data_8YXT # _model_server_result.job_id bbMnyxXgXDn3hPuVwuU1iw _model_server_result.datetime_utc '2024-11-20 14:25:09' _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 8yxt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 8YXT # _exptl.entry_id 8YXT _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 90 _cell.angle_gamma 90 _cell.entry_id 8YXT _cell.length_a 88.712 _cell.length_b 88.712 _cell.length_c 139.892 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YXT _symmetry.cell_setting ? _symmetry.Int_Tables_number 95 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 2 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 5_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # _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 # _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 8YXT _atom_sites.fract_transf_matrix[1][1] 0.011272 _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] 0.011272 _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] 0.007148 _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 DRG . C 3 HOH A 1 601 6 HOH HOH . C 3 HOH A 2 602 18 HOH HOH . C 3 HOH A 3 603 5 HOH HOH . C 3 HOH A 4 604 19 HOH HOH . C 3 HOH A 5 605 1 HOH HOH . C 3 HOH A 6 606 17 HOH HOH . C 3 HOH A 7 607 11 HOH HOH . C 3 HOH A 8 608 10 HOH HOH . C 3 HOH A 9 609 16 HOH HOH . C 3 HOH A 10 610 4 HOH HOH . C 3 HOH A 11 611 3 HOH HOH . C 3 HOH A 12 612 13 HOH HOH . C 3 HOH A 13 613 14 HOH HOH . C 3 HOH A 14 614 15 HOH HOH . C 3 HOH A 15 615 9 HOH HOH . C 3 HOH A 16 616 2 HOH HOH . C 3 HOH A 17 617 12 HOH HOH . C 3 HOH A 18 618 7 HOH HOH . C 3 HOH A 19 619 20 HOH HOH . C 3 HOH A 20 620 21 HOH HOH . C 3 HOH A 21 621 8 HOH HOH . C 3 HOH A 22 622 22 HOH HOH . C 3 HOH A 23 623 24 HOH HOH . C 3 HOH A 24 624 23 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 -22.235 -31.957 -11.834 1 55.5 ? CHA HEM 501 A 1 HETATM 2 C CHB HEM . . . B 2 -21.612 -31.093 -7.077 1 48.4 ? CHB HEM 501 A 1 HETATM 3 C CHC HEM . . . B 2 -20.888 -35.846 -6.428 1 48.07 ? CHC HEM 501 A 1 HETATM 4 C CHD HEM . . . B 2 -21.082 -36.636 -11.252 1 47.96 ? CHD HEM 501 A 1 HETATM 5 C C1A HEM . . . B 2 -22.294 -31.327 -10.58 1 51.38 ? C1A HEM 501 A 1 HETATM 6 C C2A HEM . . . B 2 -22.679 -29.952 -10.351 1 51.48 ? C2A HEM 501 A 1 HETATM 7 C C3A HEM . . . B 2 -22.415 -29.676 -9.04 1 50.17 ? C3A HEM 501 A 1 HETATM 8 C C4A HEM . . . B 2 -21.976 -30.919 -8.426 1 49.06 ? C4A HEM 501 A 1 HETATM 9 C CMA HEM . . . B 2 -22.562 -28.351 -8.353 1 42.21 ? CMA HEM 501 A 1 HETATM 10 C CAA HEM . . . B 2 -23.234 -29.034 -11.396 1 50.86 ? CAA HEM 501 A 1 HETATM 11 C CBA HEM . . . B 2 -22.127 -28.414 -12.258 1 52.46 ? CBA HEM 501 A 1 HETATM 12 C CGA HEM . . . B 2 -22.607 -27.404 -13.291 1 52.54 ? CGA HEM 501 A 1 HETATM 13 O O1A HEM . . . B 2 -23.817 -27.064 -13.283 1 54.66 ? O1A HEM 501 A 1 HETATM 14 O O2A HEM . . . B 2 -21.771 -26.963 -14.113 1 52.1 -1 O2A HEM 501 A 1 HETATM 15 C C1B HEM . . . B 2 -21.305 -32.296 -6.426 1 47.74 ? C1B HEM 501 A 1 HETATM 16 C C2B HEM . . . B 2 -21.106 -32.484 -4.996 1 49.1 ? C2B HEM 501 A 1 HETATM 17 C C3B HEM . . . B 2 -20.879 -33.891 -4.852 1 50.57 ? C3B HEM 501 A 1 HETATM 18 C C4B HEM . . . B 2 -20.961 -34.478 -6.116 1 46.14 ? C4B HEM 501 A 1 HETATM 19 C CMB HEM . . . B 2 -21.132 -31.435 -3.921 1 40.38 ? CMB HEM 501 A 1 HETATM 20 C CAB HEM . . . B 2 -20.66 -34.663 -3.699 1 51.67 ? CAB HEM 501 A 1 HETATM 21 C CBB HEM . . . B 2 -20.981 -34.394 -2.454 1 52.77 ? CBB HEM 501 A 1 HETATM 22 C C1C HEM . . . B 2 -20.906 -36.523 -7.642 1 52.46 ? C1C HEM 501 A 1 HETATM 23 C C2C HEM . . . B 2 -20.747 -37.957 -7.822 1 53.2 ? C2C HEM 501 A 1 HETATM 24 C C3C HEM . . . B 2 -20.688 -38.134 -9.249 1 55.76 ? C3C HEM 501 A 1 HETATM 25 C C4C HEM . . . B 2 -20.962 -36.913 -9.852 1 51.92 ? C4C HEM 501 A 1 HETATM 26 C CMC HEM . . . B 2 -20.657 -38.992 -6.74 1 48.17 ? CMC HEM 501 A 1 HETATM 27 C CAC HEM . . . B 2 -20.403 -39.267 -10.009 1 56.73 ? CAC HEM 501 A 1 HETATM 28 C CBC HEM . . . B 2 -19.933 -40.411 -9.595 1 55.62 ? CBC HEM 501 A 1 HETATM 29 C C1D HEM . . . B 2 -21.429 -35.435 -11.878 1 55.1 ? C1D HEM 501 A 1 HETATM 30 C C2D HEM . . . B 2 -21.408 -35.165 -13.316 1 64.02 ? C2D HEM 501 A 1 HETATM 31 C C3D HEM . . . B 2 -21.784 -33.864 -13.48 1 62.19 ? C3D HEM 501 A 1 HETATM 32 C C4D HEM . . . B 2 -21.967 -33.303 -12.141 1 56.06 ? C4D HEM 501 A 1 HETATM 33 C CMD HEM . . . B 2 -21.066 -36.142 -14.403 1 63.98 ? CMD HEM 501 A 1 HETATM 34 C CAD HEM . . . B 2 -22.01 -33.13 -14.767 1 62.17 ? CAD HEM 501 A 1 HETATM 35 C CBD HEM . . . B 2 -23.483 -33.112 -15.189 1 69.63 ? CBD HEM 501 A 1 HETATM 36 C CGD HEM . . . B 2 -23.74 -32.426 -16.522 1 77.12 ? CGD HEM 501 A 1 HETATM 37 O O1D HEM . . . B 2 -22.781 -32.306 -17.329 1 88.69 ? O1D HEM 501 A 1 HETATM 38 O O2D HEM . . . B 2 -24.897 -32 -16.745 1 66.61 -1 O2D HEM 501 A 1 HETATM 39 N NA HEM . . . B 2 -22.009 -31.918 -9.374 1 44.64 ? NA HEM 501 A 1 HETATM 40 N NB HEM . . . B 2 -21.109 -33.495 -7.058 1 45.76 ? NB HEM 501 A 1 HETATM 41 N NC HEM . . . B 2 -21.081 -35.951 -8.871 1 47.54 ? NC HEM 501 A 1 HETATM 42 N ND HEM . . . B 2 -21.875 -34.313 -11.219 1 51.25 ? ND HEM 501 A 1 HETATM 43 FE FE HEM . . . B 2 -20.613 -33.756 -9.481 1 45.07 ? FE HEM 501 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 43 #