data_4PK5 # _model_server_result.job_id DhbpO-36_S1dp8oSk7eIMA _model_server_result.datetime_utc '2024-11-28 12:01:50' _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 4pk5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 4PK5 # _exptl.entry_id 4PK5 _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 4PK5 _cell.length_a 84.799 _cell.length_b 90.414 _cell.length_c 131.757 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PK5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _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 # 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 disulf ? disulf1 A SG CYS 328 A CYS 308 1_555 B SG CYS 328 B CYS 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc1 A NE2 HIS 366 A HIS 346 1_555 C FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc2 C FE HEM . A HEM 501 1_555 D N17 PKJ . A PKJ 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc3 B NE2 HIS 366 B HIS 346 1_555 E FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.908 ? metalc ? metalc4 E FE HEM . B HEM 501 1_555 F N17 PKJ . B PKJ 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? # _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 4PK5 _atom_sites.fract_transf_matrix[1][1] 0.011793 _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] 0.01106 _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] 0.00759 _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 1 501 404 HEM HEM . D 3 PKJ A 1 502 2 PKJ UNL . E 2 HEM B 1 501 404 HEM HEM . F 3 PKJ B 1 502 1 PKJ UNL . G 4 HOH A 1 601 1 HOH HOH . G 4 HOH A 2 602 3 HOH HOH . G 4 HOH A 3 603 4 HOH HOH . G 4 HOH A 4 604 5 HOH HOH . G 4 HOH A 5 605 8 HOH HOH . H 4 HOH B 1 601 2 HOH HOH . H 4 HOH B 2 602 6 HOH HOH . H 4 HOH B 3 603 7 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 . . . E 2 -21.096 49.203 20.16 1 38.72 ? CHA HEM 501 B 1 HETATM 2 C CHB HEM . . . E 2 -22.787 53.472 21.647 1 41.38 ? CHB HEM 501 B 1 HETATM 3 C CHC HEM . . . E 2 -24.034 54.562 17.071 1 38 ? CHC HEM 501 B 1 HETATM 4 C CHD HEM . . . E 2 -21.92 50.481 15.63 1 37.62 ? CHD HEM 501 B 1 HETATM 5 C C1A HEM . . . E 2 -21.512 50.256 20.93 1 42.01 ? C1A HEM 501 B 1 HETATM 6 C C2A HEM . . . E 2 -21.384 50.27 22.352 1 44.43 ? C2A HEM 501 B 1 HETATM 7 C C3A HEM . . . E 2 -21.865 51.461 22.769 1 40.65 ? C3A HEM 501 B 1 HETATM 8 C C4A HEM . . . E 2 -22.258 52.204 21.63 1 40.73 ? C4A HEM 501 B 1 HETATM 9 C CMA HEM . . . E 2 -21.918 51.873 24.205 1 39.99 ? CMA HEM 501 B 1 HETATM 10 C CAA HEM . . . E 2 -20.821 49.197 23.265 1 46.5 ? CAA HEM 501 B 1 HETATM 11 C CBA HEM . . . E 2 -21.409 47.825 22.915 1 53.76 ? CBA HEM 501 B 1 HETATM 12 C CGA HEM . . . E 2 -22.595 47.522 23.766 1 60.52 ? CGA HEM 501 B 1 HETATM 13 O O1A HEM . . . E 2 -23.264 46.511 23.483 1 64.75 ? O1A HEM 501 B 1 HETATM 14 O O2A HEM . . . E 2 -22.921 48.262 24.734 1 71.93 ? O2A HEM 501 B 1 HETATM 15 C C1B HEM . . . E 2 -23.258 54.133 20.502 1 40.17 ? C1B HEM 501 B 1 HETATM 16 C C2B HEM . . . E 2 -23.841 55.426 20.568 1 40.12 ? C2B HEM 501 B 1 HETATM 17 C C3B HEM . . . E 2 -24.182 55.752 19.281 1 39.25 ? C3B HEM 501 B 1 HETATM 18 C C4B HEM . . . E 2 -23.796 54.612 18.435 1 38.86 ? C4B HEM 501 B 1 HETATM 19 C CMB HEM . . . E 2 -24.027 56.249 21.836 1 37.86 ? CMB HEM 501 B 1 HETATM 20 C CAB HEM . . . E 2 -24.834 56.97 18.785 1 41.32 ? CAB HEM 501 B 1 HETATM 21 C CBB HEM . . . E 2 -25.643 57.681 19.572 1 42.6 ? CBB HEM 501 B 1 HETATM 22 C C1C HEM . . . E 2 -23.613 53.531 16.253 1 38.8 ? C1C HEM 501 B 1 HETATM 23 C C2C HEM . . . E 2 -23.842 53.385 14.864 1 38.54 ? C2C HEM 501 B 1 HETATM 24 C C3C HEM . . . E 2 -23.23 52.214 14.462 1 40.14 ? C3C HEM 501 B 1 HETATM 25 C C4C HEM . . . E 2 -22.625 51.654 15.637 1 40.02 ? C4C HEM 501 B 1 HETATM 26 C CMC HEM . . . E 2 -24.584 54.308 13.943 1 38.67 ? CMC HEM 501 B 1 HETATM 27 C CAC HEM . . . E 2 -23.177 51.637 13.085 1 39.44 ? CAC HEM 501 B 1 HETATM 28 C CBC HEM . . . E 2 -23.895 50.548 12.766 1 35.46 ? CBC HEM 501 B 1 HETATM 29 C C1D HEM . . . E 2 -21.53 49.847 16.772 1 37.46 ? C1D HEM 501 B 1 HETATM 30 C C2D HEM . . . E 2 -20.859 48.531 16.701 1 38.26 ? C2D HEM 501 B 1 HETATM 31 C C3D HEM . . . E 2 -20.61 48.179 17.968 1 39.2 ? C3D HEM 501 B 1 HETATM 32 C C4D HEM . . . E 2 -21.142 49.287 18.791 1 40.4 ? C4D HEM 501 B 1 HETATM 33 C CMD HEM . . . E 2 -20.513 47.733 15.46 1 35.04 ? CMD HEM 501 B 1 HETATM 34 C CAD HEM . . . E 2 -19.964 46.892 18.434 1 39.75 ? CAD HEM 501 B 1 HETATM 35 C CBD HEM . . . E 2 -18.516 47.055 18.921 1 41.64 ? CBD HEM 501 B 1 HETATM 36 C CGD HEM . . . E 2 -17.516 47.102 17.787 1 43.47 ? CGD HEM 501 B 1 HETATM 37 O O1D HEM . . . E 2 -16.586 47.938 17.805 1 44.81 ? O1D HEM 501 B 1 HETATM 38 O O2D HEM . . . E 2 -17.58 46.312 16.817 1 45.92 ? O2D HEM 501 B 1 HETATM 39 N NA HEM . . . E 2 -22.103 51.43 20.521 1 38.3 ? NA HEM 501 B 1 HETATM 40 N NB HEM . . . E 2 -23.282 53.7 19.245 1 38.17 ? NB HEM 501 B 1 HETATM 41 N NC HEM . . . E 2 -22.953 52.435 16.702 1 37.92 ? NC HEM 501 B 1 HETATM 42 N ND HEM . . . E 2 -21.714 50.26 18.027 1 40.79 ? ND HEM 501 B 1 HETATM 43 FE FE HEM . . . E 2 -22.461 51.902 18.645 1 38.44 ? FE HEM 501 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 43 #