data_3PI4 # _model_server_result.job_id hhvyCDvatGexyUrnr1w-iw _model_server_result.datetime_utc '2024-11-14 23:07:34' _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 3pi4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 3PI4 # _exptl.entry_id 3PI4 _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 3PI4 _cell.length_a 72.237 _cell.length_b 72.237 _cell.length_c 146.288 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PI4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 42 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA tetrameric 4 software_defined_assembly 2 PISA tetrameric 4 software_defined_assembly 3 PISA octameric 8 software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F 1 1 A,B,C,D,E,F 2 1,2 A,B,C,D,E,F 3 1,3 A,B,C,D,E,F 4 1,3,2,4 # 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 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 3 'crystal symmetry operation' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 4 'crystal symmetry operation' 8_555 -y,-x,-z 0 -1 0 -1 0 0 0 0 -1 0 0 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 D 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 covale ? covale1 A C ACE 1 A ACE 0 1_555 A N THR 2 A THR 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale2 B C ACE 1 B ACE 0 1_555 B N THR 2 B THR 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? metalc ? metalc1 A NE2 HIS 98 A HIS 97 1_555 C FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? metalc ? metalc2 C FE HEM . A HEM 500 1_555 E O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc3 B NE2 HIS 98 B HIS 97 1_555 D FE HEM . B HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc4 D FE HEM . B HEM 500 1_555 F O HOH . B HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? # _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 135 n n CHA C4D HEM doub 136 n n CHA HHA HEM sing 137 n n CHB C4A HEM sing 138 n n CHB C1B HEM doub 139 n n CHB HHB HEM sing 140 n n CHC C4B HEM sing 141 n n CHC C1C HEM doub 142 n n CHC HHC HEM sing 143 n n CHD C4C HEM doub 144 n n CHD C1D HEM sing 145 n n CHD HHD HEM sing 146 n n C1A C2A HEM doub 147 n y C1A NA HEM sing 148 n y C2A C3A HEM sing 149 n y C2A CAA HEM sing 150 n n C3A C4A HEM doub 151 n y C3A CMA HEM sing 152 n n C4A NA HEM sing 153 n y CMA HMA HEM sing 154 n n CMA HMAA HEM sing 155 n n CMA HMAB HEM sing 156 n n CAA CBA HEM sing 157 n n CAA HAA HEM sing 158 n n CAA HAAA HEM sing 159 n n CBA CGA HEM sing 160 n n CBA HBA HEM sing 161 n n CBA HBAA HEM sing 162 n n CGA O1A HEM doub 163 n n CGA O2A HEM sing 164 n n C1B C2B HEM sing 165 n n C1B NB HEM sing 166 n n C2B C3B HEM doub 167 n n C2B CMB HEM sing 168 n n C3B C4B HEM sing 169 n n C3B CAB HEM sing 170 n n C4B NB HEM doub 171 n n CMB HMB HEM sing 172 n n CMB HMBA HEM sing 173 n n CMB HMBB HEM sing 174 n n CAB CBB HEM doub 175 n n CAB HAB HEM sing 176 n n CBB HBB HEM sing 177 n n CBB HBBA HEM sing 178 n n C1C C2C HEM sing 179 n y C1C NC HEM sing 180 n y C2C C3C HEM doub 181 n y C2C CMC HEM sing 182 n n C3C C4C HEM sing 183 n y C3C CAC HEM sing 184 n n C4C NC HEM sing 185 n y CMC HMC HEM sing 186 n n CMC HMCA HEM sing 187 n n CMC HMCB HEM sing 188 n n CAC CBC HEM doub 189 n n CAC HAC HEM sing 190 n n CBC HBC HEM sing 191 n n CBC HBCA HEM sing 192 n n C1D C2D HEM sing 193 n n C1D ND HEM doub 194 n n C2D C3D HEM doub 195 n n C2D CMD HEM sing 196 n n C3D C4D HEM sing 197 n n C3D CAD HEM sing 198 n n C4D ND HEM sing 199 n n CMD HMD HEM sing 200 n n CMD HMDA HEM sing 201 n n CMD HMDB HEM sing 202 n n CAD CBD HEM sing 203 n n CAD HAD HEM sing 204 n n CAD HADA HEM sing 205 n n CBD CGD HEM sing 206 n n CBD HBD HEM sing 207 n n CBD HBDA HEM sing 208 n n CGD O1D HEM doub 209 n n CGD O2D HEM sing 210 n n O2A H2A HEM sing 211 n n O2D H2D HEM sing 212 n n FE NA HEM sing 213 n n FE NB HEM sing 214 n n FE NC HEM sing 215 n n FE ND HEM sing 216 n n # _atom_sites.entry_id 3PI4 _atom_sites.fract_transf_matrix[1][1] 0.013843 _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] 0.013843 _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] 0.006836 _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 1 500 500 HEM HEM . D 2 HEM B 1 500 500 HEM HEM . E 3 HOH A 1 501 501 HOH HOH . F 3 HOH B 1 501 501 HOH HOH . F 3 HOH B 2 502 502 HOH HOH . F 3 HOH B 3 503 503 HOH HOH . F 3 HOH B 4 504 504 HOH HOH . F 3 HOH B 5 505 505 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 . . . D 2 -10.928 -15.892 -16.755 1 82.48 ? CHA HEM 500 B 1 HETATM 2 C CHB HEM . . . D 2 -14.622 -13.469 -18.764 1 80.3 ? CHB HEM 500 B 1 HETATM 3 C CHC HEM . . . D 2 -16.522 -13.642 -14.404 1 79.45 ? CHC HEM 500 B 1 HETATM 4 C CHD HEM . . . D 2 -13.59 -17.267 -13.006 1 80.24 ? CHD HEM 500 B 1 HETATM 5 C C1A HEM . . . D 2 -11.802 -15.355 -17.684 1 82.72 ? C1A HEM 500 B 1 HETATM 6 C C2A HEM . . . D 2 -11.715 -15.491 -19.13 1 84.48 ? C2A HEM 500 B 1 HETATM 7 C C3A HEM . . . D 2 -12.737 -14.824 -19.682 1 83.89 ? C3A HEM 500 B 1 HETATM 8 C C4A HEM . . . D 2 -13.498 -14.232 -18.609 1 81.71 ? C4A HEM 500 B 1 HETATM 9 C CMA HEM . . . D 2 -13.07 -14.698 -21.191 1 84.95 ? CMA HEM 500 B 1 HETATM 10 C CAA HEM . . . D 2 -10.64 -16.284 -19.901 1 86.38 ? CAA HEM 500 B 1 HETATM 11 C CBA HEM . . . D 2 -11.027 -17.751 -19.79 1 89.71 ? CBA HEM 500 B 1 HETATM 12 C CGA HEM . . . D 2 -10.501 -18.349 -18.51 1 91.39 ? CGA HEM 500 B 1 HETATM 13 O O1A HEM . . . D 2 -9.285 -18.153 -18.229 1 91.8 ? O1A HEM 500 B 1 HETATM 14 O O2A HEM . . . D 2 -11.293 -19.008 -17.772 1 92.67 ? O2A HEM 500 B 1 HETATM 15 C C1B HEM . . . D 2 -15.457 -13.218 -17.721 1 79.28 ? C1B HEM 500 B 1 HETATM 16 C C2B HEM . . . D 2 -16.609 -12.342 -17.705 1 79.27 ? C2B HEM 500 B 1 HETATM 17 C C3B HEM . . . D 2 -17.128 -12.407 -16.469 1 79.42 ? C3B HEM 500 B 1 HETATM 18 C C4B HEM . . . D 2 -16.316 -13.319 -15.706 1 79.43 ? C4B HEM 500 B 1 HETATM 19 C CMB HEM . . . D 2 -17.109 -11.498 -18.905 1 78.46 ? CMB HEM 500 B 1 HETATM 20 C CAB HEM . . . D 2 -18.372 -11.694 -15.878 1 79.56 ? CAB HEM 500 B 1 HETATM 21 C CBB HEM . . . D 2 -18.52 -10.365 -15.843 1 79.23 ? CBB HEM 500 B 1 HETATM 22 C C1C HEM . . . D 2 -15.883 -14.627 -13.713 1 79.78 ? C1C HEM 500 B 1 HETATM 23 C C2C HEM . . . D 2 -16.227 -14.96 -12.365 1 80.89 ? C2C HEM 500 B 1 HETATM 24 C C3C HEM . . . D 2 -15.427 -15.958 -11.974 1 81.16 ? C3C HEM 500 B 1 HETATM 25 C C4C HEM . . . D 2 -14.55 -16.289 -13.064 1 80.28 ? C4C HEM 500 B 1 HETATM 26 C CMC HEM . . . D 2 -17.338 -14.25 -11.553 1 81.88 ? CMC HEM 500 B 1 HETATM 27 C CAC HEM . . . D 2 -15.411 -16.666 -10.602 1 81.88 ? CAC HEM 500 B 1 HETATM 28 C CBC HEM . . . D 2 -16.465 -17.407 -10.236 1 82.57 ? CBC HEM 500 B 1 HETATM 29 C C1D HEM . . . D 2 -12.514 -17.25 -13.836 1 81.17 ? C1D HEM 500 B 1 HETATM 30 C C2D HEM . . . D 2 -11.318 -18.059 -13.73 1 82.32 ? C2D HEM 500 B 1 HETATM 31 C C3D HEM . . . D 2 -10.464 -17.615 -14.932 1 83.41 ? C3D HEM 500 B 1 HETATM 32 C C4D HEM . . . D 2 -11.258 -16.599 -15.623 1 82.22 ? C4D HEM 500 B 1 HETATM 33 C CMD HEM . . . D 2 -10.965 -19.124 -12.66 1 81.19 ? CMD HEM 500 B 1 HETATM 34 C CAD HEM . . . D 2 -9.063 -18.168 -15.311 1 85.6 ? CAD HEM 500 B 1 HETATM 35 C CBD HEM . . . D 2 -7.92 -17.658 -14.421 1 87.92 ? CBD HEM 500 B 1 HETATM 36 C CGD HEM . . . D 2 -6.567 -18.191 -14.878 1 89.51 ? CGD HEM 500 B 1 HETATM 37 O O1D HEM . . . D 2 -6.501 -19.082 -15.783 1 90.34 ? O1D HEM 500 B 1 HETATM 38 O O2D HEM . . . D 2 -5.525 -17.729 -14.329 1 89.52 ? O2D HEM 500 B 1 HETATM 39 N NA HEM . . . D 2 -12.91 -14.578 -17.406 1 81.11 ? NA HEM 500 B 1 HETATM 40 N NB HEM . . . D 2 -15.302 -13.8 -16.488 1 79.44 ? NB HEM 500 B 1 HETATM 41 N NC HEM . . . D 2 -14.86 -15.456 -14.127 1 79.63 ? NC HEM 500 B 1 HETATM 42 N ND HEM . . . D 2 -12.446 -16.416 -14.945 1 80.87 ? ND HEM 500 B 1 HETATM 43 FE FE HEM . . . D 2 -13.87 -15.078 -15.734 1 78.99 ? FE HEM 500 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 347 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #