data_7M8I # _model_server_result.job_id yNFJY2uugtIEMEGIkcbvIQ _model_server_result.datetime_utc '2024-10-12 12:21:04' _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":"H","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 . . . H 3 13.365 -64.218 44.91 1 37.48 ? CHA HEM 1602 B 1 HETATM 2 C CHB HEM . . . H 3 15.444 -59.868 45.07 1 38.53 ? CHB HEM 1602 B 1 HETATM 3 C CHC HEM . . . H 3 13.631 -58.867 40.741 1 27 ? CHC HEM 1602 B 1 HETATM 4 C CHD HEM . . . H 3 10.941 -62.839 40.994 1 33.58 ? CHD HEM 1602 B 1 HETATM 5 C C1A HEM . . . H 3 14.105 -63.145 45.31 1 43.87 ? C1A HEM 1602 B 1 HETATM 6 C C2A HEM . . . H 3 14.901 -63.077 46.507 1 34.05 ? C2A HEM 1602 B 1 HETATM 7 C C3A HEM . . . H 3 15.471 -61.878 46.552 1 32.3 ? C3A HEM 1602 B 1 HETATM 8 C C4A HEM . . . H 3 15.061 -61.141 45.381 1 41.38 ? C4A HEM 1602 B 1 HETATM 9 C CMA HEM . . . H 3 16.411 -61.371 47.661 1 39.75 ? CMA HEM 1602 B 1 HETATM 10 C CAA HEM . . . H 3 15.051 -64.195 47.553 1 44.02 ? CAA HEM 1602 B 1 HETATM 11 C CBA HEM . . . H 3 16.434 -64.819 47.431 1 52.57 ? CBA HEM 1602 B 1 HETATM 12 C CGA HEM . . . H 3 16.514 -66.003 48.352 1 56.2 ? CGA HEM 1602 B 1 HETATM 13 O O1A HEM . . . H 3 15.536 -66.252 49.1 1 60.19 ? O1A HEM 1602 B 1 HETATM 14 O O2A HEM . . . H 3 17.559 -66.698 48.338 1 54.7 ? O2A HEM 1602 B 1 HETATM 15 C C1B HEM . . . H 3 15.186 -59.241 43.886 1 34.18 ? C1B HEM 1602 B 1 HETATM 16 C C2B HEM . . . H 3 15.758 -57.991 43.438 1 31.71 ? C2B HEM 1602 B 1 HETATM 17 C C3B HEM . . . H 3 15.241 -57.716 42.232 1 25.68 ? C3B HEM 1602 B 1 HETATM 18 C C4B HEM . . . H 3 14.348 -58.789 41.895 1 33.11 ? C4B HEM 1602 B 1 HETATM 19 C CMB HEM . . . H 3 16.77 -57.159 44.252 1 34.12 ? CMB HEM 1602 B 1 HETATM 20 C CAB HEM . . . H 3 15.5 -56.527 41.284 1 29.86 ? CAB HEM 1602 B 1 HETATM 21 C CBB HEM . . . H 3 16.486 -55.66 41.524 1 47.75 ? CBB HEM 1602 B 1 HETATM 22 C C1C HEM . . . H 3 12.763 -59.868 40.436 1 25.84 ? C1C HEM 1602 B 1 HETATM 23 C C2C HEM . . . H 3 12.04 -59.983 39.201 1 35.67 ? C2C HEM 1602 B 1 HETATM 24 C C3C HEM . . . H 3 11.28 -61.08 39.273 1 37.65 ? C3C HEM 1602 B 1 HETATM 25 C C4C HEM . . . H 3 11.523 -61.691 40.55 1 31.28 ? C4C HEM 1602 B 1 HETATM 26 C CMC HEM . . . H 3 12.149 -58.968 38.05 1 38.18 ? CMC HEM 1602 B 1 HETATM 27 C CAC HEM . . . H 3 10.327 -61.681 38.223 1 29.32 ? CAC HEM 1602 B 1 HETATM 28 C CBC HEM . . . H 3 10.413 -61.324 36.941 1 31.32 ? CBC HEM 1602 B 1 HETATM 29 C C1D HEM . . . H 3 11.406 -63.58 42.04 1 33.87 ? C1D HEM 1602 B 1 HETATM 30 C C2D HEM . . . H 3 10.995 -64.919 42.364 1 35.81 ? C2D HEM 1602 B 1 HETATM 31 C C3D HEM . . . H 3 11.666 -65.307 43.444 1 37.18 ? C3D HEM 1602 B 1 HETATM 32 C C4D HEM . . . H 3 12.52 -64.219 43.841 1 40.6 ? C4D HEM 1602 B 1 HETATM 33 C CMD HEM . . . H 3 9.961 -65.745 41.579 1 36.53 ? CMD HEM 1602 B 1 HETATM 34 C CAD HEM . . . H 3 11.542 -66.669 44.157 1 40.45 ? CAD HEM 1602 B 1 HETATM 35 C CBD HEM . . . H 3 12.824 -67.475 43.977 1 57.57 ? CBD HEM 1602 B 1 HETATM 36 C CGD HEM . . . H 3 12.758 -68.778 44.737 1 50.46 ? CGD HEM 1602 B 1 HETATM 37 O O1D HEM . . . H 3 13.411 -69.752 44.286 1 47.3 ? O1D HEM 1602 B 1 HETATM 38 O O2D HEM . . . H 3 12.053 -68.856 45.777 1 48.82 ? O2D HEM 1602 B 1 HETATM 39 N NA HEM . . . H 3 14.218 -61.942 44.639 1 42.36 ? NA HEM 1602 B 1 HETATM 40 N NB HEM . . . H 3 14.326 -59.705 42.921 1 35.14 ? NB HEM 1602 B 1 HETATM 41 N NC HEM . . . H 3 12.423 -60.924 41.248 1 23.05 ? NC HEM 1602 B 1 HETATM 42 N ND HEM . . . H 3 12.342 -63.174 42.961 1 33.69 ? ND HEM 1602 B 1 HETATM 43 FE FE HEM . . . H 3 13.272 -61.415 42.97 1 43.11 ? FE HEM 1602 B 1 HETATM 44 H HHB HEM . . . H 3 15.774 -59.311 45.805 1 46.78 ? HHB HEM 1602 B 1 HETATM 45 H HHC HEM . . . H 3 13.901 -58.274 40.009 1 32.95 ? HHC HEM 1602 B 1 HETATM 46 H HHD HEM . . . H 3 10.026 -63.019 40.693 1 40.85 ? HHD HEM 1602 B 1 HETATM 47 H HMA HEM . . . H 3 15.967 -61.459 48.53 1 48.25 ? HMA HEM 1602 B 1 HETATM 48 H HMAA HEM . . . H 3 16.629 -60.429 47.501 1 48.25 ? HMAA HEM 1602 B 1 HETATM 49 H HMAB HEM . . . H 3 17.234 -61.902 47.661 1 48.25 ? HMAB HEM 1602 B 1 HETATM 50 H HAA HEM . . . H 3 14.375 -64.874 47.401 1 53.38 ? HAA HEM 1602 B 1 HETATM 51 H HAAA HEM . . . H 3 14.941 -63.823 48.442 1 53.38 ? HAAA HEM 1602 B 1 HETATM 52 H HBA HEM . . . H 3 17.109 -64.168 47.68 1 63.64 ? HBA HEM 1602 B 1 HETATM 53 H HBAA HEM . . . H 3 16.581 -65.107 46.517 1 63.64 ? HBAA HEM 1602 B 1 HETATM 54 H HMB HEM . . . H 3 16.677 -57.375 45.193 1 41.5 ? HMB HEM 1602 B 1 HETATM 55 H HMBA HEM . . . H 3 16.598 -56.213 44.125 1 41.5 ? HMBA HEM 1602 B 1 HETATM 56 H HMBB HEM . . . H 3 17.671 -57.372 43.964 1 41.5 ? HMBB HEM 1602 B 1 HETATM 57 H HAB HEM . . . H 3 14.932 -56.397 40.521 1 36.38 ? HAB HEM 1602 B 1 HETATM 58 H HBB HEM . . . H 3 16.499 -54.812 41.053 1 57.86 ? HBB HEM 1602 B 1 HETATM 59 H HBBA HEM . . . H 3 17.269 -55.94 42.02 1 57.86 ? HBBA HEM 1602 B 1 HETATM 60 H HMC HEM . . . H 3 12.229 -58.076 38.422 1 46.37 ? HMC HEM 1602 B 1 HETATM 61 H HMCA HEM . . . H 3 11.363 -59.006 37.488 1 46.37 ? HMCA HEM 1602 B 1 HETATM 62 H HMCB HEM . . . H 3 12.939 -59.163 37.522 1 46.37 ? HMCB HEM 1602 B 1 HETATM 63 H HAC HEM . . . H 3 9.653 -62.307 38.497 1 35.74 ? HAC HEM 1602 B 1 HETATM 64 H HBC HEM . . . H 3 9.664 -61.485 36.346 1 38.14 ? HBC HEM 1602 B 1 HETATM 65 H HBCA HEM . . . H 3 11.251 -60.994 36.582 1 38.14 ? HBCA HEM 1602 B 1 HETATM 66 H HMD HEM . . . H 3 9.931 -66.662 41.918 1 44.39 ? HMD HEM 1602 B 1 HETATM 67 H HMDA HEM . . . H 3 10.211 -65.759 40.632 1 44.39 ? HMDA HEM 1602 B 1 HETATM 68 H HMDB HEM . . . H 3 9.077 -65.333 41.673 1 44.39 ? HMDB HEM 1602 B 1 HETATM 69 H HAD HEM . . . H 3 10.794 -67.165 43.795 1 49.1 ? HAD HEM 1602 B 1 HETATM 70 H HADA HEM . . . H 3 11.393 -66.518 45.104 1 49.1 ? HADA HEM 1602 B 1 HETATM 71 H HBD HEM . . . H 3 13.576 -66.956 44.302 1 69.63 ? HBD HEM 1602 B 1 HETATM 72 H HBDA HEM . . . H 3 12.951 -67.663 43.034 1 69.63 ? HBDA HEM 1602 B 1 HETATM 73 H HHA HEM . . . H 3 13.58 -65.085 45.312 1 45.53 ? HHA HEM 1602 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 73 #