data_4K8F # _model_server_result.job_id oCeDRt7j7_iqRNFT9B-ntA _model_server_result.datetime_utc '2025-03-25 12:10:24' _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 4k8f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":300}' # _entry.id 4K8F # _exptl.entry_id 4K8F _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 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 90 _cell.entry_id 4K8F _cell.length_a 71.23 _cell.length_b 71.23 _cell.length_c 143.733 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4K8F _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_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,E,F,I,J 1 1 C,D,G,H,K 2 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 ? 2 E N N ? 2 F N N ? 2 G N N ? 2 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 N PRO 1 A PRO 2 1_555 F FE HEM . B HEM 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc2 A NE2 HIS 76 A HIS 77 1_555 E FE HEM . A HEM 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc3 E FE HEM . A HEM 300 1_555 B N PRO 1 B PRO 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc4 B NE2 HIS 76 B HIS 77 1_555 F FE HEM . B HEM 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc5 C N PRO 1 C PRO 2 1_555 H FE HEM . D HEM 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc6 C NE2 HIS 76 C HIS 77 1_555 G FE HEM . C HEM 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc7 G FE HEM . C HEM 300 1_555 D N PRO 1 D PRO 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc8 D NE2 HIS 76 D HIS 77 1_555 H FE HEM . D HEM 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? # _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 4K8F _atom_sites.fract_transf_matrix[1][1] 0.014039 _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] 0.014039 _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] 0.006957 _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 2 HEM A 1 300 300 HEM HEM . F 2 HEM B 1 300 300 HEM HEM . G 2 HEM C 1 300 300 HEM HEM . H 2 HEM D 1 300 300 HEM HEM . I 3 HOH A 1 401 2 HOH HOH . I 3 HOH A 2 402 8 HOH HOH . I 3 HOH A 3 403 9 HOH HOH . I 3 HOH A 4 404 10 HOH HOH . I 3 HOH A 5 405 20 HOH HOH . I 3 HOH A 6 406 21 HOH HOH . I 3 HOH A 7 407 22 HOH HOH . I 3 HOH A 8 408 24 HOH HOH . I 3 HOH A 9 409 25 HOH HOH . J 3 HOH B 1 401 4 HOH HOH . J 3 HOH B 2 402 6 HOH HOH . J 3 HOH B 3 403 11 HOH HOH . J 3 HOH B 4 404 12 HOH HOH . J 3 HOH B 5 405 15 HOH HOH . J 3 HOH B 6 406 17 HOH HOH . J 3 HOH B 7 407 18 HOH HOH . J 3 HOH B 8 408 19 HOH HOH . J 3 HOH B 9 409 23 HOH HOH . K 3 HOH C 1 401 1 HOH HOH . K 3 HOH C 2 402 3 HOH HOH . K 3 HOH C 3 403 5 HOH HOH . K 3 HOH C 4 404 7 HOH HOH . K 3 HOH C 5 405 13 HOH HOH . K 3 HOH C 6 406 14 HOH HOH . K 3 HOH C 7 407 16 HOH HOH . K 3 HOH C 8 408 26 HOH HOH . K 3 HOH C 9 409 27 HOH HOH . K 3 HOH C 10 410 28 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 . . . H 2 -6.319 17.374 36.236 1 61.38 ? CHA HEM 300 D 1 HETATM 2 C CHB HEM . . . H 2 -2.813 17.09 32.86 1 60.59 ? CHB HEM 300 D 1 HETATM 3 C CHC HEM . . . H 2 -4.394 12.64 31.618 1 59.54 ? CHC HEM 300 D 1 HETATM 4 C CHD HEM . . . H 2 -7.809 12.895 35.08 1 64.34 ? CHD HEM 300 D 1 HETATM 5 C C1A HEM . . . H 2 -5.266 17.676 35.406 1 65.98 ? C1A HEM 300 D 1 HETATM 6 C C2A HEM . . . H 2 -4.599 18.964 35.354 1 72.9 ? C2A HEM 300 D 1 HETATM 7 C C3A HEM . . . H 2 -3.63 18.893 34.427 1 72.32 ? C3A HEM 300 D 1 HETATM 8 C C4A HEM . . . H 2 -3.656 17.559 33.846 1 65.32 ? C4A HEM 300 D 1 HETATM 9 C CMA HEM . . . H 2 -2.654 20.03 34.039 1 68.15 ? CMA HEM 300 D 1 HETATM 10 C CAA HEM . . . H 2 -4.943 20.195 36.235 1 76.37 ? CAA HEM 300 D 1 HETATM 11 C CBA HEM . . . H 2 -5.846 21.187 35.491 1 84.97 ? CBA HEM 300 D 1 HETATM 12 C CGA HEM . . . H 2 -5.431 22.626 35.763 1 94.46 ? CGA HEM 300 D 1 HETATM 13 O O1A HEM . . . H 2 -4.201 22.927 35.774 1 90.95 ? O1A HEM 300 D 1 HETATM 14 O O2A HEM . . . H 2 -6.332 23.492 35.948 1 96.34 ? O2A HEM 300 D 1 HETATM 15 C C1B HEM . . . H 2 -2.964 15.899 32.193 1 59.97 ? C1B HEM 300 D 1 HETATM 16 C C2B HEM . . . H 2 -2.256 15.483 31.005 1 58.64 ? C2B HEM 300 D 1 HETATM 17 C C3B HEM . . . H 2 -2.699 14.28 30.655 1 58.22 ? C3B HEM 300 D 1 HETATM 18 C C4B HEM . . . H 2 -3.695 13.844 31.617 1 62.54 ? C4B HEM 300 D 1 HETATM 19 C CMB HEM . . . H 2 -1.192 16.288 30.242 1 62.03 ? CMB HEM 300 D 1 HETATM 20 C CAB HEM . . . H 2 -2.205 13.472 29.45 1 62.64 ? CAB HEM 300 D 1 HETATM 21 C CBB HEM . . . H 2 -2.929 12.429 29.014 1 67.53 ? CBB HEM 300 D 1 HETATM 22 C C1C HEM . . . H 2 -5.436 12.304 32.467 1 61.54 ? C1C HEM 300 D 1 HETATM 23 C C2C HEM . . . H 2 -6.15 11.036 32.527 1 64.21 ? C2C HEM 300 D 1 HETATM 24 C C3C HEM . . . H 2 -7.093 11.141 33.49 1 67.81 ? C3C HEM 300 D 1 HETATM 25 C C4C HEM . . . H 2 -6.991 12.454 34.069 1 65.08 ? C4C HEM 300 D 1 HETATM 26 C CMC HEM . . . H 2 -5.869 9.814 31.62 1 57.01 ? CMC HEM 300 D 1 HETATM 27 C CAC HEM . . . H 2 -8.139 10.116 34.014 1 70.4 ? CAC HEM 300 D 1 HETATM 28 C CBC HEM . . . H 2 -8.082 8.807 33.749 1 74.89 ? CBC HEM 300 D 1 HETATM 29 C C1D HEM . . . H 2 -7.719 14.095 35.728 1 63.3 ? C1D HEM 300 D 1 HETATM 30 C C2D HEM . . . H 2 -8.515 14.455 36.875 1 66.29 ? C2D HEM 300 D 1 HETATM 31 C C3D HEM . . . H 2 -8.048 15.872 37.248 1 71.61 ? C3D HEM 300 D 1 HETATM 32 C C4D HEM . . . H 2 -7.017 16.196 36.28 1 61.66 ? C4D HEM 300 D 1 HETATM 33 C CMD HEM . . . H 2 -9.603 13.594 37.555 1 60.73 ? CMD HEM 300 D 1 HETATM 34 C CAD HEM . . . H 2 -8.573 16.758 38.411 1 76.01 ? CAD HEM 300 D 1 HETATM 35 C CBD HEM . . . H 2 -7.961 16.304 39.74 1 78.9 ? CBD HEM 300 D 1 HETATM 36 C CGD HEM . . . H 2 -6.855 17.251 40.14 1 88.45 ? CGD HEM 300 D 1 HETATM 37 O O1D HEM . . . H 2 -5.815 16.747 40.633 1 92.31 ? O1D HEM 300 D 1 HETATM 38 O O2D HEM . . . H 2 -6.99 18.498 39.956 1 88.19 ? O2D HEM 300 D 1 HETATM 39 N NA HEM . . . H 2 -4.666 16.841 34.47 1 64.37 ? NA HEM 300 D 1 HETATM 40 N NB HEM . . . H 2 -3.832 14.874 32.536 1 63.15 ? NB HEM 300 D 1 HETATM 41 N NC HEM . . . H 2 -5.98 13.142 33.427 1 62.54 ? NC HEM 300 D 1 HETATM 42 N ND HEM . . . H 2 -6.85 15.128 35.406 1 61.17 ? ND HEM 300 D 1 HETATM 43 FE FE HEM . . . H 2 -5.296 14.951 33.891 1 58.88 ? FE HEM 300 D 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 43 #