data_4JEB # _model_server_result.job_id KpbmJIoz0H_HybI-P_7r1g _model_server_result.datetime_utc '2024-11-26 17:55:33' _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 4jeb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 4JEB # _exptl.entry_id 4JEB _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 120 _cell.entry_id 4JEB _cell.length_a 54.942 _cell.length_b 54.942 _cell.length_c 145.658 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4JEB _symmetry.cell_setting ? _symmetry.Int_Tables_number 151 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 1 2' # _pdbx_struct_assembly.method_details PISA _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,D,E,F,G,H,I _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' 4_554 -y,-x,-z-1/3 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 0 0 -48.552667 # 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 F 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 81 A CYS 81 1_555 B SG CYS 81 B CYS 81 4_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf2 A SG CYS 96 A CYS 96 1_555 A SG CYS 96 A CYS 96 4_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf3 B SG CYS 96 B CYS 96 1_555 B SG CYS 96 B CYS 96 4_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc1 A SD MET 7 A MET 7 1_555 C FE HEM . A HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc2 A OD1 ASP 39 A ASP 39 1_555 E ZN ZN . A ZN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc3 A NE2 HIS 63 A HIS 63 1_555 G ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc4 A NE2 HIS 73 A HIS 73 1_555 D ZN ZN . A ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc5 A NE2 HIS 77 A HIS 77 1_555 D ZN ZN . A ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc6 A NE2 HIS 102 A HIS 102 1_555 C FE HEM . A HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc7 D ZN ZN . A ZN 202 1_555 H O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc8 D ZN ZN . A ZN 202 1_555 B NE2 HIS 63 B HIS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc9 E ZN ZN . A ZN 203 1_555 H O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc10 B SD MET 7 B MET 7 1_555 F FE HEM . B HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc11 B NE2 HIS 73 B HIS 73 1_555 G ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc12 B NE2 HIS 77 B HIS 77 1_555 G ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc13 B NE2 HIS 102 B HIS 102 1_555 F FE HEM . B HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc14 G ZN ZN . B ZN 202 1_555 I O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? # _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 4JEB _atom_sites.fract_transf_matrix[1][1] 0.018201 _atom_sites.fract_transf_matrix[1][2] 0.010508 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021017 _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] 0.006865 _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 1 201 150 HEM HEM . D 3 ZN A 1 202 3 ZN ZN . E 3 ZN A 1 203 4 ZN ZN . F 2 HEM B 1 201 150 HEM HEM . G 3 ZN B 1 202 2 ZN ZN . H 4 HOH A 1 301 2 HOH HOH . H 4 HOH A 2 302 3 HOH HOH . H 4 HOH A 3 303 5 HOH HOH . H 4 HOH A 4 304 7 HOH HOH . H 4 HOH A 5 305 8 HOH HOH . H 4 HOH A 6 306 9 HOH HOH . H 4 HOH A 7 307 10 HOH HOH . H 4 HOH A 8 308 15 HOH HOH . H 4 HOH A 9 309 16 HOH HOH . H 4 HOH A 10 310 17 HOH HOH . H 4 HOH A 11 311 20 HOH HOH . H 4 HOH A 12 312 21 HOH HOH . H 4 HOH A 13 313 24 HOH HOH . H 4 HOH A 14 314 25 HOH HOH . H 4 HOH A 15 315 27 HOH HOH . H 4 HOH A 16 316 28 HOH HOH . H 4 HOH A 17 317 33 HOH HOH . H 4 HOH A 18 318 34 HOH HOH . H 4 HOH A 19 319 35 HOH HOH . I 4 HOH B 1 301 1 HOH HOH . I 4 HOH B 2 302 4 HOH HOH . I 4 HOH B 3 303 6 HOH HOH . I 4 HOH B 4 304 11 HOH HOH . I 4 HOH B 5 305 12 HOH HOH . I 4 HOH B 6 306 13 HOH HOH . I 4 HOH B 7 307 14 HOH HOH . I 4 HOH B 8 308 18 HOH HOH . I 4 HOH B 9 309 19 HOH HOH . I 4 HOH B 10 310 22 HOH HOH . I 4 HOH B 11 311 23 HOH HOH . I 4 HOH B 12 312 26 HOH HOH . I 4 HOH B 13 313 29 HOH HOH . I 4 HOH B 14 314 30 HOH HOH . I 4 HOH B 15 315 31 HOH HOH . I 4 HOH B 16 316 32 HOH HOH . I 4 HOH B 17 317 36 HOH HOH . I 4 HOH B 18 318 37 HOH HOH . I 4 HOH B 19 319 38 HOH HOH . I 4 HOH B 20 320 39 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 . . . C 2 18.497 -1.854 -9.277 1 49.41 ? CHA HEM 201 A 1 HETATM 2 C CHB HEM . . . C 2 15.596 -5.587 -10.405 1 47.52 ? CHB HEM 201 A 1 HETATM 3 C CHC HEM . . . C 2 12.709 -2.545 -12.859 1 41.62 ? CHC HEM 201 A 1 HETATM 4 C CHD HEM . . . C 2 15.774 1.095 -12.071 1 45.89 ? CHD HEM 201 A 1 HETATM 5 C C1A HEM . . . C 2 17.993 -3.129 -9.358 1 48.71 ? C1A HEM 201 A 1 HETATM 6 C C2A HEM . . . C 2 18.526 -4.34 -8.74 1 51.91 ? C2A HEM 201 A 1 HETATM 7 C C3A HEM . . . C 2 17.713 -5.361 -9.052 1 49.97 ? C3A HEM 201 A 1 HETATM 8 C C4A HEM . . . C 2 16.636 -4.845 -9.879 1 50.62 ? C4A HEM 201 A 1 HETATM 9 C CMA HEM . . . C 2 17.881 -6.824 -8.612 1 49.82 ? CMA HEM 201 A 1 HETATM 10 C CAA HEM . . . C 2 19.805 -4.435 -7.851 1 54.14 ? CAA HEM 201 A 1 HETATM 11 C CBA HEM . . . C 2 19.477 -3.818 -6.499 1 58.55 ? CBA HEM 201 A 1 HETATM 12 C CGA HEM . . . C 2 20.561 -4.074 -5.491 1 61.51 ? CGA HEM 201 A 1 HETATM 13 O O1A HEM . . . C 2 20.338 -4.765 -4.481 1 62.22 ? O1A HEM 201 A 1 HETATM 14 O O2A HEM . . . C 2 21.665 -3.543 -5.678 1 63.49 ? O2A HEM 201 A 1 HETATM 15 C C1B HEM . . . C 2 14.549 -5.061 -11.142 1 46.3 ? C1B HEM 201 A 1 HETATM 16 C C2B HEM . . . C 2 13.416 -5.811 -11.641 1 41.02 ? C2B HEM 201 A 1 HETATM 17 C C3B HEM . . . C 2 12.622 -4.978 -12.299 1 42.17 ? C3B HEM 201 A 1 HETATM 18 C C4B HEM . . . C 2 13.244 -3.666 -12.259 1 43.06 ? C4B HEM 201 A 1 HETATM 19 C CMB HEM . . . C 2 13.194 -7.308 -11.392 1 45.27 ? CMB HEM 201 A 1 HETATM 20 C CAB HEM . . . C 2 11.257 -5.284 -13.015 1 43.79 ? CAB HEM 201 A 1 HETATM 21 C CBB HEM . . . C 2 10.414 -6.314 -12.732 1 38.55 ? CBB HEM 201 A 1 HETATM 22 C C1C HEM . . . C 2 13.291 -1.303 -12.884 1 42.92 ? C1C HEM 201 A 1 HETATM 23 C C2C HEM . . . C 2 12.761 -0.127 -13.584 1 43.28 ? C2C HEM 201 A 1 HETATM 24 C C3C HEM . . . C 2 13.616 0.891 -13.358 1 42.39 ? C3C HEM 201 A 1 HETATM 25 C C4C HEM . . . C 2 14.702 0.378 -12.523 1 45.87 ? C4C HEM 201 A 1 HETATM 26 C CMC HEM . . . C 2 11.441 -0.033 -14.398 1 41.77 ? CMC HEM 201 A 1 HETATM 27 C CAC HEM . . . C 2 13.513 2.37 -13.844 1 45.56 ? CAC HEM 201 A 1 HETATM 28 C CBC HEM . . . C 2 12.387 3.008 -14.283 1 47.57 ? CBC HEM 201 A 1 HETATM 29 C C1D HEM . . . C 2 16.77 0.627 -11.253 1 47.65 ? C1D HEM 201 A 1 HETATM 30 C C2D HEM . . . C 2 17.87 1.444 -10.803 1 47.92 ? C2D HEM 201 A 1 HETATM 31 C C3D HEM . . . C 2 18.734 0.538 -9.937 1 51.47 ? C3D HEM 201 A 1 HETATM 32 C C4D HEM . . . C 2 18.035 -0.739 -9.932 1 49.51 ? C4D HEM 201 A 1 HETATM 33 C CMD HEM . . . C 2 18.173 2.922 -11.142 1 47.9 ? CMD HEM 201 A 1 HETATM 34 C CAD HEM . . . C 2 20.06 0.958 -9.208 1 54.87 ? CAD HEM 201 A 1 HETATM 35 C CBD HEM . . . C 2 19.748 1.26 -7.739 1 57.73 ? CBD HEM 201 A 1 HETATM 36 C CGD HEM . . . C 2 20.982 1.514 -6.876 1 62.28 ? CGD HEM 201 A 1 HETATM 37 O O1D HEM . . . C 2 22.129 1.256 -7.322 1 63.8 ? O1D HEM 201 A 1 HETATM 38 O O2D HEM . . . C 2 20.832 1.981 -5.703 1 63.05 ? O2D HEM 201 A 1 HETATM 39 N NA HEM . . . C 2 16.846 -3.458 -10.051 1 49.85 ? NA HEM 201 A 1 HETATM 40 N NB HEM . . . C 2 14.447 -3.76 -11.561 1 43.89 ? NB HEM 201 A 1 HETATM 41 N NC HEM . . . C 2 14.509 -0.959 -12.254 1 44.84 ? NC HEM 201 A 1 HETATM 42 N ND HEM . . . C 2 16.88 -0.644 -10.72 1 46.63 ? ND HEM 201 A 1 HETATM 43 FE FE HEM . . . C 2 15.728 -2.19 -11.137 1 47.02 ? FE HEM 201 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 234 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #