data_3ONZ
#
_model_server_result.job_id            p1e_WAp4vIIcIuljjsB0xA 
_model_server_result.datetime_utc      '2025-06-20 20:42:26' 
_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          3onz 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":148}' 
#
_entry.id    3ONZ 
#
_exptl.entry_id    3ONZ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          3 
_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            3ONZ 
_cell.length_a            53.27 
_cell.length_b            53.27 
_cell.length_c            193.62 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3ONZ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 C N N 
? 3 G 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 NE2 HIS 87 A HIS 87 1_555 C FE HEM . A HEM 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? 
metalc ? metalc2 D O1 NO2 . A NO2 142 1_555 C FE HEM . A HEM 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.92 ? 
metalc ? metalc3 D N NO2 . A NO2 142 1_555 C FE HEM . A HEM 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.67 ? 
metalc ? metalc4 B NE2 HIS 63 B HIS 63 1_555 G FE HEM . B HEM 148 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.287 ? 
#
_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                     3ONZ 
_atom_sites.fract_transf_matrix[1][1]    0.018772 
_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]    0.018772 
_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]    0.005165 
_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
C 3 HEM A 1 143 143 HEM HEM . 
D 4 NO2 A 1 142 1 NO2 NO2 . 
E 5 MBN A 1 144 5 MBN MBN . 
F 5 MBN A 1 145 6 MBN MBN . 
G 3 HEM B 1 148 148 HEM HEM . 
H 4 NO2 B 1 147 2 NO2 NO2 . 
I 5 MBN B 1 149 3 MBN MBN . 
J 5 MBN B 1 150 4 MBN MBN . 
K 6 HOH A 1 146 2 HOH HOH . 
K 6 HOH A 2 147 3 HOH HOH . 
K 6 HOH A 3 148 5 HOH HOH . 
K 6 HOH A 4 149 6 HOH HOH . 
K 6 HOH A 5 150 7 HOH HOH . 
K 6 HOH A 6 151 9 HOH HOH . 
K 6 HOH A 7 152 10 HOH HOH . 
K 6 HOH A 8 153 11 HOH HOH . 
K 6 HOH A 9 154 12 HOH HOH . 
K 6 HOH A 10 155 13 HOH HOH . 
K 6 HOH A 11 156 14 HOH HOH . 
K 6 HOH A 12 157 15 HOH HOH . 
K 6 HOH A 13 158 16 HOH HOH . 
K 6 HOH A 14 159 17 HOH HOH . 
K 6 HOH A 15 160 18 HOH HOH . 
K 6 HOH A 16 161 19 HOH HOH . 
K 6 HOH A 17 162 20 HOH HOH . 
K 6 HOH A 18 163 21 HOH HOH . 
K 6 HOH A 19 164 23 HOH HOH . 
K 6 HOH A 20 165 25 HOH HOH . 
K 6 HOH A 21 166 26 HOH HOH . 
K 6 HOH A 22 167 27 HOH HOH . 
K 6 HOH A 23 168 28 HOH HOH . 
K 6 HOH A 24 169 29 HOH HOH . 
K 6 HOH A 25 170 30 HOH HOH . 
K 6 HOH A 26 171 35 HOH HOH . 
K 6 HOH A 27 172 37 HOH HOH . 
K 6 HOH A 28 173 39 HOH HOH . 
K 6 HOH A 29 174 40 HOH HOH . 
K 6 HOH A 30 175 41 HOH HOH . 
K 6 HOH A 31 176 43 HOH HOH . 
K 6 HOH A 32 177 44 HOH HOH . 
K 6 HOH A 33 178 45 HOH HOH . 
K 6 HOH A 34 179 46 HOH HOH . 
K 6 HOH A 35 180 47 HOH HOH . 
K 6 HOH A 36 181 49 HOH HOH . 
K 6 HOH A 37 182 50 HOH HOH . 
K 6 HOH A 38 183 54 HOH HOH . 
K 6 HOH A 39 184 55 HOH HOH . 
K 6 HOH A 40 185 57 HOH HOH . 
K 6 HOH A 41 186 58 HOH HOH . 
K 6 HOH A 42 187 62 HOH HOH . 
K 6 HOH A 43 188 63 HOH HOH . 
K 6 HOH A 44 189 64 HOH HOH . 
K 6 HOH A 45 190 66 HOH HOH . 
K 6 HOH A 46 191 68 HOH HOH . 
K 6 HOH A 47 192 70 HOH HOH . 
K 6 HOH A 48 193 71 HOH HOH . 
K 6 HOH A 49 194 72 HOH HOH . 
K 6 HOH A 50 195 73 HOH HOH . 
K 6 HOH A 51 196 77 HOH HOH . 
K 6 HOH A 52 197 78 HOH HOH . 
K 6 HOH A 53 198 79 HOH HOH . 
K 6 HOH A 54 199 81 HOH HOH . 
K 6 HOH A 55 200 82 HOH HOH . 
K 6 HOH A 56 201 83 HOH HOH . 
K 6 HOH A 57 202 84 HOH HOH . 
K 6 HOH A 58 203 85 HOH HOH . 
K 6 HOH A 59 204 86 HOH HOH . 
K 6 HOH A 60 205 87 HOH HOH . 
K 6 HOH A 61 206 89 HOH HOH . 
K 6 HOH A 62 207 90 HOH HOH . 
K 6 HOH A 63 208 91 HOH HOH . 
K 6 HOH A 64 209 92 HOH HOH . 
K 6 HOH A 65 210 94 HOH HOH . 
L 6 HOH B 1 151 1 HOH HOH . 
L 6 HOH B 2 152 4 HOH HOH . 
L 6 HOH B 3 153 8 HOH HOH . 
L 6 HOH B 4 154 22 HOH HOH . 
L 6 HOH B 5 155 24 HOH HOH . 
L 6 HOH B 6 156 31 HOH HOH . 
L 6 HOH B 7 157 32 HOH HOH . 
L 6 HOH B 8 158 33 HOH HOH . 
L 6 HOH B 9 159 34 HOH HOH . 
L 6 HOH B 10 160 36 HOH HOH . 
L 6 HOH B 11 161 38 HOH HOH . 
L 6 HOH B 12 162 42 HOH HOH . 
L 6 HOH B 13 163 48 HOH HOH . 
L 6 HOH B 14 164 51 HOH HOH . 
L 6 HOH B 15 165 52 HOH HOH . 
L 6 HOH B 16 166 53 HOH HOH . 
L 6 HOH B 17 167 56 HOH HOH . 
L 6 HOH B 18 168 59 HOH HOH . 
L 6 HOH B 19 169 60 HOH HOH . 
L 6 HOH B 20 170 61 HOH HOH . 
L 6 HOH B 21 171 65 HOH HOH . 
L 6 HOH B 22 172 67 HOH HOH . 
L 6 HOH B 23 173 69 HOH HOH . 
L 6 HOH B 24 174 74 HOH HOH . 
L 6 HOH B 25 175 75 HOH HOH . 
L 6 HOH B 26 176 76 HOH HOH . 
L 6 HOH B 27 177 80 HOH HOH . 
L 6 HOH B 28 178 88 HOH HOH . 
L 6 HOH B 29 179 93 HOH HOH . 
L 6 HOH B 30 180 95 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 . A . G 3 -25.25 6.874 -0.886 0.62 39.72 ? CHA HEM 148 B 1 
HETATM 2 C CHB HEM . A . G 3 -21.807 5.107 2.075 0.62 34.01 ? CHB HEM 148 B 1 
HETATM 3 C CHC HEM . A . G 3 -18.326 7.217 -0.55 0.62 37.42 ? CHC HEM 148 B 1 
HETATM 4 C CHD HEM . A . G 3 -21.769 9.543 -3.042 0.62 35.73 ? CHD HEM 148 B 1 
HETATM 5 C C1A HEM . A . G 3 -24.624 6.171 0.127 0.62 40.95 ? C1A HEM 148 B 1 
HETATM 6 C C2A HEM . A . G 3 -25.265 5.28 1.083 0.62 43.55 ? C2A HEM 148 B 1 
HETATM 7 C C3A HEM . A . G 3 -24.328 4.796 1.897 0.62 40.62 ? C3A HEM 148 B 1 
HETATM 8 C C4A HEM . A . G 3 -23.039 5.351 1.493 0.62 38.68 ? C4A HEM 148 B 1 
HETATM 9 C CMA HEM . A . G 3 -24.603 3.814 3.055 0.62 39.75 ? CMA HEM 148 B 1 
HETATM 10 C CAA HEM . A . G 3 -26.774 4.948 1.158 0.62 44.7 ? CAA HEM 148 B 1 
HETATM 11 C CBA HEM . A . G 3 -27.43 5.936 2.119 0.62 48.07 ? CBA HEM 148 B 1 
HETATM 12 C CGA HEM . A . G 3 -28.879 6.155 1.762 0.62 50.15 ? CGA HEM 148 B 1 
HETATM 13 O O1A HEM . A . G 3 -29.557 5.183 1.336 0.62 52.84 ? O1A HEM 148 B 1 
HETATM 14 O O2A HEM . A . G 3 -29.362 7.309 1.907 0.62 51.4 ? O2A HEM 148 B 1 
HETATM 15 C C1B HEM . A . G 3 -20.562 5.486 1.599 0.62 37.86 ? C1B HEM 148 B 1 
HETATM 16 C C2B HEM . A . G 3 -19.259 5.05 2.107 0.62 34.7 ? C2B HEM 148 B 1 
HETATM 17 C C3B HEM . A . G 3 -18.305 5.639 1.383 0.62 39.14 ? C3B HEM 148 B 1 
HETATM 18 C C4B HEM . A . G 3 -18.969 6.456 0.39 0.62 37.74 ? C4B HEM 148 B 1 
HETATM 19 C CMB HEM . A . G 3 -19.026 4.084 3.285 0.62 37.14 ? CMB HEM 148 B 1 
HETATM 20 C CAB HEM . A . G 3 -16.762 5.507 1.517 0.62 35.9 ? CAB HEM 148 B 1 
HETATM 21 C CBB HEM . A . G 3 -16.166 4.693 2.395 0.62 37.96 ? CBB HEM 148 B 1 
HETATM 22 C C1C HEM . A . G 3 -18.962 8.02 -1.459 0.62 36.51 ? C1C HEM 148 B 1 
HETATM 23 C C2C HEM . A . G 3 -18.308 8.818 -2.463 0.62 34.18 ? C2C HEM 148 B 1 
HETATM 24 C C3C HEM . A . G 3 -19.253 9.465 -3.142 0.62 36.59 ? C3C HEM 148 B 1 
HETATM 25 C C4C HEM . A . G 3 -20.545 9.086 -2.605 0.62 36.68 ? C4C HEM 148 B 1 
HETATM 26 C CMC HEM . A . G 3 -16.784 8.901 -2.668 0.62 36.16 ? CMC HEM 148 B 1 
HETATM 27 C CAC HEM . A . G 3 -19.024 10.443 -4.314 0.62 38.03 ? CAC HEM 148 B 1 
HETATM 28 C CBC HEM . A . G 3 -20.015 11.261 -4.679 0.62 36.91 ? CBC HEM 148 B 1 
HETATM 29 C C1D HEM . A . G 3 -23.009 9.005 -2.784 0.62 35.78 ? C1D HEM 148 B 1 
HETATM 30 C C2D HEM . A . G 3 -24.21 9.286 -3.529 0.62 37.49 ? C2D HEM 148 B 1 
HETATM 31 C C3D HEM . A . G 3 -25.315 8.463 -2.859 0.62 41.11 ? C3D HEM 148 B 1 
HETATM 32 C C4D HEM . A . G 3 -24.661 7.75 -1.775 0.62 40.34 ? C4D HEM 148 B 1 
HETATM 33 C CMD HEM . A . G 3 -24.366 10.226 -4.741 0.62 34.47 ? CMD HEM 148 B 1 
HETATM 34 C CAD HEM . A . G 3 -26.796 8.414 -3.312 0.62 38.92 ? CAD HEM 148 B 1 
HETATM 35 C CBD HEM . A . G 3 -27.741 8.767 -2.175 0.62 43.28 ? CBD HEM 148 B 1 
HETATM 36 C CGD HEM . A . G 3 -28.353 7.498 -1.645 0.62 46.51 ? CGD HEM 148 B 1 
HETATM 37 O O1D HEM . A . G 3 -29.239 6.906 -2.319 0.62 47.41 ? O1D HEM 148 B 1 
HETATM 38 O O2D HEM . A . G 3 -27.947 7.084 -0.532 0.62 44.76 ? O2D HEM 148 B 1 
HETATM 39 N NA HEM . A . G 3 -23.27 6.183 0.411 0.62 35.78 ? NA HEM 148 B 1 
HETATM 40 N NB HEM . A . G 3 -20.335 6.345 0.543 0.62 33.08 ? NB HEM 148 B 1 
HETATM 41 N NC HEM . A . G 3 -20.325 8.199 -1.576 0.62 35.13 ? NC HEM 148 B 1 
HETATM 42 N ND HEM . A . G 3 -23.318 8.105 -1.772 0.62 38.75 ? ND HEM 148 B 1 
HETATM 43 FE FE HEM . A . G 3 -21.877 7.138 -0.675 0.62 36.51 ? FE HEM 148 B 1 
HETATM 44 FE FE HEM . B . G 3 -17.183 6.888 0.103 0.28 35.18 ? FE HEM 148 B 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           311 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           44 
#