data_1D06 # _model_server_result.job_id DT-vjM030MLGbuZDXDJEuA _model_server_result.datetime_utc '2025-08-02 03:43:58' _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 1d06 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 1D06 # _exptl.entry_id 1D06 _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 115.43 _cell.angle_gamma 90 _cell.entry_id 1D06 _cell.length_a 60.6 _cell.length_b 37.15 _cell.length_c 53.99 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D06 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 PISA,PQS dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C 1 1 A,B,C 2 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' 2_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 37.416259 0 48.75894 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NE2 _struct_conn.ptnr1_label_comp_id HIS _struct_conn.ptnr1_label_seq_id 73 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id HIS _struct_conn.ptnr1_auth_seq_id 194 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id FE _struct_conn.ptnr2_label_comp_id HEM _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id HEM _struct_conn.ptnr2_auth_seq_id 501 _struct_conn.ptnr2_symmetry 1_555 _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 2.14 _struct_conn.pdbx_value_order ? # _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 116 n n CHA C4D HEM doub 117 n n CHA HHA HEM sing 118 n n CHB C4A HEM sing 119 n n CHB C1B HEM doub 120 n n CHB HHB HEM sing 121 n n CHC C4B HEM sing 122 n n CHC C1C HEM doub 123 n n CHC HHC HEM sing 124 n n CHD C4C HEM doub 125 n n CHD C1D HEM sing 126 n n CHD HHD HEM sing 127 n n C1A C2A HEM doub 128 n y C1A NA HEM sing 129 n y C2A C3A HEM sing 130 n y C2A CAA HEM sing 131 n n C3A C4A HEM doub 132 n y C3A CMA HEM sing 133 n n C4A NA HEM sing 134 n y CMA HMA HEM sing 135 n n CMA HMAA HEM sing 136 n n CMA HMAB HEM sing 137 n n CAA CBA HEM sing 138 n n CAA HAA HEM sing 139 n n CAA HAAA HEM sing 140 n n CBA CGA HEM sing 141 n n CBA HBA HEM sing 142 n n CBA HBAA HEM sing 143 n n CGA O1A HEM doub 144 n n CGA O2A HEM sing 145 n n C1B C2B HEM sing 146 n n C1B NB HEM sing 147 n n C2B C3B HEM doub 148 n n C2B CMB HEM sing 149 n n C3B C4B HEM sing 150 n n C3B CAB HEM sing 151 n n C4B NB HEM doub 152 n n CMB HMB HEM sing 153 n n CMB HMBA HEM sing 154 n n CMB HMBB HEM sing 155 n n CAB CBB HEM doub 156 n n CAB HAB HEM sing 157 n n CBB HBB HEM sing 158 n n CBB HBBA HEM sing 159 n n C1C C2C HEM sing 160 n y C1C NC HEM sing 161 n y C2C C3C HEM doub 162 n y C2C CMC HEM sing 163 n n C3C C4C HEM sing 164 n y C3C CAC HEM sing 165 n n C4C NC HEM sing 166 n y CMC HMC HEM sing 167 n n CMC HMCA HEM sing 168 n n CMC HMCB HEM sing 169 n n CAC CBC HEM doub 170 n n CAC HAC HEM sing 171 n n CBC HBC HEM sing 172 n n CBC HBCA HEM sing 173 n n C1D C2D HEM sing 174 n n C1D ND HEM doub 175 n n C2D C3D HEM doub 176 n n C2D CMD HEM sing 177 n n C3D C4D HEM sing 178 n n C3D CAD HEM sing 179 n n C4D ND HEM sing 180 n n CMD HMD HEM sing 181 n n CMD HMDA HEM sing 182 n n CMD HMDB HEM sing 183 n n CAD CBD HEM sing 184 n n CAD HAD HEM sing 185 n n CAD HADA HEM sing 186 n n CBD CGD HEM sing 187 n n CBD HBD HEM sing 188 n n CBD HBDA HEM sing 189 n n CGD O1D HEM doub 190 n n CGD O2D HEM sing 191 n n O2A H2A HEM sing 192 n n O2D H2D HEM sing 193 n n FE NA HEM sing 194 n n FE NB HEM sing 195 n n FE NC HEM sing 196 n n FE ND HEM sing 197 n n # _atom_sites.entry_id 1D06 _atom_sites.fract_transf_matrix[1][1] 0.016502 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007846 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.026918 _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] 0.020509 _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 B 2 HEM A 1 501 501 HEM HEM . C 3 HOH A 1 1 1 HOH HOH . C 3 HOH A 2 2 2 HOH HOH . C 3 HOH A 3 3 3 HOH HOH . C 3 HOH A 4 4 4 HOH HOH . C 3 HOH A 5 5 5 HOH HOH . C 3 HOH A 6 6 6 HOH HOH . C 3 HOH A 7 7 7 HOH HOH . C 3 HOH A 8 8 8 HOH HOH . C 3 HOH A 9 9 9 HOH HOH . C 3 HOH A 10 10 10 HOH HOH . C 3 HOH A 11 11 11 HOH HOH . C 3 HOH A 12 12 12 HOH HOH . C 3 HOH A 13 13 13 HOH HOH . C 3 HOH A 14 14 14 HOH HOH . C 3 HOH A 15 15 15 HOH HOH . C 3 HOH A 16 16 16 HOH HOH . C 3 HOH A 17 17 17 HOH HOH . C 3 HOH A 18 18 18 HOH HOH . C 3 HOH A 19 19 19 HOH HOH . C 3 HOH A 20 20 20 HOH HOH . C 3 HOH A 21 21 21 HOH HOH . C 3 HOH A 22 22 22 HOH HOH . C 3 HOH A 23 23 23 HOH HOH . C 3 HOH A 24 24 24 HOH HOH . C 3 HOH A 25 25 25 HOH HOH . C 3 HOH A 26 26 26 HOH HOH . C 3 HOH A 27 27 27 HOH HOH . C 3 HOH A 28 28 28 HOH HOH . C 3 HOH A 29 29 29 HOH HOH . C 3 HOH A 30 30 30 HOH HOH . C 3 HOH A 31 31 31 HOH HOH . C 3 HOH A 32 32 32 HOH HOH . C 3 HOH A 33 33 33 HOH HOH . C 3 HOH A 34 34 34 HOH HOH . C 3 HOH A 35 35 35 HOH HOH . C 3 HOH A 36 36 36 HOH HOH . C 3 HOH A 37 37 37 HOH HOH . C 3 HOH A 38 38 38 HOH HOH . C 3 HOH A 39 39 39 HOH HOH . C 3 HOH A 40 40 40 HOH HOH . C 3 HOH A 41 41 41 HOH HOH . C 3 HOH A 42 42 42 HOH HOH . C 3 HOH A 43 43 43 HOH HOH . C 3 HOH A 44 44 44 HOH HOH . C 3 HOH A 45 45 45 HOH HOH . C 3 HOH A 46 46 46 HOH HOH . C 3 HOH A 47 47 47 HOH HOH . C 3 HOH A 48 48 48 HOH HOH . C 3 HOH A 49 49 49 HOH HOH . C 3 HOH A 50 50 50 HOH HOH . C 3 HOH A 51 51 51 HOH HOH . C 3 HOH A 52 52 52 HOH HOH . C 3 HOH A 53 53 53 HOH HOH . C 3 HOH A 54 54 54 HOH HOH . C 3 HOH A 55 55 55 HOH HOH . C 3 HOH A 56 56 56 HOH HOH . C 3 HOH A 57 57 57 HOH HOH . C 3 HOH A 58 58 58 HOH HOH . C 3 HOH A 59 59 59 HOH HOH . C 3 HOH A 60 60 60 HOH HOH . C 3 HOH A 61 61 61 HOH HOH . C 3 HOH A 62 62 62 HOH HOH . C 3 HOH A 63 63 63 HOH HOH . C 3 HOH A 64 64 64 HOH HOH . C 3 HOH A 65 65 65 HOH HOH . C 3 HOH A 66 66 66 HOH HOH . C 3 HOH A 67 67 67 HOH HOH . C 3 HOH A 68 68 68 HOH HOH . C 3 HOH A 69 69 69 HOH HOH . C 3 HOH A 70 70 70 HOH HOH . C 3 HOH A 71 71 71 HOH HOH . C 3 HOH A 72 72 72 HOH HOH . C 3 HOH A 73 73 73 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 . . . B 2 14.574 0.017 7.167 1 10.83 ? CHA HEM 501 A 1 HETATM 2 C CHB HEM . . . B 2 18.683 -2.607 7.255 1 8.99 ? CHB HEM 501 A 1 HETATM 3 C CHC HEM . . . B 2 20.716 0.768 10.067 1 9.95 ? CHC HEM 501 A 1 HETATM 4 C CHD HEM . . . B 2 16.706 3.456 9.808 1 7.38 ? CHD HEM 501 A 1 HETATM 5 C C1A HEM . . . B 2 15.517 -1.016 7.05 1 10.72 ? C1A HEM 501 A 1 HETATM 6 C C2A HEM . . . B 2 15.157 -2.344 6.602 1 12.41 ? C2A HEM 501 A 1 HETATM 7 C C3A HEM . . . B 2 16.316 -3.059 6.524 1 11.52 ? C3A HEM 501 A 1 HETATM 8 C C4A HEM . . . B 2 17.373 -2.198 7.016 1 9.75 ? C4A HEM 501 A 1 HETATM 9 C CMA HEM . . . B 2 16.449 -4.459 5.903 1 12.63 ? CMA HEM 501 A 1 HETATM 10 C CAA HEM . . . B 2 13.75 -2.868 6.421 1 15.68 ? CAA HEM 501 A 1 HETATM 11 C CBA HEM . . . B 2 13.504 -3.106 4.952 1 18.48 ? CBA HEM 501 A 1 HETATM 12 C CGA HEM . . . B 2 12.299 -3.994 4.717 1 18.78 ? CGA HEM 501 A 1 HETATM 13 O O1A HEM . . . B 2 11.64 -3.808 3.683 1 19.78 ? O1A HEM 501 A 1 HETATM 14 O O2A HEM . . . B 2 12.016 -4.867 5.571 1 21.95 ? O2A HEM 501 A 1 HETATM 15 C C1B HEM . . . B 2 19.63 -1.879 7.937 1 8.39 ? C1B HEM 501 A 1 HETATM 16 C C2B HEM . . . B 2 20.949 -2.352 8.254 1 8.52 ? C2B HEM 501 A 1 HETATM 17 C C3B HEM . . . B 2 21.546 -1.46 9.105 1 7.68 ? C3B HEM 501 A 1 HETATM 18 C C4B HEM . . . B 2 20.541 -0.381 9.274 1 7.81 ? C4B HEM 501 A 1 HETATM 19 C CMB HEM . . . B 2 21.565 -3.654 7.714 1 9.08 ? CMB HEM 501 A 1 HETATM 20 C CAB HEM . . . B 2 22.853 -1.62 9.625 1 8.31 ? CAB HEM 501 A 1 HETATM 21 C CBB HEM . . . B 2 23.783 -0.647 10.086 1 8.11 ? CBB HEM 501 A 1 HETATM 22 C C1C HEM . . . B 2 19.783 1.802 10.224 1 7.55 ? C1C HEM 501 A 1 HETATM 23 C C2C HEM . . . B 2 19.989 2.894 11.174 1 7.78 ? C2C HEM 501 A 1 HETATM 24 C C3C HEM . . . B 2 18.849 3.68 11.084 1 7.34 ? C3C HEM 501 A 1 HETATM 25 C C4C HEM . . . B 2 17.974 3.023 10.119 1 7.49 ? C4C HEM 501 A 1 HETATM 26 C CMC HEM . . . B 2 21.209 3.048 12.099 1 7.62 ? CMC HEM 501 A 1 HETATM 27 C CAC HEM . . . B 2 18.525 4.886 11.758 1 8.51 ? CAC HEM 501 A 1 HETATM 28 C CBC HEM . . . B 2 19.387 5.905 12.216 1 8 ? CBC HEM 501 A 1 HETATM 29 C C1D HEM . . . B 2 15.824 2.79 8.98 1 8.53 ? C1D HEM 501 A 1 HETATM 30 C C2D HEM . . . B 2 14.489 3.257 8.693 1 9.86 ? C2D HEM 501 A 1 HETATM 31 C C3D HEM . . . B 2 13.914 2.307 7.929 1 9.82 ? C3D HEM 501 A 1 HETATM 32 C C4D HEM . . . B 2 14.881 1.236 7.768 1 10.08 ? C4D HEM 501 A 1 HETATM 33 C CMD HEM . . . B 2 13.85 4.588 9.111 1 9.26 ? CMD HEM 501 A 1 HETATM 34 C CAD HEM . . . B 2 12.531 2.351 7.327 1 12.68 ? CAD HEM 501 A 1 HETATM 35 C CBD HEM . . . B 2 11.586 2.166 8.488 1 14.56 ? CBD HEM 501 A 1 HETATM 36 C CGD HEM . . . B 2 10.966 0.79 8.51 1 16.19 ? CGD HEM 501 A 1 HETATM 37 O O1D HEM . . . B 2 10.93 0.145 7.434 1 17.54 ? O1D HEM 501 A 1 HETATM 38 O O2D HEM . . . B 2 10.516 0.372 9.606 1 14.52 ? O2D HEM 501 A 1 HETATM 39 N NA HEM . . . B 2 16.868 -0.936 7.352 1 7.58 ? NA HEM 501 A 1 HETATM 40 N NB HEM . . . B 2 19.397 -0.616 8.513 1 8.43 ? NB HEM 501 A 1 HETATM 41 N NC HEM . . . B 2 18.562 1.876 9.571 1 8.32 ? NC HEM 501 A 1 HETATM 42 N ND HEM . . . B 2 16.089 1.561 8.349 1 8.08 ? ND HEM 501 A 1 HETATM 43 FE FE HEM . . . B 2 17.835 0.605 8.178 1 7.86 ? FE HEM 501 A 1 # _model_server_stats.io_time_ms 40 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 43 #