data_7M8I # _model_server_result.job_id 2BOZTU408qTE4HrL9V8QPA _model_server_result.datetime_utc '2024-10-12 12:23:30' _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":"K","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 . . . K 3 -38.304 -51.66 12.829 1 38.87 ? CHA HEM 1602 C 1 HETATM 2 C CHB HEM . . . K 3 -35.351 -55.434 13.496 1 27.42 ? CHB HEM 1602 C 1 HETATM 3 C CHC HEM . . . K 3 -31.534 -52.637 12.54 1 43.29 ? CHC HEM 1602 C 1 HETATM 4 C CHD HEM . . . K 3 -34.427 -48.751 12.561 1 34.67 ? CHD HEM 1602 C 1 HETATM 5 C C1A HEM . . . K 3 -37.843 -52.936 13.047 1 37.29 ? C1A HEM 1602 C 1 HETATM 6 C C2A HEM . . . K 3 -38.659 -54.12 13.218 1 35.83 ? C2A HEM 1602 C 1 HETATM 7 C C3A HEM . . . K 3 -37.838 -55.153 13.408 1 40.56 ? C3A HEM 1602 C 1 HETATM 8 C C4A HEM . . . K 3 -36.48 -54.664 13.351 1 29.18 ? C4A HEM 1602 C 1 HETATM 9 C CMA HEM . . . K 3 -38.24 -56.628 13.64 1 52.83 ? CMA HEM 1602 C 1 HETATM 10 C CAA HEM . . . K 3 -40.204 -54.172 13.208 1 34.19 ? CAA HEM 1602 C 1 HETATM 11 C CBA HEM . . . K 3 -40.733 -54.525 11.821 1 48.93 ? CBA HEM 1602 C 1 HETATM 12 C CGA HEM . . . K 3 -42.207 -54.818 11.908 1 62.73 ? CGA HEM 1602 C 1 HETATM 13 O O1A HEM . . . K 3 -42.761 -54.813 13.036 1 55.76 ? O1A HEM 1602 C 1 HETATM 14 O O2A HEM . . . K 3 -42.833 -55.057 10.846 1 56.78 ? O2A HEM 1602 C 1 HETATM 15 C C1B HEM . . . K 3 -34.064 -55.021 13.25 1 33.05 ? C1B HEM 1602 C 1 HETATM 16 C C2B HEM . . . K 3 -32.89 -55.868 13.203 1 36.23 ? C2B HEM 1602 C 1 HETATM 17 C C3B HEM . . . K 3 -31.832 -55.091 12.935 1 35.69 ? C3B HEM 1602 C 1 HETATM 18 C C4B HEM . . . K 3 -32.312 -53.733 12.81 1 36.8 ? C4B HEM 1602 C 1 HETATM 19 C CMB HEM . . . K 3 -32.921 -57.394 13.434 1 40.78 ? CMB HEM 1602 C 1 HETATM 20 C CAB HEM . . . K 3 -30.339 -55.468 12.783 1 40.43 ? CAB HEM 1602 C 1 HETATM 21 C CBB HEM . . . K 3 -29.901 -56.709 13.007 1 54.09 ? CBB HEM 1602 C 1 HETATM 22 C C1C HEM . . . K 3 -31.982 -51.341 12.481 1 39.51 ? C1C HEM 1602 C 1 HETATM 23 C C2C HEM . . . K 3 -31.147 -50.183 12.271 1 25.24 ? C2C HEM 1602 C 1 HETATM 24 C C3C HEM . . . K 3 -31.944 -49.096 12.281 1 29.47 ? C3C HEM 1602 C 1 HETATM 25 C C4C HEM . . . K 3 -33.305 -49.547 12.489 1 37.04 ? C4C HEM 1602 C 1 HETATM 26 C CMC HEM . . . K 3 -29.616 -50.274 12.085 1 33.16 ? CMC HEM 1602 C 1 HETATM 27 C CAC HEM . . . K 3 -31.579 -47.602 12.092 1 38.12 ? CAC HEM 1602 C 1 HETATM 28 C CBC HEM . . . K 3 -30.351 -47.232 11.725 1 49.23 ? CBC HEM 1602 C 1 HETATM 29 C C1D HEM . . . K 3 -35.728 -49.202 12.579 1 33.42 ? C1D HEM 1602 C 1 HETATM 30 C C2D HEM . . . K 3 -36.916 -48.39 12.427 1 30.42 ? C2D HEM 1602 C 1 HETATM 31 C C3D HEM . . . K 3 -37.989 -49.192 12.495 1 29.7 ? C3D HEM 1602 C 1 HETATM 32 C C4D HEM . . . K 3 -37.513 -50.542 12.701 1 32.25 ? C4D HEM 1602 C 1 HETATM 33 C CMD HEM . . . K 3 -36.912 -46.862 12.216 1 38.16 ? CMD HEM 1602 C 1 HETATM 34 C CAD HEM . . . K 3 -39.478 -48.779 12.39 1 34.26 ? CAD HEM 1602 C 1 HETATM 35 C CBD HEM . . . K 3 -40.022 -49.1 11 1 36.51 ? CBD HEM 1602 C 1 HETATM 36 C CGD HEM . . . K 3 -41.447 -48.62 10.872 1 40.8 ? CGD HEM 1602 C 1 HETATM 37 O O1D HEM . . . K 3 -41.819 -48.139 9.767 1 37.82 ? O1D HEM 1602 C 1 HETATM 38 O O2D HEM . . . K 3 -42.21 -48.705 11.87 1 45.71 ? O2D HEM 1602 C 1 HETATM 39 N NA HEM . . . K 3 -36.513 -53.3 13.131 1 45.77 ? NA HEM 1602 C 1 HETATM 40 N NB HEM . . . K 3 -33.674 -53.723 13.006 1 30.97 ? NB HEM 1602 C 1 HETATM 41 N NC HEM . . . K 3 -33.285 -50.918 12.613 1 36.42 ? NC HEM 1602 C 1 HETATM 42 N ND HEM . . . K 3 -36.13 -50.512 12.745 1 36.51 ? ND HEM 1602 C 1 HETATM 43 FE FE HEM . . . K 3 -34.84 -52.067 12.826 1 38.23 ? FE HEM 1602 C 1 HETATM 44 H HHB HEM . . . K 3 -35.46 -56.299 13.943 1 33.45 ? HHB HEM 1602 C 1 HETATM 45 H HHC HEM . . . K 3 -30.62 -52.806 12.231 1 52.5 ? HHC HEM 1602 C 1 HETATM 46 H HHD HEM . . . K 3 -34.285 -47.796 12.728 1 42.16 ? HHD HEM 1602 C 1 HETATM 47 H HMA HEM . . . K 3 -38.856 -56.681 14.401 1 63.95 ? HMA HEM 1602 C 1 HETATM 48 H HMAA HEM . . . K 3 -37.441 -57.162 13.831 1 63.95 ? HMAA HEM 1602 C 1 HETATM 49 H HMAB HEM . . . K 3 -38.683 -56.976 12.838 1 63.95 ? HMAB HEM 1602 C 1 HETATM 50 H HAA HEM . . . K 3 -40.554 -53.307 13.472 1 41.58 ? HAA HEM 1602 C 1 HETATM 51 H HAAA HEM . . . K 3 -40.5 -54.842 13.843 1 41.58 ? HAAA HEM 1602 C 1 HETATM 52 H HBA HEM . . . K 3 -40.262 -55.304 11.491 1 59.27 ? HBA HEM 1602 C 1 HETATM 53 H HBAA HEM . . . K 3 -40.586 -53.778 11.22 1 59.27 ? HBAA HEM 1602 C 1 HETATM 54 H HMB HEM . . . K 3 -33.804 -57.658 13.735 1 49.49 ? HMB HEM 1602 C 1 HETATM 55 H HMBA HEM . . . K 3 -32.269 -57.635 14.11 1 49.49 ? HMBA HEM 1602 C 1 HETATM 56 H HMBB HEM . . . K 3 -32.716 -57.852 12.604 1 49.49 ? HMBB HEM 1602 C 1 HETATM 57 H HAB HEM . . . K 3 -29.711 -54.792 12.518 1 49.07 ? HAB HEM 1602 C 1 HETATM 58 H HBB HEM . . . K 3 -28.945 -56.859 13.029 1 65.47 ? HBB HEM 1602 C 1 HETATM 59 H HBBA HEM . . . K 3 -30.481 -57.463 12.838 1 65.47 ? HBBA HEM 1602 C 1 HETATM 60 H HMC HEM . . . K 3 -29.269 -50.993 12.635 1 40.35 ? HMC HEM 1602 C 1 HETATM 61 H HMCA HEM . . . K 3 -29.194 -49.446 12.341 1 40.35 ? HMCA HEM 1602 C 1 HETATM 62 H HMCB HEM . . . K 3 -29.42 -50.46 11.154 1 40.35 ? HMCB HEM 1602 C 1 HETATM 63 H HAC HEM . . . K 3 -32.249 -46.931 12.239 1 46.3 ? HAC HEM 1602 C 1 HETATM 64 H HBC HEM . . . K 3 -30.077 -46.31 11.853 1 59.64 ? HBC HEM 1602 C 1 HETATM 65 H HBCA HEM . . . K 3 -29.833 -47.802 11.138 1 59.64 ? HBCA HEM 1602 C 1 HETATM 66 H HMD HEM . . . K 3 -37.83 -46.54 12.103 1 46.34 ? HMD HEM 1602 C 1 HETATM 67 H HMDA HEM . . . K 3 -36.391 -46.646 11.415 1 46.34 ? HMDA HEM 1602 C 1 HETATM 68 H HMDB HEM . . . K 3 -36.507 -46.426 12.995 1 46.34 ? HMDB HEM 1602 C 1 HETATM 69 H HAD HEM . . . K 3 -39.564 -47.828 12.557 1 41.67 ? HAD HEM 1602 C 1 HETATM 70 H HADA HEM . . . K 3 -39.991 -49.266 13.053 1 41.67 ? HADA HEM 1602 C 1 HETATM 71 H HBD HEM . . . K 3 -39.992 -50.059 10.858 1 44.37 ? HBD HEM 1602 C 1 HETATM 72 H HBDA HEM . . . K 3 -39.474 -48.66 10.332 1 44.37 ? HBDA HEM 1602 C 1 HETATM 73 H HHA HEM . . . K 3 -39.269 -51.514 12.917 1 47.19 ? HHA HEM 1602 C 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 33 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 73 #