data_1DKH # _model_server_result.job_id Ps3XWzuRL8aLyr0gOTtgiw _model_server_result.datetime_utc '2024-11-15 13:08:08' _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 1dkh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":200}' # _entry.id 1DKH # _exptl.entry_id 1DKH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 4 _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 90 _cell.angle_gamma 120 _cell.entry_id 1DKH _cell.length_a 111.65 _cell.length_b 111.65 _cell.length_c 52.79 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DKH _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 OD1 ASP 8 A ASP 8 1_555 B ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.506 ? metalc ? metalc2 A OD2 ASP 8 A ASP 8 1_555 B ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? metalc ? metalc3 A ND1 HIS 17 A HIS 17 3_665 B ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc4 A OD2 ASP 18 A ASP 18 3_665 C ZN ZN . A ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.675 ? metalc ? metalc5 A NE2 HIS 32 A HIS 32 1_555 F FE HEM . A HEM 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.724 ? metalc ? metalc6 A OH TYR 75 A TYR 75 1_555 F FE HEM . A HEM 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? metalc ? metalc7 A OD2 ASP 96 A ASP 96 1_555 C ZN ZN . A ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? metalc ? metalc8 A OD1 ASP 112 A ASP 112 1_555 D ZN ZN . A ZN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc9 A OE2 GLU 148 A GLU 148 3_665 B ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? metalc ? metalc10 A OE1 GLU 148 A GLU 148 3_665 B ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc11 A O GLY 153 A GLY 153 1_555 E SM SM . A SM 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.027 ? metalc ? metalc12 A OD2 ASP 156 A ASP 156 1_555 E SM SM . A SM 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc13 A OD1 ASP 156 A ASP 156 1_555 E SM SM . A SM 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? metalc ? metalc14 A OD2 ASP 157 A ASP 157 1_555 E SM SM . A SM 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? metalc ? metalc15 A OD1 ASP 157 A ASP 157 1_555 E SM SM . A SM 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? # _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 90 n n CHA C4D HEM doub 91 n n CHA HHA HEM sing 92 n n CHB C4A HEM sing 93 n n CHB C1B HEM doub 94 n n CHB HHB HEM sing 95 n n CHC C4B HEM sing 96 n n CHC C1C HEM doub 97 n n CHC HHC HEM sing 98 n n CHD C4C HEM doub 99 n n CHD C1D HEM sing 100 n n CHD HHD HEM sing 101 n n C1A C2A HEM doub 102 n y C1A NA HEM sing 103 n y C2A C3A HEM sing 104 n y C2A CAA HEM sing 105 n n C3A C4A HEM doub 106 n y C3A CMA HEM sing 107 n n C4A NA HEM sing 108 n y CMA HMA HEM sing 109 n n CMA HMAA HEM sing 110 n n CMA HMAB HEM sing 111 n n CAA CBA HEM sing 112 n n CAA HAA HEM sing 113 n n CAA HAAA HEM sing 114 n n CBA CGA HEM sing 115 n n CBA HBA HEM sing 116 n n CBA HBAA HEM sing 117 n n CGA O1A HEM doub 118 n n CGA O2A HEM sing 119 n n C1B C2B HEM sing 120 n n C1B NB HEM sing 121 n n C2B C3B HEM doub 122 n n C2B CMB HEM sing 123 n n C3B C4B HEM sing 124 n n C3B CAB HEM sing 125 n n C4B NB HEM doub 126 n n CMB HMB HEM sing 127 n n CMB HMBA HEM sing 128 n n CMB HMBB HEM sing 129 n n CAB CBB HEM doub 130 n n CAB HAB HEM sing 131 n n CBB HBB HEM sing 132 n n CBB HBBA HEM sing 133 n n C1C C2C HEM sing 134 n y C1C NC HEM sing 135 n y C2C C3C HEM doub 136 n y C2C CMC HEM sing 137 n n C3C C4C HEM sing 138 n y C3C CAC HEM sing 139 n n C4C NC HEM sing 140 n y CMC HMC HEM sing 141 n n CMC HMCA HEM sing 142 n n CMC HMCB HEM sing 143 n n CAC CBC HEM doub 144 n n CAC HAC HEM sing 145 n n CBC HBC HEM sing 146 n n CBC HBCA HEM sing 147 n n C1D C2D HEM sing 148 n n C1D ND HEM doub 149 n n C2D C3D HEM doub 150 n n C2D CMD HEM sing 151 n n C3D C4D HEM sing 152 n n C3D CAD HEM sing 153 n n C4D ND HEM sing 154 n n CMD HMD HEM sing 155 n n CMD HMDA HEM sing 156 n n CMD HMDB HEM sing 157 n n CAD CBD HEM sing 158 n n CAD HAD HEM sing 159 n n CAD HADA HEM sing 160 n n CBD CGD HEM sing 161 n n CBD HBD HEM sing 162 n n CBD HBDA HEM sing 163 n n CGD O1D HEM doub 164 n n CGD O2D HEM sing 165 n n O2A H2A HEM sing 166 n n O2D H2D HEM sing 167 n n FE NA HEM sing 168 n n FE NB HEM sing 169 n n FE NC HEM sing 170 n n FE ND HEM sing 171 n n # _atom_sites.entry_id 1DKH _atom_sites.fract_transf_matrix[1][1] 0.008957 _atom_sites.fract_transf_matrix[1][2] 0.005171 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010342 _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] 0.018943 _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 ZN A 1 201 201 ZN ZN . C 2 ZN A 1 202 202 ZN ZN . D 2 ZN A 1 203 203 ZN ZN . E 3 SM A 1 204 204 SM SM . F 4 HEM A 1 200 200 HEM HEM . G 5 HOH A 1 300 300 HOH WAT . G 5 HOH A 2 301 301 HOH WAT . G 5 HOH A 3 302 302 HOH WAT . G 5 HOH A 4 303 303 HOH WAT . G 5 HOH A 5 304 304 HOH WAT . G 5 HOH A 6 305 305 HOH WAT . G 5 HOH A 7 306 306 HOH WAT . G 5 HOH A 8 307 307 HOH WAT . # 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 . . . F 4 31.605 48.693 19.921 1 72.89 ? CHA HEM 200 A 1 HETATM 2 C CHB HEM . . . F 4 35.629 49.976 17.72 1 72.63 ? CHB HEM 200 A 1 HETATM 3 C CHC HEM . . . F 4 37.255 51.341 21.917 1 72.62 ? CHC HEM 200 A 1 HETATM 4 C CHD HEM . . . F 4 32.84 50.942 23.809 1 72.73 ? CHD HEM 200 A 1 HETATM 5 C C1A HEM . . . F 4 32.595 48.837 19.013 1 73.14 ? C1A HEM 200 A 1 HETATM 6 C C2A HEM . . . F 4 32.425 48.476 17.615 1 73.32 ? C2A HEM 200 A 1 HETATM 7 C C3A HEM . . . F 4 33.538 48.876 16.996 1 73.05 ? C3A HEM 200 A 1 HETATM 8 C C4A HEM . . . F 4 34.335 49.583 17.961 1 72.91 ? C4A HEM 200 A 1 HETATM 9 C CMA HEM . . . F 4 33.94 48.482 15.592 1 73.16 ? CMA HEM 200 A 1 HETATM 10 C CAA HEM . . . F 4 31.193 48.062 16.846 1 73.8 ? CAA HEM 200 A 1 HETATM 11 C CBA HEM . . . F 4 30.164 47.032 17.271 1 74.47 ? CBA HEM 200 A 1 HETATM 12 C CGA HEM . . . F 4 29.182 46.748 16.142 1 75.12 ? CGA HEM 200 A 1 HETATM 13 O O1A HEM . . . F 4 28.663 47.734 15.535 1 75.12 ? O1A HEM 200 A 1 HETATM 14 O O2A HEM . . . F 4 28.939 45.542 15.861 1 75.43 ? O2A HEM 200 A 1 HETATM 15 C C1B HEM . . . F 4 36.457 50.35 18.721 1 72.36 ? C1B HEM 200 A 1 HETATM 16 C C2B HEM . . . F 4 37.89 50.412 18.517 1 72.25 ? C2B HEM 200 A 1 HETATM 17 C C3B HEM . . . F 4 38.297 50.574 19.763 1 72.36 ? C3B HEM 200 A 1 HETATM 18 C C4B HEM . . . F 4 37.179 50.684 20.694 1 72.42 ? C4B HEM 200 A 1 HETATM 19 C CMB HEM . . . F 4 38.808 50.371 17.27 1 71.8 ? CMB HEM 200 A 1 HETATM 20 C CAB HEM . . . F 4 39.623 50.745 20.025 1 72.5 ? CAB HEM 200 A 1 HETATM 21 C CBB HEM . . . F 4 40.257 52.035 19.529 1 72.53 ? CBB HEM 200 A 1 HETATM 22 C C1C HEM . . . F 4 36.163 51.697 22.689 1 72.72 ? C1C HEM 200 A 1 HETATM 23 C C2C HEM . . . F 4 36.269 52.141 24.085 1 72.86 ? C2C HEM 200 A 1 HETATM 24 C C3C HEM . . . F 4 35.072 51.868 24.675 1 72.95 ? C3C HEM 200 A 1 HETATM 25 C C4C HEM . . . F 4 34.193 51.369 23.61 1 72.92 ? C4C HEM 200 A 1 HETATM 26 C CMC HEM . . . F 4 37.472 52.8 24.774 1 72.83 ? CMC HEM 200 A 1 HETATM 27 C CAC HEM . . . F 4 34.771 51.977 26.043 1 73.19 ? CAC HEM 200 A 1 HETATM 28 C CBC HEM . . . F 4 33.95 50.945 26.885 1 73.38 ? CBC HEM 200 A 1 HETATM 29 C C1D HEM . . . F 4 32.087 50.347 22.833 1 72.41 ? C1D HEM 200 A 1 HETATM 30 C C2D HEM . . . F 4 30.688 50.02 22.933 1 72.23 ? C2D HEM 200 A 1 HETATM 31 C C3D HEM . . . F 4 30.249 49.596 21.748 1 72.13 ? C3D HEM 200 A 1 HETATM 32 C C4D HEM . . . F 4 31.527 49.413 21.046 1 72.4 ? C4D HEM 200 A 1 HETATM 33 C CMD HEM . . . F 4 29.891 49.744 24.165 1 72.16 ? CMD HEM 200 A 1 HETATM 34 C CAD HEM . . . F 4 28.777 49.266 21.238 1 71.55 ? CAD HEM 200 A 1 HETATM 35 C CBD HEM . . . F 4 27.637 50.246 20.898 1 70.28 ? CBD HEM 200 A 1 HETATM 36 C CGD HEM . . . F 4 26.443 49.564 20.249 1 69.91 ? CGD HEM 200 A 1 HETATM 37 O O1D HEM . . . F 4 25.872 48.615 20.842 1 69.33 ? O1D HEM 200 A 1 HETATM 38 O O2D HEM . . . F 4 26.076 49.981 19.135 1 69.67 ? O2D HEM 200 A 1 HETATM 39 N NA HEM . . . F 4 33.728 49.589 19.207 1 72.9 ? NA HEM 200 A 1 HETATM 40 N NB HEM . . . F 4 36.032 50.505 20.034 1 72.42 ? NB HEM 200 A 1 HETATM 41 N NC HEM . . . F 4 34.89 51.298 22.389 1 72.79 ? NC HEM 200 A 1 HETATM 42 N ND HEM . . . F 4 32.576 50.018 21.603 1 72.41 ? ND HEM 200 A 1 HETATM 43 FE FE HEM . . . F 4 34.216 50.598 20.728 1 72.58 ? FE HEM 200 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 43 #