data_3ODQ # _model_server_result.job_id Bbh-eRqaYAzJsrlxBvgYOQ _model_server_result.datetime_utc '2025-04-16 07:40:28' _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 3odq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":142}' # _entry.id 3ODQ # _exptl.entry_id 3ODQ _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 4 _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 120 _cell.entry_id 3ODQ _cell.length_a 54.6 _cell.length_b 54.6 _cell.length_c 677.42 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ODQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 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 _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 ? 3 E N N ? 3 F N N ? 3 G N N ? 3 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 NE2 HIS 87 A HIS 87 1_555 E FE HEM . A HEM 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc2 B NE2 HIS 92 B HIS 92 1_555 F FE HEM . B HEM 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc3 C NE2 HIS 87 C HIS 87 1_555 G FE HEM . C HEM 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc4 D NE2 HIS 92 D HIS 92 1_555 H FE HEM . D HEM 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? # _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 3ODQ _atom_sites.fract_transf_matrix[1][1] 0.018315 _atom_sites.fract_transf_matrix[1][2] 0.010574 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021148 _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] 0.001476 _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 3 HEM A 1 142 142 HEM HEM . F 3 HEM B 1 147 147 HEM HEM . G 3 HEM C 1 142 142 HEM HEM . H 3 HEM D 1 147 147 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 . . . E 3 60.701 17.593 89.071 1 150.45 ? CHA HEM 142 A 1 HETATM 2 C CHB HEM . . . E 3 61.109 22.142 90.538 1 143.95 ? CHB HEM 142 A 1 HETATM 3 C CHC HEM . . . E 3 56.381 22.83 89.916 1 133.17 ? CHC HEM 142 A 1 HETATM 4 C CHD HEM . . . E 3 55.899 18.117 88.947 1 145.03 ? CHD HEM 142 A 1 HETATM 5 C C1A HEM . . . E 3 61.245 18.742 89.485 1 154.11 ? C1A HEM 142 A 1 HETATM 6 C C2A HEM . . . E 3 62.616 18.92 89.774 1 160.44 ? C2A HEM 142 A 1 HETATM 7 C C3A HEM . . . E 3 62.732 20.229 90.306 1 158.37 ? C3A HEM 142 A 1 HETATM 8 C C4A HEM . . . E 3 61.507 20.822 90.196 1 151.86 ? C4A HEM 142 A 1 HETATM 9 C CMA HEM . . . E 3 64.01 20.95 90.653 1 161.51 ? CMA HEM 142 A 1 HETATM 10 C CAA HEM . . . E 3 63.694 18.001 89.669 1 166.06 ? CAA HEM 142 A 1 HETATM 11 C CBA HEM . . . E 3 64.277 18.085 88.348 1 171.36 ? CBA HEM 142 A 1 HETATM 12 C CGA HEM . . . E 3 65.403 16.504 88.06 1 172.43 ? CGA HEM 142 A 1 HETATM 13 O O1A HEM . . . E 3 65.535 15.691 88.881 1 173.83 ? O1A HEM 142 A 1 HETATM 14 O O2A HEM . . . E 3 66.079 17.367 86.994 1 171.76 ? O2A HEM 142 A 1 HETATM 15 C C1B HEM . . . E 3 59.919 22.777 90.419 1 134.56 ? C1B HEM 142 A 1 HETATM 16 C C2B HEM . . . E 3 59.676 24.152 90.739 1 130.9 ? C2B HEM 142 A 1 HETATM 17 C C3B HEM . . . E 3 58.31 24.38 90.566 1 130.6 ? C3B HEM 142 A 1 HETATM 18 C C4B HEM . . . E 3 57.792 23.083 90.104 1 132.27 ? C4B HEM 142 A 1 HETATM 19 C CMB HEM . . . E 3 60.765 25.153 91.115 1 123.58 ? CMB HEM 142 A 1 HETATM 20 C CAB HEM . . . E 3 57.537 25.613 90.823 1 129.81 ? CAB HEM 142 A 1 HETATM 21 C CBB HEM . . . E 3 57.762 26.523 91.732 1 129.01 ? CBB HEM 142 A 1 HETATM 22 C C1C HEM . . . E 3 55.84 21.642 89.6 1 138.5 ? C1C HEM 142 A 1 HETATM 23 C C2C HEM . . . E 3 54.476 21.383 89.535 1 138.99 ? C2C HEM 142 A 1 HETATM 24 C C3C HEM . . . E 3 54.28 20.085 89.358 1 142.49 ? C3C HEM 142 A 1 HETATM 25 C C4C HEM . . . E 3 55.604 19.499 89.201 1 143.9 ? C4C HEM 142 A 1 HETATM 26 C CMC HEM . . . E 3 53.382 22.491 89.743 1 138.54 ? CMC HEM 142 A 1 HETATM 27 C CAC HEM . . . E 3 53.048 19.314 89.24 1 141.31 ? CAC HEM 142 A 1 HETATM 28 C CBC HEM . . . E 3 51.926 19.512 89.985 1 139.6 ? CBC HEM 142 A 1 HETATM 29 C C1D HEM . . . E 3 57.137 17.606 88.887 1 143.63 ? C1D HEM 142 A 1 HETATM 30 C C2D HEM . . . E 3 57.427 16.177 88.632 1 144.8 ? C2D HEM 142 A 1 HETATM 31 C C3D HEM . . . E 3 58.793 15.985 88.629 1 147.06 ? C3D HEM 142 A 1 HETATM 32 C C4D HEM . . . E 3 59.355 17.368 88.844 1 147.01 ? C4D HEM 142 A 1 HETATM 33 C CMD HEM . . . E 3 56.294 15.2 88.43 1 140.68 ? CMD HEM 142 A 1 HETATM 34 C CAD HEM . . . E 3 59.541 14.735 88.361 1 147.82 ? CAD HEM 142 A 1 HETATM 35 C CBD HEM . . . E 3 59.497 13.918 89.57 1 149.14 ? CBD HEM 142 A 1 HETATM 36 C CGD HEM . . . E 3 60.527 12.524 89.266 1 151.4 ? CGD HEM 142 A 1 HETATM 37 O O1D HEM . . . E 3 60.747 11.839 89.958 1 156.94 ? O1D HEM 142 A 1 HETATM 38 O O2D HEM . . . E 3 59.838 12.048 87.985 1 151.49 ? O2D HEM 142 A 1 HETATM 39 N NA HEM . . . E 3 60.515 19.909 89.777 1 149.33 ? NA HEM 142 A 1 HETATM 40 N NB HEM . . . E 3 58.756 22.171 90.065 1 134.42 ? NB HEM 142 A 1 HETATM 41 N NC HEM . . . E 3 56.525 20.502 89.384 1 141.45 ? NC HEM 142 A 1 HETATM 42 N ND HEM . . . E 3 58.31 18.195 89.073 1 143.67 ? ND HEM 142 A 1 HETATM 43 FE FE HEM . . . E 3 58.514 20.207 89.616 1 136.91 ? FE HEM 142 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 43 #