPznqzf0Kgw 
_model_server_result.datetime_utc      '2024-11-25 13:41:59' 
_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          3zj4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":4000}' 
#
_entry.id    3ZJ4 
#
_exptl.entry_id    3ZJ4 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          2 
_entity.src_method                  syn 
_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         82.08 
_cell.angle_beta          82.48 
_cell.angle_gamma         62.33 
_cell.entry_id            3ZJ4 
_cell.length_a            85.445 
_cell.length_b            88.207 
_cell.length_c            104.398 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3ZJ4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H 
_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
? 2 E N N 
? 2 F N N 
? 2 G N N 
? 2 H 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 A OH TYR 416 A TYR 389 1_555 E FE HEM . A HEM 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? 
metalc ? metalc2 B OH TYR 416 B TYR 389 1_555 F FE HEM . B HEM 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? 
metalc ? metalc3 C OH TYR 416 C TYR 389 1_555 G FE HEM . C HEM 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? 
metalc ? metalc4 D OH TYR 416 D TYR 389 1_555 H FE HEM . D HEM 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? 
#
_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 129 n n 
CHA C4D HEM doub 130 n n 
CHA HHA HEM sing 131 n n 
CHB C4A HEM sing 132 n n 
CHB C1B HEM doub 133 n n 
CHB HHB HEM sing 134 n n 
CHC C4B HEM sing 135 n n 
CHC C1C HEM doub 136 n n 
CHC HHC HEM sing 137 n n 
CHD C4C HEM doub 138 n n 
CHD C1D HEM sing 139 n n 
CHD HHD HEM sing 140 n n 
C1A C2A HEM doub 141 n y 
C1A NA HEM sing 142 n y 
C2A C3A HEM sing 143 n y 
C2A CAA HEM sing 144 n n 
C3A C4A HEM doub 145 n y 
C3A CMA HEM sing 146 n n 
C4A NA HEM sing 147 n y 
CMA HMA HEM sing 148 n n 
CMA HMAA HEM sing 149 n n 
CMA HMAB HEM sing 150 n n 
CAA CBA HEM sing 151 n n 
CAA HAA HEM sing 152 n n 
CAA HAAA HEM sing 153 n n 
CBA CGA HEM sing 154 n n 
CBA HBA HEM sing 155 n n 
CBA HBAA HEM sing 156 n n 
CGA O1A HEM doub 157 n n 
CGA O2A HEM sing 158 n n 
C1B C2B HEM sing 159 n n 
C1B NB HEM sing 160 n n 
C2B C3B HEM doub 161 n n 
C2B CMB HEM sing 162 n n 
C3B C4B HEM sing 163 n n 
C3B CAB HEM sing 164 n n 
C4B NB HEM doub 165 n n 
CMB HMB HEM sing 166 n n 
CMB HMBA HEM sing 167 n n 
CMB HMBB HEM sing 168 n n 
CAB CBB HEM doub 169 n n 
CAB HAB HEM sing 170 n n 
CBB HBB HEM sing 171 n n 
CBB HBBA HEM sing 172 n n 
C1C C2C HEM sing 173 n y 
C1C NC HEM sing 174 n y 
C2C C3C HEM doub 175 n y 
C2C CMC HEM sing 176 n n 
C3C C4C HEM sing 177 n y 
C3C CAC HEM sing 178 n n 
C4C NC HEM sing 179 n y 
CMC HMC HEM sing 180 n n 
CMC HMCA HEM sing 181 n n 
CMC HMCB HEM sing 182 n n 
CAC CBC HEM doub 183 n n 
CAC HAC HEM sing 184 n n 
CBC HBC HEM sing 185 n n 
CBC HBCA HEM sing 186 n n 
C1D C2D HEM sing 187 n n 
C1D ND HEM doub 188 n n 
C2D C3D HEM doub 189 n n 
C2D CMD HEM sing 190 n n 
C3D C4D HEM sing 191 n n 
C3D CAD HEM sing 192 n n 
C4D ND HEM sing 193 n n 
CMD HMD HEM sing 194 n n 
CMD HMDA HEM sing 195 n n 
CMD HMDB HEM sing 196 n n 
CAD CBD HEM sing 197 n n 
CAD HAD HEM sing 198 n n 
CAD HADA HEM sing 199 n n 
CBD CGD HEM sing 200 n n 
CBD HBD HEM sing 201 n n 
CBD HBDA HEM sing 202 n n 
CGD O1D HEM doub 203 n n 
CGD O2D HEM sing 204 n n 
O2A H2A HEM sing 205 n n 
O2D H2D HEM sing 206 n n 
FE NA HEM sing 207 n n 
FE NB HEM sing 208 n n 
FE NC HEM sing 209 n n 
FE ND HEM sing 210 n n 
#
_atom_sites.entry_id                     3ZJ4 
_atom_sites.fract_transf_matrix[1][1]    0.011703 
_atom_sites.fract_transf_matrix[1][2]    -0.006137 
_atom_sites.fract_transf_matrix[1][3]    -0.001011 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012801 
_atom_sites.fract_transf_matrix[2][3]    -0.001127 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.009699 
_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
E 2 HEM A 1 4000 4000 HEM HEM . 
F 2 HEM B 1 4000 4000 HEM HEM . 
G 2 HEM C 1 4000 4000 HEM HEM . 
H 2 HEM D 1 4000 4000 HEM HEM . 
#
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 2 -10.537 18.852 -53.354 1 29.3 ? CHA HEM 4000 D 1 
HETATM 2 C CHB HEM . . . H 2 -14.391 21.21 -51.573 1 30.59 ? CHB HEM 4000 D 1 
HETATM 3 C CHC HEM . . . H 2 -11.572 25.08 -50.862 1 25.29 ? CHC HEM 4000 D 1 
HETATM 4 C CHD HEM . . . H 2 -8.313 23.192 -53.894 1 26.63 ? CHD HEM 4000 D 1 
HETATM 5 C C1A HEM . . . H 2 -11.813 19.117 -52.898 1 23.66 ? C1A HEM 4000 D 1 
HETATM 6 C C2A HEM . . . H 2 -12.924 18.187 -52.803 1 23.52 ? C2A HEM 4000 D 1 
HETATM 7 C C3A HEM . . . H 2 -13.977 18.84 -52.31 1 21.68 ? C3A HEM 4000 D 1 
HETATM 8 C C4A HEM . . . H 2 -13.587 20.212 -52.075 1 28.66 ? C4A HEM 4000 D 1 
HETATM 9 C CMA HEM . . . H 2 -15.372 18.232 -52.043 1 28.2 ? CMA HEM 4000 D 1 
HETATM 10 C CAA HEM . . . H 2 -12.922 16.694 -53.182 1 25.72 ? CAA HEM 4000 D 1 
HETATM 11 C CBA HEM . . . H 2 -13.072 16.49 -54.681 1 21.92 ? CBA HEM 4000 D 1 
HETATM 12 C CGA HEM . . . H 2 -13.265 15.014 -54.893 1 28.29 ? CGA HEM 4000 D 1 
HETATM 13 O O1A HEM . . . H 2 -12.76 14.482 -55.915 1 22.91 ? O1A HEM 4000 D 1 
HETATM 14 O O2A HEM . . . H 2 -13.909 14.372 -54.021 1 25.29 ? O2A HEM 4000 D 1 
HETATM 15 C C1B HEM . . . H 2 -13.977 22.488 -51.272 1 41.63 ? C1B HEM 4000 D 1 
HETATM 16 C C2B HEM . . . H 2 -14.83 23.585 -50.865 1 32.62 ? C2B HEM 4000 D 1 
HETATM 17 C C3B HEM . . . H 2 -14.057 24.67 -50.666 1 31.8 ? C3B HEM 4000 D 1 
HETATM 18 C C4B HEM . . . H 2 -12.687 24.276 -50.939 1 29.63 ? C4B HEM 4000 D 1 
HETATM 19 C CMB HEM . . . H 2 -16.359 23.44 -50.72 1 33.46 ? CMB HEM 4000 D 1 
HETATM 20 C CAB HEM . . . H 2 -14.441 26.106 -50.22 1 23.82 ? CAB HEM 4000 D 1 
HETATM 21 C CBB HEM . . . H 2 -15.671 26.498 -49.869 1 39 ? CBB HEM 4000 D 1 
HETATM 22 C C1C HEM . . . H 2 -10.501 24.975 -51.722 1 21.24 ? C1C HEM 4000 D 1 
HETATM 23 C C2C HEM . . . H 2 -9.616 26.041 -52.146 1 28.91 ? C2C HEM 4000 D 1 
HETATM 24 C C3C HEM . . . H 2 -8.708 25.513 -52.99 1 20.44 ? C3C HEM 4000 D 1 
HETATM 25 C C4C HEM . . . H 2 -9.006 24.1 -53.124 1 27.02 ? C4C HEM 4000 D 1 
HETATM 26 C CMC HEM . . . H 2 -9.753 27.501 -51.663 1 24.35 ? CMC HEM 4000 D 1 
HETATM 27 C CAC HEM . . . H 2 -7.534 26.193 -53.744 1 27.67 ? CAC HEM 4000 D 1 
HETATM 28 C CBC HEM . . . H 2 -7.281 27.507 -53.75 1 27.88 ? CBC HEM 4000 D 1 
HETATM 29 C C1D HEM . . . H 2 -8.568 21.839 -54.006 1 20.4 ? C1D HEM 4000 D 1 
HETATM 30 C C2D HEM . . . H 2 -7.744 20.898 -54.729 1 28.17 ? C2D HEM 4000 D 1 
HETATM 31 C C3D HEM . . . H 2 -8.431 19.536 -54.569 1 26.75 ? C3D HEM 4000 D 1 
HETATM 32 C C4D HEM . . . H 2 -9.607 19.79 -53.76 1 26.4 ? C4D HEM 4000 D 1 
HETATM 33 C CMD HEM . . . H 2 -6.446 21.21 -55.503 1 24.49 ? CMD HEM 4000 D 1 
HETATM 34 C CAD HEM . . . H 2 -7.955 18.188 -55.156 1 22.22 ? CAD HEM 4000 D 1 
HETATM 35 C CBD HEM . . . H 2 -8.932 17.76 -56.247 1 24.69 ? CBD HEM 4000 D 1 
HETATM 36 C CGD HEM . . . H 2 -8.475 16.478 -56.893 1 20.96 ? CGD HEM 4000 D 1 
HETATM 37 O O1D HEM . . . H 2 -9.251 15.927 -57.719 1 21.3 ? O1D HEM 4000 D 1 
HETATM 38 O O2D HEM . . . H 2 -7.348 16.007 -56.585 1 21.67 ? O2D HEM 4000 D 1 
HETATM 39 N NA HEM . . . H 2 -12.261 20.344 -52.444 1 22.02 ? NA HEM 4000 D 1 
HETATM 40 N NB HEM . . . H 2 -12.676 22.945 -51.307 1 26.35 ? NB HEM 4000 D 1 
HETATM 41 N NC HEM . . . H 2 -10.099 23.81 -52.338 1 23.81 ? NC HEM 4000 D 1 
HETATM 42 N ND HEM . . . H 2 -9.644 21.149 -53.455 1 24.11 ? ND HEM 4000 D 1 
HETATM 43 FE FE HEM . . . H 2 -11.094 22.024 -52.261 1 28.59 ? FE HEM 4000 D 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    40 
_model_server_stats.query_time_ms           262 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           43 
#