data_1PBX # _model_server_result.job_id GXaZJ7bTPcgqyobvF2lTHw _model_server_result.datetime_utc '2024-10-23 21:23:25' _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 1pbx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":148}' # _entry.id 1PBX # _exptl.entry_id 1PBX _exptl.method 'X-RAY DIFFRACTION' # _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 97.16 _cell.angle_gamma 90 _cell.entry_id 1PBX _cell.length_a 91.38 _cell.length_b 88.54 _cell.length_c 55.34 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1PBX _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 1,2 # 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' 2_555 -x,y,-z -1 0 0 0 1 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 ? 3 C N N ? 3 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 covale ? covale1 A C ACE 1 A ACE 0 1_555 A N SER 2 A SER 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? metalc ? metalc1 A NE2 HIS 89 A HIS 88 1_555 C FE HEM . A HEM 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc2 C FE HEM . A HEM 144 1_555 D C CMO . A CMO 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.654 ? metalc ? metalc3 C FE HEM . A HEM 144 1_555 D O CMO . A CMO 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.694 ? metalc ? metalc4 B NE2 HIS 92 B HIS 92 1_555 E FE HEM . B HEM 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc5 E FE HEM . B HEM 148 1_555 F C CMO . B CMO 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? metalc ? metalc6 E FE HEM . B HEM 148 1_555 F O CMO . B CMO 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.78 ? # _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 136 n n CHA C4D HEM doub 137 n n CHA HHA HEM sing 138 n n CHB C4A HEM sing 139 n n CHB C1B HEM doub 140 n n CHB HHB HEM sing 141 n n CHC C4B HEM sing 142 n n CHC C1C HEM doub 143 n n CHC HHC HEM sing 144 n n CHD C4C HEM doub 145 n n CHD C1D HEM sing 146 n n CHD HHD HEM sing 147 n n C1A C2A HEM doub 148 n y C1A NA HEM sing 149 n y C2A C3A HEM sing 150 n y C2A CAA HEM sing 151 n n C3A C4A HEM doub 152 n y C3A CMA HEM sing 153 n n C4A NA HEM sing 154 n y CMA HMA HEM sing 155 n n CMA HMAA HEM sing 156 n n CMA HMAB HEM sing 157 n n CAA CBA HEM sing 158 n n CAA HAA HEM sing 159 n n CAA HAAA HEM sing 160 n n CBA CGA HEM sing 161 n n CBA HBA HEM sing 162 n n CBA HBAA HEM sing 163 n n CGA O1A HEM doub 164 n n CGA O2A HEM sing 165 n n C1B C2B HEM sing 166 n n C1B NB HEM sing 167 n n C2B C3B HEM doub 168 n n C2B CMB HEM sing 169 n n C3B C4B HEM sing 170 n n C3B CAB HEM sing 171 n n C4B NB HEM doub 172 n n CMB HMB HEM sing 173 n n CMB HMBA HEM sing 174 n n CMB HMBB HEM sing 175 n n CAB CBB HEM doub 176 n n CAB HAB HEM sing 177 n n CBB HBB HEM sing 178 n n CBB HBBA HEM sing 179 n n C1C C2C HEM sing 180 n y C1C NC HEM sing 181 n y C2C C3C HEM doub 182 n y C2C CMC HEM sing 183 n n C3C C4C HEM sing 184 n y C3C CAC HEM sing 185 n n C4C NC HEM sing 186 n y CMC HMC HEM sing 187 n n CMC HMCA HEM sing 188 n n CMC HMCB HEM sing 189 n n CAC CBC HEM doub 190 n n CAC HAC HEM sing 191 n n CBC HBC HEM sing 192 n n CBC HBCA HEM sing 193 n n C1D C2D HEM sing 194 n n C1D ND HEM doub 195 n n C2D C3D HEM doub 196 n n C2D CMD HEM sing 197 n n C3D C4D HEM sing 198 n n C3D CAD HEM sing 199 n n C4D ND HEM sing 200 n n CMD HMD HEM sing 201 n n CMD HMDA HEM sing 202 n n CMD HMDB HEM sing 203 n n CAD CBD HEM sing 204 n n CAD HAD HEM sing 205 n n CAD HADA HEM sing 206 n n CBD CGD HEM sing 207 n n CBD HBD HEM sing 208 n n CBD HBDA HEM sing 209 n n CGD O1D HEM doub 210 n n CGD O2D HEM sing 211 n n O2A H2A HEM sing 212 n n O2D H2D HEM sing 213 n n FE NA HEM sing 214 n n FE NB HEM sing 215 n n FE NC HEM sing 216 n n FE ND HEM sing 217 n n # _atom_sites.entry_id 1PBX _atom_sites.fract_transf_matrix[1][1] 0.010943 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001375 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011294 _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] 0.018212 _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 3 HEM A 1 144 144 HEM HEM . D 4 CMO A 1 145 144 CMO HEM . E 3 HEM B 1 148 148 HEM HEM . F 4 CMO B 1 149 148 CMO HEM . G 5 HOH A 1 450 450 HOH HOH . G 5 HOH A 2 451 451 HOH HOH . G 5 HOH A 3 455 455 HOH HOH . G 5 HOH A 4 457 457 HOH HOH . G 5 HOH A 5 458 458 HOH HOH . G 5 HOH A 6 459 459 HOH HOH . G 5 HOH A 7 463 463 HOH HOH . G 5 HOH A 8 469 469 HOH HOH . G 5 HOH A 9 470 470 HOH HOH . G 5 HOH A 10 480 480 HOH HOH . G 5 HOH A 11 481 481 HOH HOH . G 5 HOH A 12 482 482 HOH HOH . G 5 HOH A 13 484 484 HOH HOH . G 5 HOH A 14 485 485 HOH HOH . G 5 HOH A 15 487 487 HOH HOH . H 5 HOH B 1 452 452 HOH HOH . H 5 HOH B 2 453 453 HOH HOH . H 5 HOH B 3 454 454 HOH HOH . H 5 HOH B 4 456 456 HOH HOH . H 5 HOH B 5 461 461 HOH HOH . H 5 HOH B 6 466 466 HOH HOH . H 5 HOH B 7 467 467 HOH HOH . H 5 HOH B 8 468 468 HOH HOH . H 5 HOH B 9 471 471 HOH HOH . H 5 HOH B 10 472 472 HOH HOH . H 5 HOH B 11 483 483 HOH HOH . H 5 HOH B 12 486 486 HOH HOH . H 5 HOH B 13 488 488 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 3 8.54 11.47 -18.338 1 33.94 ? CHA HEM 148 B 1 HETATM 2 C CHB HEM . . . E 3 10.352 12.851 -14.019 1 31.04 ? CHB HEM 148 B 1 HETATM 3 C CHC HEM . . . E 3 8.245 9.009 -11.894 1 30.23 ? CHC HEM 148 B 1 HETATM 4 C CHD HEM . . . E 3 6.465 7.584 -16.163 1 30.56 ? CHD HEM 148 B 1 HETATM 5 C C1A HEM . . . E 3 9.236 12.163 -17.382 1 36.25 ? C1A HEM 148 B 1 HETATM 6 C C2A HEM . . . E 3 10.071 13.346 -17.595 1 37.43 ? C2A HEM 148 B 1 HETATM 7 C C3A HEM . . . E 3 10.541 13.715 -16.397 1 37 ? C3A HEM 148 B 1 HETATM 8 C C4A HEM . . . E 3 10.044 12.784 -15.382 1 36.25 ? C4A HEM 148 B 1 HETATM 9 C CMA HEM . . . E 3 11.482 14.874 -15.997 1 36.82 ? CMA HEM 148 B 1 HETATM 10 C CAA HEM . . . E 3 10.374 14.023 -18.941 1 38.32 ? CAA HEM 148 B 1 HETATM 11 C CBA HEM . . . E 3 9.58 15.27 -19.267 1 45.09 ? CBA HEM 148 B 1 HETATM 12 C CGA HEM . . . E 3 9.705 15.797 -20.699 1 50.57 ? CGA HEM 148 B 1 HETATM 13 O O1A HEM . . . E 3 10.794 15.491 -21.316 1 52.08 ? O1A HEM 148 B 1 HETATM 14 O O2A HEM . . . E 3 8.741 16.507 -21.186 1 51.37 ? O2A HEM 148 B 1 HETATM 15 C C1B HEM . . . E 3 9.95 11.927 -13.079 1 31.61 ? C1B HEM 148 B 1 HETATM 16 C C2B HEM . . . E 3 10.244 11.963 -11.64 1 31.85 ? C2B HEM 148 B 1 HETATM 17 C C3B HEM . . . E 3 9.663 10.896 -11.067 1 30.84 ? C3B HEM 148 B 1 HETATM 18 C C4B HEM . . . E 3 8.978 10.153 -12.117 1 31.03 ? C4B HEM 148 B 1 HETATM 19 C CMB HEM . . . E 3 11.11 13.059 -10.981 1 26.78 ? CMB HEM 148 B 1 HETATM 20 C CAB HEM . . . E 3 9.638 10.409 -9.605 1 30.13 ? CAB HEM 148 B 1 HETATM 21 C CBB HEM . . . E 3 9.434 9.079 -9.39 1 30.69 ? CBB HEM 148 B 1 HETATM 22 C C1C HEM . . . E 3 7.588 8.27 -12.865 1 30.63 ? C1C HEM 148 B 1 HETATM 23 C C2C HEM . . . E 3 7.003 6.954 -12.629 1 29.84 ? C2C HEM 148 B 1 HETATM 24 C C3C HEM . . . E 3 6.535 6.558 -13.806 1 30.48 ? C3C HEM 148 B 1 HETATM 25 C C4C HEM . . . E 3 6.826 7.556 -14.809 1 30.8 ? C4C HEM 148 B 1 HETATM 26 C CMC HEM . . . E 3 6.954 6.196 -11.281 1 25.48 ? CMC HEM 148 B 1 HETATM 27 C CAC HEM . . . E 3 5.875 5.176 -14.01 1 31.35 ? CAC HEM 148 B 1 HETATM 28 C CBC HEM . . . E 3 5.484 4.817 -15.219 1 33.48 ? CBC HEM 148 B 1 HETATM 29 C C1D HEM . . . E 3 6.81 8.543 -17.096 1 33.85 ? C1D HEM 148 B 1 HETATM 30 C C2D HEM . . . E 3 6.53 8.528 -18.501 1 37.31 ? C2D HEM 148 B 1 HETATM 31 C C3D HEM . . . E 3 7.103 9.604 -19.073 1 37.89 ? C3D HEM 148 B 1 HETATM 32 C C4D HEM . . . E 3 7.815 10.342 -18.068 1 34.87 ? C4D HEM 148 B 1 HETATM 33 C CMD HEM . . . E 3 5.675 7.43 -19.194 1 39.2 ? CMD HEM 148 B 1 HETATM 34 C CAD HEM . . . E 3 7.117 10.03 -20.56 1 41.24 ? CAD HEM 148 B 1 HETATM 35 C CBD HEM . . . E 3 8 9.091 -21.404 1 44.89 ? CBD HEM 148 B 1 HETATM 36 C CGD HEM . . . E 3 7.822 9.53 -22.857 1 50.01 ? CGD HEM 148 B 1 HETATM 37 O O1D HEM . . . E 3 6.617 9.742 -23.207 1 48.92 ? O1D HEM 148 B 1 HETATM 38 O O2D HEM . . . E 3 8.941 9.656 -23.471 1 52.73 ? O2D HEM 148 B 1 HETATM 39 N NA HEM . . . E 3 9.233 11.823 -16.041 1 36.01 ? NA HEM 148 B 1 HETATM 40 N NB HEM . . . E 3 9.151 10.79 -13.335 1 32.71 ? NB HEM 148 B 1 HETATM 41 N NC HEM . . . E 3 7.497 8.612 -14.195 1 31.42 ? NC HEM 148 B 1 HETATM 42 N ND HEM . . . E 3 7.615 9.668 -16.884 1 34.28 ? ND HEM 148 B 1 HETATM 43 FE FE HEM . . . E 3 8.374 10.216 -15.134 1 34.36 ? FE HEM 148 B 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 43 #