data_8YZ8 # _model_server_result.job_id guRfRoIMWrHa4UsoUAfPQw _model_server_result.datetime_utc '2024-11-20 16:35:37' _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 8yz8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 8YZ8 # _exptl.entry_id 8YZ8 _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 2 _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 8YZ8 _cell.length_a 145.406 _cell.length_b 145.406 _cell.length_c 129.178 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YZ8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 80 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 C N N ? 2 E N N # _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 145 n n CHA C4D HEM doub 146 n n CHA HHA HEM sing 147 n n CHB C4A HEM sing 148 n n CHB C1B HEM doub 149 n n CHB HHB HEM sing 150 n n CHC C4B HEM sing 151 n n CHC C1C HEM doub 152 n n CHC HHC HEM sing 153 n n CHD C4C HEM doub 154 n n CHD C1D HEM sing 155 n n CHD HHD HEM sing 156 n n C1A C2A HEM doub 157 n y C1A NA HEM sing 158 n y C2A C3A HEM sing 159 n y C2A CAA HEM sing 160 n n C3A C4A HEM doub 161 n y C3A CMA HEM sing 162 n n C4A NA HEM sing 163 n y CMA HMA HEM sing 164 n n CMA HMAA HEM sing 165 n n CMA HMAB HEM sing 166 n n CAA CBA HEM sing 167 n n CAA HAA HEM sing 168 n n CAA HAAA HEM sing 169 n n CBA CGA HEM sing 170 n n CBA HBA HEM sing 171 n n CBA HBAA HEM sing 172 n n CGA O1A HEM doub 173 n n CGA O2A HEM sing 174 n n C1B C2B HEM sing 175 n n C1B NB HEM sing 176 n n C2B C3B HEM doub 177 n n C2B CMB HEM sing 178 n n C3B C4B HEM sing 179 n n C3B CAB HEM sing 180 n n C4B NB HEM doub 181 n n CMB HMB HEM sing 182 n n CMB HMBA HEM sing 183 n n CMB HMBB HEM sing 184 n n CAB CBB HEM doub 185 n n CAB HAB HEM sing 186 n n CBB HBB HEM sing 187 n n CBB HBBA HEM sing 188 n n C1C C2C HEM sing 189 n y C1C NC HEM sing 190 n y C2C C3C HEM doub 191 n y C2C CMC HEM sing 192 n n C3C C4C HEM sing 193 n y C3C CAC HEM sing 194 n n C4C NC HEM sing 195 n y CMC HMC HEM sing 196 n n CMC HMCA HEM sing 197 n n CMC HMCB HEM sing 198 n n CAC CBC HEM doub 199 n n CAC HAC HEM sing 200 n n CBC HBC HEM sing 201 n n CBC HBCA HEM sing 202 n n C1D C2D HEM sing 203 n n C1D ND HEM doub 204 n n C2D C3D HEM doub 205 n n C2D CMD HEM sing 206 n n C3D C4D HEM sing 207 n n C3D CAD HEM sing 208 n n C4D ND HEM sing 209 n n CMD HMD HEM sing 210 n n CMD HMDA HEM sing 211 n n CMD HMDB HEM sing 212 n n CAD CBD HEM sing 213 n n CAD HAD HEM sing 214 n n CAD HADA HEM sing 215 n n CBD CGD HEM sing 216 n n CBD HBD HEM sing 217 n n CBD HBDA HEM sing 218 n n CGD O1D HEM doub 219 n n CGD O2D HEM sing 220 n n O2A H2A HEM sing 221 n n O2D H2D HEM sing 222 n n FE NA HEM sing 223 n n FE NB HEM sing 224 n n FE NC HEM sing 225 n n FE ND HEM sing 226 n n # _atom_sites.entry_id 8YZ8 _atom_sites.fract_transf_matrix[1][1] 0.006877 _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] 0.006877 _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] 0.007741 _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 C 2 HEM A 1 501 468 HEM DRG . D 3 ADE A 1 502 470 ADE ADF . E 2 HEM B 1 501 468 HEM DRG . F 3 ADE B 1 502 470 ADE ADF . # 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 2 55.934 2.456 18.68 1 47.31 ? CHA HEM 501 B 1 HETATM 2 C CHB HEM . . . E 2 55.961 3.316 13.988 1 42.32 ? CHB HEM 501 B 1 HETATM 3 C CHC HEM . . . E 2 55.01 -1.306 13.259 1 38.8 ? CHC HEM 501 B 1 HETATM 4 C CHD HEM . . . E 2 54.456 -1.992 17.98 1 37.62 ? CHD HEM 501 B 1 HETATM 5 C C1A HEM . . . E 2 55.893 3.106 17.483 1 45.51 ? C1A HEM 501 B 1 HETATM 6 C C2A HEM . . . E 2 55.931 4.53 17.318 1 46.88 ? C2A HEM 501 B 1 HETATM 7 C C3A HEM . . . E 2 56.144 4.76 15.999 1 46.73 ? C3A HEM 501 B 1 HETATM 8 C C4A HEM . . . E 2 55.973 3.499 15.334 1 44.16 ? C4A HEM 501 B 1 HETATM 9 C CMA HEM . . . E 2 56.457 6.077 15.357 1 43.08 ? CMA HEM 501 B 1 HETATM 10 C CAA HEM . . . E 2 55.726 5.534 18.409 1 43.1 ? CAA HEM 501 B 1 HETATM 11 C CBA HEM . . . E 2 56.821 5.492 19.47 1 51.27 ? CBA HEM 501 B 1 HETATM 12 C CGA HEM . . . E 2 57.183 6.856 20.014 1 54.29 ? CGA HEM 501 B 1 HETATM 13 O O1A HEM . . . E 2 58.308 7.307 19.74 1 65.12 ? O1A HEM 501 B 1 HETATM 14 O O2A HEM . . . E 2 56.343 7.457 20.709 1 43 -1 O2A HEM 501 B 1 HETATM 15 C C1B HEM . . . E 2 55.496 2.19 13.389 1 35.92 ? C1B HEM 501 B 1 HETATM 16 C C2B HEM . . . E 2 55.042 2.089 12.015 1 39.47 ? C2B HEM 501 B 1 HETATM 17 C C3B HEM . . . E 2 54.804 0.712 11.826 1 41.73 ? C3B HEM 501 B 1 HETATM 18 C C4B HEM . . . E 2 55.064 0.058 13.018 1 38.91 ? C4B HEM 501 B 1 HETATM 19 C CMB HEM . . . E 2 54.867 3.207 11.032 1 38.68 ? CMB HEM 501 B 1 HETATM 20 C CAB HEM . . . E 2 54.366 0.041 10.692 1 38.58 ? CAB HEM 501 B 1 HETATM 21 C CBB HEM . . . E 2 54.925 0.049 9.518 1 40.38 ? CBB HEM 501 B 1 HETATM 22 C C1C HEM . . . E 2 54.611 -1.891 14.446 1 39.77 ? C1C HEM 501 B 1 HETATM 23 C C2C HEM . . . E 2 54.299 -3.298 14.622 1 38.28 ? C2C HEM 501 B 1 HETATM 24 C C3C HEM . . . E 2 54.024 -3.424 16.004 1 37.57 ? C3C HEM 501 B 1 HETATM 25 C C4C HEM . . . E 2 54.32 -2.219 16.605 1 37.92 ? C4C HEM 501 B 1 HETATM 26 C CMC HEM . . . E 2 54.277 -4.359 13.563 1 37.33 ? CMC HEM 501 B 1 HETATM 27 C CAC HEM . . . E 2 53.52 -4.501 16.723 1 42.1 ? CAC HEM 501 B 1 HETATM 28 C CBC HEM . . . E 2 53.984 -5.715 16.757 1 48.56 ? CBC HEM 501 B 1 HETATM 29 C C1D HEM . . . E 2 54.733 -0.82 18.627 1 42.08 ? C1D HEM 501 B 1 HETATM 30 C C2D HEM . . . E 2 55.053 -0.694 20.027 1 44.42 ? C2D HEM 501 B 1 HETATM 31 C C3D HEM . . . E 2 55.439 0.593 20.228 1 48.61 ? C3D HEM 501 B 1 HETATM 32 C C4D HEM . . . E 2 55.397 1.234 18.95 1 49.19 ? C4D HEM 501 B 1 HETATM 33 C CMD HEM . . . E 2 54.961 -1.771 21.063 1 56.7 ? CMD HEM 501 B 1 HETATM 34 C CAD HEM . . . E 2 55.823 1.257 21.516 1 51.66 ? CAD HEM 501 B 1 HETATM 35 C CBD HEM . . . E 2 57.332 1.402 21.723 1 60.6 ? CBD HEM 501 B 1 HETATM 36 C CGD HEM . . . E 2 57.708 1.935 23.092 1 60.98 ? CGD HEM 501 B 1 HETATM 37 O O1D HEM . . . E 2 58.831 1.657 23.543 1 60 ? O1D HEM 501 B 1 HETATM 38 O O2D HEM . . . E 2 56.873 2.623 23.701 1 63.22 -1 O2D HEM 501 B 1 HETATM 39 N NA HEM . . . E 2 55.798 2.497 16.262 1 40.83 ? NA HEM 501 B 1 HETATM 40 N NB HEM . . . E 2 55.389 0.969 13.993 1 39.63 ? NB HEM 501 B 1 HETATM 41 N NC HEM . . . E 2 54.453 -1.241 15.64 1 34.83 ? NC HEM 501 B 1 HETATM 42 N ND HEM . . . E 2 54.758 0.424 18.039 1 51.26 ? ND HEM 501 B 1 HETATM 43 FE FE HEM . . . E 2 55.285 1.149 15.866 1 44.83 ? FE HEM 501 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 1065 _model_server_stats.encode_time_ms 24 _model_server_stats.element_count 43 #