data_8PVD # _model_server_result.job_id gMwH9RzZdXq1Mn8BrpnhDA _model_server_result.datetime_utc '2025-01-07 01:13:05' _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 8pvd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":602}' # _entry.id 8PVD # _exptl.entry_id 8PVD _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 616.487 _entity.id 3 _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 8PVD _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8PVD _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 1,2,3,4 # 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 'point symmetry operation' ? ? -1 0 0 0 -1 0 0 0 1 211.328 211.328 0 3 'point symmetry operation' ? ? 1 0 0 0 -1 0 0 0 -1 0 211.328 211.328 4 'point symmetry operation' ? ? -1 0 0 0 1 0 0 0 -1 211.328 0 211.328 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id OH _struct_conn.ptnr1_label_comp_id TYR _struct_conn.ptnr1_label_seq_id 358 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id TYR _struct_conn.ptnr1_auth_seq_id 358 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id FE _struct_conn.ptnr2_label_comp_id HEM _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id HEM _struct_conn.ptnr2_auth_seq_id 602 _struct_conn.ptnr2_symmetry 1_555 _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 1.919 _struct_conn.pdbx_value_order ? # _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 8PVD _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 B 2 NDP A 1 601 601 NDP NDP . C 3 HEM A 1 602 602 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 . . . C 3 119.459 90.963 110.39 1 74.85 ? CHA HEM 602 A 1 HETATM 2 C CHB HEM . . . C 3 122.124 93.107 107.116 1 74.52 ? CHB HEM 602 A 1 HETATM 3 C CHC HEM . . . C 3 125.646 90.042 108.153 1 80.99 ? CHC HEM 602 A 1 HETATM 4 C CHD HEM . . . C 3 123.204 88.305 111.81 1 77.57 ? CHD HEM 602 A 1 HETATM 5 C C1A HEM . . . C 3 119.833 91.815 109.379 1 72.19 ? C1A HEM 602 A 1 HETATM 6 C C2A HEM . . . C 3 119.015 92.822 108.788 1 67.91 ? C2A HEM 602 A 1 HETATM 7 C C3A HEM . . . C 3 119.783 93.433 107.848 1 71.65 ? C3A HEM 602 A 1 HETATM 8 C C4A HEM . . . C 3 121.045 92.783 107.883 1 72.06 ? C4A HEM 602 A 1 HETATM 9 C CMA HEM . . . C 3 119.465 94.606 106.914 1 71.62 ? CMA HEM 602 A 1 HETATM 10 C CAA HEM . . . C 3 117.569 93.101 109.084 1 67.32 ? CAA HEM 602 A 1 HETATM 11 C CBA HEM . . . C 3 117.446 93.793 110.417 1 73.55 ? CBA HEM 602 A 1 HETATM 12 C CGA HEM . . . C 3 116.016 94.201 110.738 1 78.01 ? CGA HEM 602 A 1 HETATM 13 O O1A HEM . . . C 3 115.759 94.283 111.974 1 77.93 ? O1A HEM 602 A 1 HETATM 14 O O2A HEM . . . C 3 115.116 94.487 109.877 1 72.73 ? O2A HEM 602 A 1 HETATM 15 C C1B HEM . . . C 3 123.344 92.457 107.112 1 75 ? C1B HEM 602 A 1 HETATM 16 C C2B HEM . . . C 3 124.4 92.796 106.229 1 78.06 ? C2B HEM 602 A 1 HETATM 17 C C3B HEM . . . C 3 125.409 91.907 106.49 1 77.21 ? C3B HEM 602 A 1 HETATM 18 C C4B HEM . . . C 3 124.914 91.074 107.6 1 74.92 ? C4B HEM 602 A 1 HETATM 19 C CMB HEM . . . C 3 124.374 93.886 105.188 1 77.27 ? CMB HEM 602 A 1 HETATM 20 C CAB HEM . . . C 3 126.775 91.747 105.954 1 80.34 ? CAB HEM 602 A 1 HETATM 21 C CBB HEM . . . C 3 127.504 92.592 105.279 1 86.59 ? CBB HEM 602 A 1 HETATM 22 C C1C HEM . . . C 3 125.367 89.304 109.258 1 80.73 ? C1C HEM 602 A 1 HETATM 23 C C2C HEM . . . C 3 126.26 88.5 109.995 1 79.43 ? C2C HEM 602 A 1 HETATM 24 C C3C HEM . . . C 3 125.553 87.99 111.054 1 79.81 ? C3C HEM 602 A 1 HETATM 25 C C4C HEM . . . C 3 124.233 88.518 110.927 1 81.59 ? C4C HEM 602 A 1 HETATM 26 C CMC HEM . . . C 3 127.686 88.201 109.64 1 83.85 ? CMC HEM 602 A 1 HETATM 27 C CAC HEM . . . C 3 125.996 87.17 112.198 1 82.62 ? CAC HEM 602 A 1 HETATM 28 C CBC HEM . . . C 3 127.209 87.078 112.69 1 85.49 ? CBC HEM 602 A 1 HETATM 29 C C1D HEM . . . C 3 121.959 88.911 111.7 1 74.85 ? C1D HEM 602 A 1 HETATM 30 C C2D HEM . . . C 3 120.9 88.582 112.623 1 70.75 ? C2D HEM 602 A 1 HETATM 31 C C3D HEM . . . C 3 119.861 89.326 112.249 1 73.61 ? C3D HEM 602 A 1 HETATM 32 C C4D HEM . . . C 3 120.286 90.093 111.078 1 73.85 ? C4D HEM 602 A 1 HETATM 33 C CMD HEM . . . C 3 120.948 87.632 113.786 1 77.5 ? CMD HEM 602 A 1 HETATM 34 C CAD HEM . . . C 3 118.492 89.318 112.881 1 77.51 ? CAD HEM 602 A 1 HETATM 35 C CBD HEM . . . C 3 118.436 90.274 114.055 1 78.91 ? CBD HEM 602 A 1 HETATM 36 C CGD HEM . . . C 3 117.073 90.124 114.659 1 79.25 ? CGD HEM 602 A 1 HETATM 37 O O1D HEM . . . C 3 116.78 89.02 115.191 1 79.34 ? O1D HEM 602 A 1 HETATM 38 O O2D HEM . . . C 3 116.276 91.092 114.611 1 77.04 ? O2D HEM 602 A 1 HETATM 39 N NA HEM . . . C 3 121.07 91.828 108.816 1 69.93 ? NA HEM 602 A 1 HETATM 40 N NB HEM . . . C 3 123.711 91.481 107.914 1 72.85 ? NB HEM 602 A 1 HETATM 41 N NC HEM . . . C 3 124.159 89.351 109.831 1 81.6 ? NC HEM 602 A 1 HETATM 42 N ND HEM . . . C 3 121.55 89.825 110.79 1 77.12 ? ND HEM 602 A 1 HETATM 43 FE FE HEM . . . C 3 122.528 90.623 109.381 1 70.78 ? FE HEM 602 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 338 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 43 #