data_7M8I # _model_server_result.job_id 0EOsIHGjKQ3I3xLXO1XsRg _model_server_result.datetime_utc '2024-10-12 12:21:24' _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 7m8i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1602}' # _entry.id 7M8I # _exptl.entry_id 7M8I _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 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 114.073 _cell.angle_gamma 90 _cell.entry_id 7M8I _cell.length_a 140.579 _cell.length_b 208.7 _cell.length_c 124.919 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7M8I _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,J,K,L,M _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_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 -50.954492 0 114.054357 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 H N N ? 3 K 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 metalc ? metalc1 A SG CYS 53 A CYS 112 1_555 D FE1 FES . A FES 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc2 A SG CYS 56 A CYS 115 1_555 D FE2 FES . A FES 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? metalc ? metalc3 A SG CYS 93 A CYS 152 1_555 D FE2 FES . A FES 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.636 ? metalc ? metalc4 A SG CYS 552 A CYS 1450 1_555 E FE HEM . A HEM 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? metalc ? metalc5 E FE HEM . A HEM 1602 1_555 F N06 0T3 . A 0T3 1603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc6 B SG CYS 47 B CYS 106 1_555 G FE1 FES . B FES 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc7 B SG CYS 552 B CYS 1450 1_555 H FE HEM . B HEM 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.636 ? metalc ? metalc8 H FE HEM . B HEM 1602 1_555 I N06 0T3 . B 0T3 1603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc9 C SG CYS 47 C CYS 106 1_555 J FE1 FES . C FES 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? metalc ? metalc10 C SG CYS 53 C CYS 112 1_555 J FE1 FES . C FES 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? metalc ? metalc11 C SG CYS 56 C CYS 115 1_555 J FE2 FES . C FES 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc12 C SG CYS 93 C CYS 152 1_555 J FE2 FES . C FES 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc13 C SG CYS 552 C CYS 1450 1_555 K FE HEM . C HEM 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.677 ? metalc ? metalc14 K FE HEM . C HEM 1602 1_555 L N06 0T3 . C 0T3 1603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? # _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 165 n n CHA C4D HEM doub 166 n n CHA HHA HEM sing 167 n n CHB C4A HEM sing 168 n n CHB C1B HEM doub 169 n n CHB HHB HEM sing 170 n n CHC C4B HEM sing 171 n n CHC C1C HEM doub 172 n n CHC HHC HEM sing 173 n n CHD C4C HEM doub 174 n n CHD C1D HEM sing 175 n n CHD HHD HEM sing 176 n n C1A C2A HEM doub 177 n y C1A NA HEM sing 178 n y C2A C3A HEM sing 179 n y C2A CAA HEM sing 180 n n C3A C4A HEM doub 181 n y C3A CMA HEM sing 182 n n C4A NA HEM sing 183 n y CMA HMA HEM sing 184 n n CMA HMAA HEM sing 185 n n CMA HMAB HEM sing 186 n n CAA CBA HEM sing 187 n n CAA HAA HEM sing 188 n n CAA HAAA HEM sing 189 n n CBA CGA HEM sing 190 n n CBA HBA HEM sing 191 n n CBA HBAA HEM sing 192 n n CGA O1A HEM doub 193 n n CGA O2A HEM sing 194 n n C1B C2B HEM sing 195 n n C1B NB HEM sing 196 n n C2B C3B HEM doub 197 n n C2B CMB HEM sing 198 n n C3B C4B HEM sing 199 n n C3B CAB HEM sing 200 n n C4B NB HEM doub 201 n n CMB HMB HEM sing 202 n n CMB HMBA HEM sing 203 n n CMB HMBB HEM sing 204 n n CAB CBB HEM doub 205 n n CAB HAB HEM sing 206 n n CBB HBB HEM sing 207 n n CBB HBBA HEM sing 208 n n C1C C2C HEM sing 209 n y C1C NC HEM sing 210 n y C2C C3C HEM doub 211 n y C2C CMC HEM sing 212 n n C3C C4C HEM sing 213 n y C3C CAC HEM sing 214 n n C4C NC HEM sing 215 n y CMC HMC HEM sing 216 n n CMC HMCA HEM sing 217 n n CMC HMCB HEM sing 218 n n CAC CBC HEM doub 219 n n CAC HAC HEM sing 220 n n CBC HBC HEM sing 221 n n CBC HBCA HEM sing 222 n n C1D C2D HEM sing 223 n n C1D ND HEM doub 224 n n C2D C3D HEM doub 225 n n C2D CMD HEM sing 226 n n C3D C4D HEM sing 227 n n C3D CAD HEM sing 228 n n C4D ND HEM sing 229 n n CMD HMD HEM sing 230 n n CMD HMDA HEM sing 231 n n CMD HMDB HEM sing 232 n n CAD CBD HEM sing 233 n n CAD HAD HEM sing 234 n n CAD HADA HEM sing 235 n n CBD CGD HEM sing 236 n n CBD HBD HEM sing 237 n n CBD HBDA HEM sing 238 n n CGD O1D HEM doub 239 n n CGD O2D HEM sing 240 n n O2A H2A HEM sing 241 n n O2D H2D HEM sing 242 n n FE NA HEM sing 243 n n FE NB HEM sing 244 n n FE NC HEM sing 245 n n FE ND HEM sing 246 n n # _atom_sites.entry_id 7M8I _atom_sites.fract_transf_matrix[1][1] 0.007113 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003178 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004792 _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] 0.008768 _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 D 2 FES A 1 1601 901 FES FES . E 3 HEM A 1 1602 601 HEM HEM . F 4 0T3 A 1 1603 801 0T3 LIG . G 2 FES B 1 1601 901 FES FES . H 3 HEM B 1 1602 601 HEM HEM . I 4 0T3 B 1 1603 801 0T3 LIG . J 2 FES C 1 1601 901 FES FES . K 3 HEM C 1 1602 601 HEM HEM . L 4 0T3 C 1 1603 801 0T3 LIG . M 5 HOH A 1 1701 901 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 -3.051 -5.386 34.626 1 27.55 ? CHA HEM 1602 A 1 HETATM 2 C CHB HEM . . . E 3 -6.477 -6.005 31.287 1 23.22 ? CHB HEM 1602 A 1 HETATM 3 C CHC HEM . . . E 3 -4.107 -9.819 29.595 1 26.8 ? CHC HEM 1602 A 1 HETATM 4 C CHD HEM . . . E 3 -1.192 -9.649 33.409 1 29.94 ? CHD HEM 1602 A 1 HETATM 5 C C1A HEM . . . E 3 -4.16 -5.208 33.853 1 37.15 ? C1A HEM 1602 A 1 HETATM 6 C C2A HEM . . . E 3 -5.088 -4.113 33.96 1 28.33 ? C2A HEM 1602 A 1 HETATM 7 C C3A HEM . . . E 3 -6.032 -4.285 33.042 1 25.29 ? C3A HEM 1602 A 1 HETATM 8 C C4A HEM . . . E 3 -5.736 -5.495 32.314 1 24.81 ? C4A HEM 1602 A 1 HETATM 9 C CMA HEM . . . E 3 -7.23 -3.349 32.798 1 34.21 ? CMA HEM 1602 A 1 HETATM 10 C CAA HEM . . . E 3 -5.002 -2.956 34.971 1 31.72 ? CAA HEM 1602 A 1 HETATM 11 C CBA HEM . . . E 3 -4.571 -1.687 34.251 1 35.42 ? CBA HEM 1602 A 1 HETATM 12 C CGA HEM . . . E 3 -4.347 -0.605 35.269 1 47.14 ? CGA HEM 1602 A 1 HETATM 13 O O1A HEM . . . E 3 -4.603 -0.849 36.475 1 53.29 ? O1A HEM 1602 A 1 HETATM 14 O O2A HEM . . . E 3 -3.912 0.504 34.873 1 41.94 ? O2A HEM 1602 A 1 HETATM 15 C C1B HEM . . . E 3 -6.103 -7.054 30.498 1 27.87 ? C1B HEM 1602 A 1 HETATM 16 C C2B HEM . . . E 3 -6.748 -7.477 29.275 1 22.12 ? C2B HEM 1602 A 1 HETATM 17 C C3B HEM . . . E 3 -6.084 -8.546 28.814 1 27.58 ? C3B HEM 1602 A 1 HETATM 18 C C4B HEM . . . E 3 -5.007 -8.807 29.727 1 31.15 ? C4B HEM 1602 A 1 HETATM 19 C CMB HEM . . . E 3 -7.985 -6.788 28.664 1 20.56 ? CMB HEM 1602 A 1 HETATM 20 C CAB HEM . . . E 3 -6.319 -9.395 27.548 1 29.02 ? CAB HEM 1602 A 1 HETATM 21 C CBB HEM . . . E 3 -7.187 -9.006 26.612 1 35.93 ? CBB HEM 1602 A 1 HETATM 22 C C1C HEM . . . E 3 -3.106 -10.084 30.476 1 28.45 ? C1C HEM 1602 A 1 HETATM 23 C C2C HEM . . . E 3 -2.123 -11.119 30.319 1 31.61 ? C2C HEM 1602 A 1 HETATM 24 C C3C HEM . . . E 3 -1.318 -11.084 31.385 1 26.49 ? C3C HEM 1602 A 1 HETATM 25 C C4C HEM . . . E 3 -1.766 -10.011 32.229 1 30.76 ? C4C HEM 1602 A 1 HETATM 26 C CMC HEM . . . E 3 -2.082 -12.083 29.12 1 27.94 ? CMC HEM 1602 A 1 HETATM 27 C CAC HEM . . . E 3 -0.092 -11.955 31.715 1 33.66 ? CAC HEM 1602 A 1 HETATM 28 C CBC HEM . . . E 3 0.518 -12.661 30.763 1 47.53 ? CBC HEM 1602 A 1 HETATM 29 C C1D HEM . . . E 3 -1.404 -8.454 34.031 1 26.77 ? C1D HEM 1602 A 1 HETATM 30 C C2D HEM . . . E 3 -0.622 -7.926 35.116 1 26.75 ? C2D HEM 1602 A 1 HETATM 31 C C3D HEM . . . E 3 -1.13 -6.744 35.453 1 28.26 ? C3D HEM 1602 A 1 HETATM 32 C C4D HEM . . . E 3 -2.256 -6.492 34.594 1 28.95 ? C4D HEM 1602 A 1 HETATM 33 C CMD HEM . . . E 3 0.592 -8.621 35.756 1 30.42 ? CMD HEM 1602 A 1 HETATM 34 C CAD HEM . . . E 3 -0.619 -5.817 36.574 1 31.89 ? CAD HEM 1602 A 1 HETATM 35 C CBD HEM . . . E 3 -0.008 -4.555 35.975 1 33.25 ? CBD HEM 1602 A 1 HETATM 36 C CGD HEM . . . E 3 0.424 -3.593 37.056 1 38.01 ? CGD HEM 1602 A 1 HETATM 37 O O1D HEM . . . E 3 1.39 -2.829 36.807 1 32.4 ? O1D HEM 1602 A 1 HETATM 38 O O2D HEM . . . E 3 -0.177 -3.591 38.162 1 40.9 ? O2D HEM 1602 A 1 HETATM 39 N NA HEM . . . E 3 -4.583 -6.044 32.837 1 32.99 ? NA HEM 1602 A 1 HETATM 40 N NB HEM . . . E 3 -5.041 -7.888 30.75 1 31.71 ? NB HEM 1602 A 1 HETATM 41 N NC HEM . . . E 3 -2.868 -9.424 31.658 1 30.56 ? NC HEM 1602 A 1 HETATM 42 N ND HEM . . . E 3 -2.399 -7.556 33.73 1 33.38 ? ND HEM 1602 A 1 HETATM 43 FE FE HEM . . . E 3 -3.753 -7.766 32.287 1 31.72 ? FE HEM 1602 A 1 HETATM 44 H HHB HEM . . . E 3 -7.409 -5.71 31.222 1 28.42 ? HHB HEM 1602 A 1 HETATM 45 H HHC HEM . . . E 3 -4.058 -10.26 28.721 1 32.72 ? HHC HEM 1602 A 1 HETATM 46 H HHD HEM . . . E 3 -0.785 -10.363 33.943 1 36.48 ? HHD HEM 1602 A 1 HETATM 47 H HMA HEM . . . E 3 -7.704 -3.201 33.643 1 41.61 ? HMA HEM 1602 A 1 HETATM 48 H HMAA HEM . . . E 3 -7.84 -3.759 32.15 1 41.61 ? HMAA HEM 1602 A 1 HETATM 49 H HMAB HEM . . . E 3 -6.91 -2.491 32.45 1 41.61 ? HMAB HEM 1602 A 1 HETATM 50 H HAA HEM . . . E 3 -4.354 -3.174 35.659 1 38.62 ? HAA HEM 1602 A 1 HETATM 51 H HAAA HEM . . . E 3 -5.871 -2.817 35.378 1 38.62 ? HAAA HEM 1602 A 1 HETATM 52 H HBA HEM . . . E 3 -5.265 -1.412 33.632 1 43.06 ? HBA HEM 1602 A 1 HETATM 53 H HBAA HEM . . . E 3 -3.748 -1.852 33.765 1 43.06 ? HBAA HEM 1602 A 1 HETATM 54 H HMB HEM . . . E 3 -8.464 -6.315 29.362 1 25.22 ? HMB HEM 1602 A 1 HETATM 55 H HMBA HEM . . . E 3 -8.572 -7.452 28.27 1 25.22 ? HMBA HEM 1602 A 1 HETATM 56 H HMBB HEM . . . E 3 -7.702 -6.154 27.986 1 25.22 ? HMBB HEM 1602 A 1 HETATM 57 H HAB HEM . . . E 3 -5.849 -10.225 27.441 1 35.38 ? HAB HEM 1602 A 1 HETATM 58 H HBB HEM . . . E 3 -7.482 -9.643 25.943 1 43.67 ? HBB HEM 1602 A 1 HETATM 59 H HBBA HEM . . . E 3 -7.382 -8.065 26.491 1 43.67 ? HBBA HEM 1602 A 1 HETATM 60 H HMC HEM . . . E 3 -2.99 -12.307 28.863 1 34.09 ? HMC HEM 1602 A 1 HETATM 61 H HMCA HEM . . . E 3 -1.611 -12.895 29.353 1 34.09 ? HMCA HEM 1602 A 1 HETATM 62 H HMCB HEM . . . E 3 -1.64 -11.65 28.373 1 34.09 ? HMCB HEM 1602 A 1 HETATM 63 H HAC HEM . . . E 3 0.226 -12.003 32.619 1 40.95 ? HAC HEM 1602 A 1 HETATM 64 H HBC HEM . . . E 3 1.098 -13.399 31.008 1 57.59 ? HBC HEM 1602 A 1 HETATM 65 H HBCA HEM . . . E 3 0.46 -12.382 29.837 1 57.59 ? HBCA HEM 1602 A 1 HETATM 66 H HMD HEM . . . E 3 1.029 -8.021 36.394 1 37.06 ? HMD HEM 1602 A 1 HETATM 67 H HMDA HEM . . . E 3 1.231 -8.866 35.054 1 37.06 ? HMDA HEM 1602 A 1 HETATM 68 H HMDB HEM . . . E 3 0.295 -9.432 36.219 1 37.06 ? HMDB HEM 1602 A 1 HETATM 69 H HAD HEM . . . E 3 0.046 -6.277 37.106 1 38.82 ? HAD HEM 1602 A 1 HETATM 70 H HADA HEM . . . E 3 -1.364 -5.569 37.143 1 38.82 ? HADA HEM 1602 A 1 HETATM 71 H HBD HEM . . . E 3 -0.664 -4.121 35.407 1 40.46 ? HBD HEM 1602 A 1 HETATM 72 H HBDA HEM . . . E 3 0.763 -4.799 35.44 1 40.46 ? HBDA HEM 1602 A 1 HETATM 73 H HHA HEM . . . E 3 -2.712 -4.604 35.11 1 33.62 ? HHA HEM 1602 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 73 #