data_8FDJ # _model_server_result.job_id YFs8R-924_FH11rlMfbYVQ _model_server_result.datetime_utc '2024-11-16 23:33:30' _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 8fdj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 8FDJ # _exptl.entry_id 8FDJ _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 104.55 _cell.angle_gamma 90 _cell.entry_id 8FDJ _cell.length_a 34.529 _cell.length_b 30.049 _cell.length_c 64.622 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8FDJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _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 NE2 HIS 94 A HIS 93 1_555 B FE HEM . A HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc2 B FE HEM . A HEM 201 1_555 C N NBE . A NBE 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? # _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 116 n n CHA C4D HEM doub 117 n n CHA HHA HEM sing 118 n n CHB C4A HEM sing 119 n n CHB C1B HEM doub 120 n n CHB HHB HEM sing 121 n n CHC C4B HEM sing 122 n n CHC C1C HEM doub 123 n n CHC HHC HEM sing 124 n n CHD C4C HEM doub 125 n n CHD C1D HEM sing 126 n n CHD HHD HEM sing 127 n n C1A C2A HEM doub 128 n y C1A NA HEM sing 129 n y C2A C3A HEM sing 130 n y C2A CAA HEM sing 131 n n C3A C4A HEM doub 132 n y C3A CMA HEM sing 133 n n C4A NA HEM sing 134 n y CMA HMA HEM sing 135 n n CMA HMAA HEM sing 136 n n CMA HMAB HEM sing 137 n n CAA CBA HEM sing 138 n n CAA HAA HEM sing 139 n n CAA HAAA HEM sing 140 n n CBA CGA HEM sing 141 n n CBA HBA HEM sing 142 n n CBA HBAA HEM sing 143 n n CGA O1A HEM doub 144 n n CGA O2A HEM sing 145 n n C1B C2B HEM sing 146 n n C1B NB HEM sing 147 n n C2B C3B HEM doub 148 n n C2B CMB HEM sing 149 n n C3B C4B HEM sing 150 n n C3B CAB HEM sing 151 n n C4B NB HEM doub 152 n n CMB HMB HEM sing 153 n n CMB HMBA HEM sing 154 n n CMB HMBB HEM sing 155 n n CAB CBB HEM doub 156 n n CAB HAB HEM sing 157 n n CBB HBB HEM sing 158 n n CBB HBBA HEM sing 159 n n C1C C2C HEM sing 160 n y C1C NC HEM sing 161 n y C2C C3C HEM doub 162 n y C2C CMC HEM sing 163 n n C3C C4C HEM sing 164 n y C3C CAC HEM sing 165 n n C4C NC HEM sing 166 n y CMC HMC HEM sing 167 n n CMC HMCA HEM sing 168 n n CMC HMCB HEM sing 169 n n CAC CBC HEM doub 170 n n CAC HAC HEM sing 171 n n CBC HBC HEM sing 172 n n CBC HBCA HEM sing 173 n n C1D C2D HEM sing 174 n n C1D ND HEM doub 175 n n C2D C3D HEM doub 176 n n C2D CMD HEM sing 177 n n C3D C4D HEM sing 178 n n C3D CAD HEM sing 179 n n C4D ND HEM sing 180 n n CMD HMD HEM sing 181 n n CMD HMDA HEM sing 182 n n CMD HMDB HEM sing 183 n n CAD CBD HEM sing 184 n n CAD HAD HEM sing 185 n n CAD HADA HEM sing 186 n n CBD CGD HEM sing 187 n n CBD HBD HEM sing 188 n n CBD HBDA HEM sing 189 n n CGD O1D HEM doub 190 n n CGD O2D HEM sing 191 n n O2A H2A HEM sing 192 n n O2D H2D HEM sing 193 n n FE NA HEM sing 194 n n FE NB HEM sing 195 n n FE NC HEM sing 196 n n FE ND HEM sing 197 n n # _atom_sites.entry_id 8FDJ _atom_sites.fract_transf_matrix[1][1] 0.028961 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007516 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.033279 _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] 0.015987 _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 1 201 201 HEM HEM . C 3 NBE A 1 202 202 NBE NBE . D 4 SO4 A 1 203 203 SO4 SO4 . E 5 HOH A 1 301 301 HOH HOH . E 5 HOH A 2 302 302 HOH HOH . E 5 HOH A 3 303 303 HOH HOH . E 5 HOH A 4 304 304 HOH HOH . E 5 HOH A 5 305 305 HOH HOH . E 5 HOH A 6 306 306 HOH HOH . E 5 HOH A 7 307 307 HOH HOH . E 5 HOH A 8 308 308 HOH HOH . E 5 HOH A 9 309 309 HOH HOH . E 5 HOH A 10 310 310 HOH HOH . E 5 HOH A 11 311 311 HOH HOH . E 5 HOH A 12 312 312 HOH HOH . E 5 HOH A 13 313 313 HOH HOH . E 5 HOH A 14 314 314 HOH HOH . E 5 HOH A 15 315 315 HOH HOH . E 5 HOH A 16 316 316 HOH HOH . E 5 HOH A 17 317 317 HOH HOH . E 5 HOH A 18 318 318 HOH HOH . E 5 HOH A 19 319 319 HOH HOH . E 5 HOH A 20 320 320 HOH HOH . E 5 HOH A 21 321 321 HOH HOH . E 5 HOH A 22 322 322 HOH HOH . E 5 HOH A 23 323 323 HOH HOH . E 5 HOH A 24 324 324 HOH HOH . E 5 HOH A 25 325 325 HOH HOH . E 5 HOH A 26 326 326 HOH HOH . E 5 HOH A 27 327 327 HOH HOH . E 5 HOH A 28 328 328 HOH HOH . E 5 HOH A 29 329 329 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 -0.884 -6.15 -16.74 1 23.26 ? CHA HEM 201 A 1 HETATM 2 C CHB HEM . . . B 2 -4.432 -2.982 -15.786 1 18.44 ? CHB HEM 201 A 1 HETATM 3 C CHC HEM . . . B 2 -1.176 0.01 -13.937 1 18.55 ? CHC HEM 201 A 1 HETATM 4 C CHD HEM . . . B 2 2.339 -2.873 -15.426 1 19.47 ? CHD HEM 201 A 1 HETATM 5 C C1A HEM . . . B 2 -2.101 -5.541 -16.609 1 21.97 ? C1A HEM 201 A 1 HETATM 6 C C2A HEM . . . B 2 -3.308 -6.206 -16.869 1 24.54 ? C2A HEM 201 A 1 HETATM 7 C C3A HEM . . . B 2 -4.319 -5.317 -16.6 1 23.34 ? C3A HEM 201 A 1 HETATM 8 C C4A HEM . . . B 2 -3.738 -4.104 -16.188 1 20.84 ? C4A HEM 201 A 1 HETATM 9 C CMA HEM . . . B 2 -5.799 -5.588 -16.75 1 26 ? CMA HEM 201 A 1 HETATM 10 C CAA HEM . . . B 2 -3.447 -7.636 -17.358 1 25.22 ? CAA HEM 201 A 1 HETATM 11 C CBA HEM . . . B 2 -3.934 -8.625 -16.301 1 25.6 ? CBA HEM 201 A 1 HETATM 12 C CGA HEM . . . B 2 -3.014 -8.829 -15.112 1 30 ? CGA HEM 201 A 1 HETATM 13 O O1A HEM . . . B 2 -3.453 -8.627 -13.937 1 32.12 ? O1A HEM 201 A 1 HETATM 14 O O2A HEM . . . B 2 -1.832 -9.231 -15.265 1 27.6 ? O2A HEM 201 A 1 HETATM 15 C C1B HEM . . . B 2 -3.817 -1.901 -15.188 1 18.05 ? C1B HEM 201 A 1 HETATM 16 C C2B HEM . . . B 2 -4.55 -0.764 -14.717 1 18.99 ? C2B HEM 201 A 1 HETATM 17 C C3B HEM . . . B 2 -3.677 0.089 -14.166 1 18.23 ? C3B HEM 201 A 1 HETATM 18 C C4B HEM . . . B 2 -2.356 -0.59 -14.32 1 20.23 ? C4B HEM 201 A 1 HETATM 19 C CMB HEM . . . B 2 -6.036 -0.628 -14.797 1 19.35 ? CMB HEM 201 A 1 HETATM 20 C CAB HEM . . . B 2 -3.828 1.444 -13.615 1 20.91 ? CAB HEM 201 A 1 HETATM 21 C CBB HEM . . . B 2 -4.785 2.309 -13.962 1 21.06 ? CBB HEM 201 A 1 HETATM 22 C C1C HEM . . . B 2 0.083 -0.434 -14.265 1 18.27 ? C1C HEM 201 A 1 HETATM 23 C C2C HEM . . . B 2 1.262 0.279 -14.167 1 19.68 ? C2C HEM 201 A 1 HETATM 24 C C3C HEM . . . B 2 2.288 -0.581 -14.623 1 20.13 ? C3C HEM 201 A 1 HETATM 25 C C4C HEM . . . B 2 1.684 -1.79 -14.921 1 18.74 ? C4C HEM 201 A 1 HETATM 26 C CMC HEM . . . B 2 1.344 1.695 -13.703 1 22.65 ? CMC HEM 201 A 1 HETATM 27 C CAC HEM . . . B 2 3.747 -0.379 -14.775 1 21.65 ? CAC HEM 201 A 1 HETATM 28 C CBC HEM . . . B 2 4.336 0.75 -14.536 1 20.96 ? CBC HEM 201 A 1 HETATM 29 C C1D HEM . . . B 2 1.706 -4.019 -15.902 1 21.98 ? C1D HEM 201 A 1 HETATM 30 C C2D HEM . . . B 2 2.488 -5.165 -16.414 1 21.51 ? C2D HEM 201 A 1 HETATM 31 C C3D HEM . . . B 2 1.589 -6.117 -16.758 1 22.73 ? C3D HEM 201 A 1 HETATM 32 C C4D HEM . . . B 2 0.266 -5.496 -16.46 1 20.23 ? C4D HEM 201 A 1 HETATM 33 C CMD HEM . . . B 2 3.985 -5.312 -16.519 1 21.36 ? CMD HEM 201 A 1 HETATM 34 C CAD HEM . . . B 2 1.908 -7.462 -17.403 1 25.16 ? CAD HEM 201 A 1 HETATM 35 C CBD HEM . . . B 2 1.802 -7.129 -18.907 1 25.51 ? CBD HEM 201 A 1 HETATM 36 C CGD HEM . . . B 2 2.32 -8.067 -19.958 1 24.82 ? CGD HEM 201 A 1 HETATM 37 O O1D HEM . . . B 2 1.543 -8.641 -20.713 1 24.9 ? O1D HEM 201 A 1 HETATM 38 O O2D HEM . . . B 2 3.537 -8.221 -20.189 1 28.31 ? O2D HEM 201 A 1 HETATM 39 N NA HEM . . . B 2 -2.38 -4.256 -16.159 1 22.21 ? NA HEM 201 A 1 HETATM 40 N NB HEM . . . B 2 -2.536 -1.744 -14.953 1 18.67 ? NB HEM 201 A 1 HETATM 41 N NC HEM . . . B 2 0.354 -1.657 -14.714 1 19.52 ? NC HEM 201 A 1 HETATM 42 N ND HEM . . . B 2 0.388 -4.286 -15.923 1 19.66 ? ND HEM 201 A 1 HETATM 43 FE FE HEM . . . B 2 -0.996 -3.04 -15.47 1 20.4 ? FE HEM 201 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 988 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 43 #