data_3ONZ # _model_server_result.job_id pNoY8zGPQAsOXjuVQcBbKQ _model_server_result.datetime_utc '2025-01-10 20:55:44' _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":"C","auth_seq_id":143}' # _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 . . . C 3 16.318 0.695 16.777 1 29.72 ? CHA HEM 143 A 1 HETATM 2 C CHB HEM . . . C 3 13.98 4.915 16.113 1 27.25 ? CHB HEM 143 A 1 HETATM 3 C CHC HEM . . . C 3 10.871 2.718 13.116 1 25.95 ? CHC HEM 143 A 1 HETATM 4 C CHD HEM . . . C 3 12.607 -1.592 14.527 1 31.35 ? CHD HEM 143 A 1 HETATM 5 C C1A HEM . . . C 3 15.962 2.034 16.876 1 30.55 ? C1A HEM 143 A 1 HETATM 6 C C2A HEM . . . C 3 16.628 3.056 17.664 1 30.89 ? C2A HEM 143 A 1 HETATM 7 C C3A HEM . . . C 3 15.982 4.22 17.475 1 33.2 ? C3A HEM 143 A 1 HETATM 8 C C4A HEM . . . C 3 14.881 3.976 16.567 1 27.54 ? C4A HEM 143 A 1 HETATM 9 C CMA HEM . . . C 3 16.292 5.6 18.116 1 32.96 ? CMA HEM 143 A 1 HETATM 10 C CAA HEM . . . C 3 17.863 2.808 18.56 1 32.7 ? CAA HEM 143 A 1 HETATM 11 C CBA HEM . . . C 3 19.012 3.626 17.973 1 41.81 ? CBA HEM 143 A 1 HETATM 12 C CGA HEM . . . C 3 20.336 3.118 18.482 1 54.53 ? CGA HEM 143 A 1 HETATM 13 O O1A HEM . . . C 3 20.363 2.188 19.341 1 51.79 ? O1A HEM 143 A 1 HETATM 14 O O2A HEM . . . C 3 21.375 3.652 18.014 1 58.09 ? O2A HEM 143 A 1 HETATM 15 C C1B HEM . . . C 3 12.964 4.708 15.203 1 31.69 ? C1B HEM 143 A 1 HETATM 16 C C2B HEM . . . C 3 12.105 5.724 14.625 1 27.28 ? C2B HEM 143 A 1 HETATM 17 C C3B HEM . . . C 3 11.256 5.106 13.784 1 28.62 ? C3B HEM 143 A 1 HETATM 18 C C4B HEM . . . C 3 11.536 3.692 13.827 1 26.65 ? C4B HEM 143 A 1 HETATM 19 C CMB HEM . . . C 3 12.221 7.239 14.948 1 26.39 ? CMB HEM 143 A 1 HETATM 20 C CAB HEM . . . C 3 10.105 5.669 12.904 1 26.4 ? CAB HEM 143 A 1 HETATM 21 C CBB HEM . . . C 3 9.513 6.837 13.135 1 32.67 ? CBB HEM 143 A 1 HETATM 22 C C1C HEM . . . C 3 11.012 1.365 13.291 1 29.61 ? C1C HEM 143 A 1 HETATM 23 C C2C HEM . . . C 3 10.129 0.341 12.758 1 29.12 ? C2C HEM 143 A 1 HETATM 24 C C3C HEM . . . C 3 10.623 -0.847 13.144 1 26.77 ? C3C HEM 143 A 1 HETATM 25 C C4C HEM . . . C 3 11.814 -0.613 13.948 1 29.33 ? C4C HEM 143 A 1 HETATM 26 C CMC HEM . . . C 3 8.88 0.649 11.896 1 28.02 ? CMC HEM 143 A 1 HETATM 27 C CAC HEM . . . C 3 10.055 -2.262 12.891 1 27.95 ? CAC HEM 143 A 1 HETATM 28 C CBC HEM . . . C 3 8.745 -2.42 12.702 1 28.17 ? CBC HEM 143 A 1 HETATM 29 C C1D HEM . . . C 3 13.751 -1.4 15.275 1 32.21 ? C1D HEM 143 A 1 HETATM 30 C C2D HEM . . . C 3 14.491 -2.458 15.928 1 34.88 ? C2D HEM 143 A 1 HETATM 31 C C3D HEM . . . C 3 15.661 -1.757 16.619 1 33.82 ? C3D HEM 143 A 1 HETATM 32 C C4D HEM . . . C 3 15.504 -0.337 16.341 1 29.45 ? C4D HEM 143 A 1 HETATM 33 C CMD HEM . . . C 3 14.185 -3.978 15.914 1 27.42 ? CMD HEM 143 A 1 HETATM 34 C CAD HEM . . . C 3 16.741 -2.46 17.469 1 31.43 ? CAD HEM 143 A 1 HETATM 35 C CBD HEM . . . C 3 16.078 -2.691 18.816 1 33.51 ? CBD HEM 143 A 1 HETATM 36 C CGD HEM . . . C 3 17.077 -3.236 19.802 1 39.11 ? CGD HEM 143 A 1 HETATM 37 O O1D HEM . . . C 3 17.771 -4.239 19.476 1 40.76 ? O1D HEM 143 A 1 HETATM 38 O O2D HEM . . . C 3 17.147 -2.672 20.921 1 35.87 ? O2D HEM 143 A 1 HETATM 39 N NA HEM . . . C 3 14.906 2.643 16.224 1 27.58 ? NA HEM 143 A 1 HETATM 40 N NB HEM . . . C 3 12.58 3.481 14.694 1 30.69 ? NB HEM 143 A 1 HETATM 41 N NC HEM . . . C 3 12.028 0.745 14.003 1 26.36 ? NC HEM 143 A 1 HETATM 42 N ND HEM . . . C 3 14.378 -0.179 15.539 1 29.64 ? ND HEM 143 A 1 HETATM 43 FE FE HEM . . . C 3 13.451 1.662 15.111 1 29.52 ? FE HEM 143 A 1 # _model_server_stats.io_time_ms 47 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 43 #