data_8S5K # _model_server_result.job_id h8HpnD_2gy05eJbkC2sC5Q _model_server_result.datetime_utc '2025-09-08 11:14:50' _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 8s5k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":601}' # _entry.id 8S5K # _exptl.entry_id 8S5K _exptl.method 'ELECTRON MICROSCOPY' # _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 8 _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 8S5K _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8S5K _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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,M,N,O,P _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 ? 2 I N N ? 2 J N N ? 2 K N N ? 2 L N N ? 2 M N N ? 2 N N N ? 2 O N N ? 2 P 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 covale ? covale1 A C VAL 119 A VAL 118 1_555 A N LLP 120 A LLP 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 A C LLP 120 A LLP 119 1_555 A N ASP 121 A ASP 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 B C VAL 119 B VAL 118 1_555 B N LLP 120 B LLP 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 B C LLP 120 B LLP 119 1_555 B N ASP 121 B ASP 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale5 C C VAL 119 C VAL 118 1_555 C N LLP 120 C LLP 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale6 C C LLP 120 C LLP 119 1_555 C N ASP 121 C ASP 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale7 D C VAL 119 D VAL 118 1_555 D N LLP 120 D LLP 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale8 D C LLP 120 D LLP 119 1_555 D N ASP 121 D ASP 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale9 E C VAL 119 E VAL 118 1_555 E N LLP 120 E LLP 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale10 E C LLP 120 E LLP 119 1_555 E N ASP 121 E ASP 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale11 F C VAL 119 F VAL 118 1_555 F N LLP 120 F LLP 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale12 F C LLP 120 F LLP 119 1_555 F N ASP 121 F ASP 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale13 G C VAL 119 G VAL 118 1_555 G N LLP 120 G LLP 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale14 G C LLP 120 G LLP 119 1_555 G N ASP 121 G ASP 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale15 H C VAL 119 H VAL 118 1_555 H N LLP 120 H LLP 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale16 H C LLP 120 H LLP 119 1_555 H N ASP 121 H ASP 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 A NE2 HIS 66 A HIS 65 1_555 I FE HEM . A HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc2 D NE2 HIS 66 D HIS 65 1_555 L FE HEM . D HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc3 E NE2 HIS 66 E HIS 65 1_555 M FE HEM . E HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc4 H NE2 HIS 66 H HIS 65 1_555 P FE HEM . H HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? # _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 8S5K _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 I 2 HEM A 1 601 1549 HEM HEM . J 2 HEM B 1 601 1549 HEM HEM . K 2 HEM C 1 601 1549 HEM HEM . L 2 HEM D 1 601 1549 HEM HEM . M 2 HEM E 1 601 1549 HEM HEM . N 2 HEM F 1 601 1549 HEM HEM . O 2 HEM G 1 601 1549 HEM HEM . P 2 HEM H 1 601 1549 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 . . . K 2 279.084 254.877 269.241 1 26.73 ? CHA HEM 601 C 1 HETATM 2 C CHB HEM . . . K 2 283.166 257.304 270.193 1 26.73 ? CHB HEM 601 C 1 HETATM 3 C CHC HEM . . . K 2 285.581 253.132 269.762 1 26.73 ? CHC HEM 601 C 1 HETATM 4 C CHD HEM . . . K 2 281.832 251.457 267.22 1 26.73 ? CHD HEM 601 C 1 HETATM 5 C C1A HEM . . . K 2 279.945 255.865 269.661 1 26.73 ? C1A HEM 601 C 1 HETATM 6 C C2A HEM . . . K 2 279.584 257.131 270.26 1 26.73 ? C2A HEM 601 C 1 HETATM 7 C C3A HEM . . . K 2 280.707 257.801 270.52 1 26.73 ? C3A HEM 601 C 1 HETATM 8 C C4A HEM . . . K 2 281.829 256.987 270.1 1 26.73 ? C4A HEM 601 C 1 HETATM 9 C CMA HEM . . . K 2 280.791 259.202 271.159 1 26.73 ? CMA HEM 601 C 1 HETATM 10 C CAA HEM . . . K 2 278.147 257.617 270.537 1 26.73 ? CAA HEM 601 C 1 HETATM 11 C CBA HEM . . . K 2 277.555 258.164 269.242 1 26.73 ? CBA HEM 601 C 1 HETATM 12 C CGA HEM . . . K 2 276.106 258.516 269.452 1 26.73 ? CGA HEM 601 C 1 HETATM 13 O O1A HEM . . . K 2 275.463 258.992 268.483 1 26.73 ? O1A HEM 601 C 1 HETATM 14 O O2A HEM . . . K 2 275.593 258.321 270.585 1 26.73 ? O2A HEM 601 C 1 HETATM 15 C C1B HEM . . . K 2 284.192 256.386 270.182 1 26.73 ? C1B HEM 601 C 1 HETATM 16 C C2B HEM . . . K 2 285.585 256.641 270.485 1 26.73 ? C2B HEM 601 C 1 HETATM 17 C C3B HEM . . . K 2 286.254 255.482 270.373 1 26.73 ? C3B HEM 601 C 1 HETATM 18 C C4B HEM . . . K 2 285.304 254.461 269.987 1 26.73 ? C4B HEM 601 C 1 HETATM 19 C CMB HEM . . . K 2 286.141 258.027 270.874 1 26.73 ? CMB HEM 601 C 1 HETATM 20 C CAB HEM . . . K 2 287.761 255.202 270.577 1 26.73 ? CAB HEM 601 C 1 HETATM 21 C CBB HEM . . . K 2 288.665 256.182 270.662 1 26.73 ? CBB HEM 601 C 1 HETATM 22 C C1C HEM . . . K 2 284.776 252.284 269.037 1 26.73 ? C1C HEM 601 C 1 HETATM 23 C C2C HEM . . . K 2 285.058 250.909 268.677 1 26.73 ? C2C HEM 601 C 1 HETATM 24 C C3C HEM . . . K 2 284.014 250.449 267.976 1 26.73 ? C3C HEM 601 C 1 HETATM 25 C C4C HEM . . . K 2 283.045 251.517 267.865 1 26.73 ? C4C HEM 601 C 1 HETATM 26 C CMC HEM . . . K 2 286.346 250.148 269.061 1 26.73 ? CMC HEM 601 C 1 HETATM 27 C CAC HEM . . . K 2 283.812 249.053 267.35 1 26.73 ? CAC HEM 601 C 1 HETATM 28 C CBC HEM . . . K 2 284.791 248.149 267.309 1 26.73 ? CBC HEM 601 C 1 HETATM 29 C C1D HEM . . . K 2 280.735 252.209 267.566 1 26.73 ? C1D HEM 601 C 1 HETATM 30 C C2D HEM . . . K 2 279.371 251.996 267.139 1 26.73 ? C2D HEM 601 C 1 HETATM 31 C C3D HEM . . . K 2 278.611 252.94 267.696 1 26.73 ? C3D HEM 601 C 1 HETATM 32 C C4D HEM . . . K 2 279.465 253.784 268.5 1 26.73 ? C4D HEM 601 C 1 HETATM 33 C CMD HEM . . . K 2 278.9 250.867 266.201 1 26.73 ? CMD HEM 601 C 1 HETATM 34 C CAD HEM . . . K 2 277.088 253.102 267.525 1 26.73 ? CAD HEM 601 C 1 HETATM 35 C CBD HEM . . . K 2 276.797 254.175 266.488 1 26.73 ? CBD HEM 601 C 1 HETATM 36 C CGD HEM . . . K 2 275.324 254.176 266.19 1 26.73 ? CGD HEM 601 C 1 HETATM 37 O O1D HEM . . . K 2 274.871 255.033 265.39 1 26.73 ? O1D HEM 601 C 1 HETATM 38 O O2D HEM . . . K 2 274.6 253.32 266.756 1 26.73 ? O2D HEM 601 C 1 HETATM 39 N NA HEM . . . K 2 281.322 255.814 269.582 1 26.73 ? NA HEM 601 C 1 HETATM 40 N NB HEM . . . K 2 284.06 255.047 269.885 1 26.73 ? NB HEM 601 C 1 HETATM 41 N NC HEM . . . K 2 283.541 252.618 268.525 1 26.73 ? NC HEM 601 C 1 HETATM 42 N ND HEM . . . K 2 280.753 253.308 268.394 1 26.73 ? ND HEM 601 C 1 HETATM 43 FE FE HEM . . . K 2 282.422 254.198 269.081 1 26.73 ? FE HEM 601 C 1 HETATM 44 H HHB HEM . . . K 2 283.389 258.219 270.465 1 26.73 ? HHB HEM 601 C 1 HETATM 45 H HHC HEM . . . K 2 286.485 252.82 269.974 1 26.73 ? HHC HEM 601 C 1 HETATM 46 H HHD HEM . . . K 2 281.68 250.694 266.624 1 26.73 ? HHD HEM 601 C 1 HETATM 47 H HMA HEM . . . K 2 280.296 259.842 270.607 1 26.73 ? HMA HEM 601 C 1 HETATM 48 H HMAA HEM . . . K 2 280.4 259.174 272.057 1 26.73 ? HMAA HEM 601 C 1 HETATM 49 H HMAB HEM . . . K 2 281.729 259.479 271.219 1 26.73 ? HMAB HEM 601 C 1 HETATM 50 H HAA HEM . . . K 2 277.609 256.873 270.851 1 26.73 ? HAA HEM 601 C 1 HETATM 51 H HAAA HEM . . . K 2 278.162 258.315 271.21 1 26.73 ? HAAA HEM 601 C 1 HETATM 52 H HBA HEM . . . K 2 278.044 258.958 268.976 1 26.73 ? HBA HEM 601 C 1 HETATM 53 H HBAA HEM . . . K 2 277.626 257.493 268.545 1 26.73 ? HBAA HEM 601 C 1 HETATM 54 H HMB HEM . . . K 2 286.467 258.478 270.08 1 26.73 ? HMB HEM 601 C 1 HETATM 55 H HMBA HEM . . . K 2 285.435 258.556 271.278 1 26.73 ? HMBA HEM 601 C 1 HETATM 56 H HMBB HEM . . . K 2 286.868 257.925 271.507 1 26.73 ? HMBB HEM 601 C 1 HETATM 57 H HAB HEM . . . K 2 288.052 254.293 270.682 1 26.73 ? HAB HEM 601 C 1 HETATM 58 H HBB HEM . . . K 2 289.555 255.983 270.991 1 26.73 ? HBB HEM 601 C 1 HETATM 59 H HBBA HEM . . . K 2 288.485 257.047 270.263 1 26.73 ? HBBA HEM 601 C 1 HETATM 60 H HMC HEM . . . K 2 286.756 250.58 269.827 1 26.73 ? HMC HEM 601 C 1 HETATM 61 H HMCA HEM . . . K 2 286.133 249.231 269.29 1 26.73 ? HMCA HEM 601 C 1 HETATM 62 H HMCB HEM . . . K 2 286.967 250.166 268.316 1 26.73 ? HMCB HEM 601 C 1 HETATM 63 H HAC HEM . . . K 2 282.959 248.834 266.966 1 26.73 ? HAC HEM 601 C 1 HETATM 64 H HBC HEM . . . K 2 285.701 248.451 267.166 1 26.73 ? HBC HEM 601 C 1 HETATM 65 H HBCA HEM . . . K 2 284.563 247.24 267.06 1 26.73 ? HBCA HEM 601 C 1 HETATM 66 H HMD HEM . . . K 2 277.964 251.01 265.951 1 26.73 ? HMD HEM 601 C 1 HETATM 67 H HMDA HEM . . . K 2 279.454 250.865 265.393 1 26.73 ? HMDA HEM 601 C 1 HETATM 68 H HMDB HEM . . . K 2 278.989 250.005 266.658 1 26.73 ? HMDB HEM 601 C 1 HETATM 69 H HAD HEM . . . K 2 276.702 252.259 267.24 1 26.73 ? HAD HEM 601 C 1 HETATM 70 H HADA HEM . . . K 2 276.696 253.362 268.374 1 26.73 ? HADA HEM 601 C 1 HETATM 71 H HBD HEM . . . K 2 277.06 255.042 266.834 1 26.73 ? HBD HEM 601 C 1 HETATM 72 H HBDA HEM . . . K 2 277.293 253.985 265.676 1 26.73 ? HBDA HEM 601 C 1 HETATM 73 H HHA HEM . . . K 2 278.124 255.059 269.312 1 26.73 ? HHA HEM 601 C 1 # _model_server_stats.io_time_ms 131 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 44 _model_server_stats.query_time_ms 343 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 73 #