data_8D9M # _model_server_result.job_id 5gRnC6cjxpoHCbpigwweOg _model_server_result.datetime_utc '2024-11-09 02:26:26' _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 8d9m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 8D9M # _exptl.entry_id 8D9M _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 618.503 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'HEME C' _entity.pdbx_number_of_molecules 8 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? heptameric 7 'representative helical assembly' 1 ? monomeric 1 'helical asymmetric unit' 2 ? monomeric 1 'helical asymmetric unit, std helical frame' 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I 1 (1-7) A,B,C,D,E,F,G,H,I 2 4 A,B,C,D,E,F,G,H,I 3 H # 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] H 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 1 'helical symmetry operation' ? ? -0.416281 -0.909236 0 0.909236 -0.416281 0 0 0 1 0 0 -174.3 2 'helical symmetry operation' ? ? 0.724172 0.68962 0 -0.68962 0.724172 0 0 0 1 0 0 -116.2 3 'helical symmetry operation' ? ? -0.928486 -0.371368 0 0.371368 -0.928486 0 0 0 1 0 0 -58.1 4 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 5 'helical symmetry operation' ? ? -0.928486 0.371368 0 -0.371368 -0.928486 0 0 0 1 0 0 58.1 6 'helical symmetry operation' ? ? 0.724172 -0.68962 0 0.68962 0.724172 0 0 0 1 0 0 116.2 7 'helical symmetry operation' ? ? -0.416281 0.909236 0 -0.909236 -0.416281 0 0 0 1 0 0 174.3 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N N ? 2 D N N ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N ? 2 I 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 SG CYS 92 A CYS 92 1_555 B CAC HEC . A HEC 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? covale ? covale2 A SG CYS 114 A CYS 114 1_555 C CAC HEC . A HEC 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.896 ? covale ? covale3 A SG CYS 134 A CYS 134 1_555 E CAC HEC . A HEC 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? covale ? covale4 A SG CYS 178 A CYS 178 1_555 H CAB HEC . A HEC 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.852 ? covale ? covale5 A SG CYS 181 A CYS 181 1_555 H CAC HEC . A HEC 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.895 ? covale ? covale6 A SG CYS 229 A CYS 229 1_555 F CAB HEC . A HEC 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.892 ? covale ? covale7 A SG CYS 232 A CYS 232 1_555 F CAC HEC . A HEC 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.903 ? metalc ? metalc1 A NE2 HIS 54 A HIS 54 1_555 D FE HEC . A HEC 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc2 A NE2 HIS 64 A HIS 64 1_555 C FE HEC . A HEC 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc3 A NE2 HIS 65 A HIS 65 1_555 B FE HEC . A HEC 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc4 A NE2 HIS 93 A HIS 93 1_555 B FE HEC . A HEC 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc5 A NE2 HIS 115 A HIS 115 1_555 C FE HEC . A HEC 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc6 A NE2 HIS 120 A HIS 120 1_555 D FE HEC . A HEC 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc7 A NE2 HIS 121 A HIS 121 1_555 E FE HEC . A HEC 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc8 A NE2 HIS 135 A HIS 135 1_555 E FE HEC . A HEC 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc9 A NE2 HIS 182 A HIS 182 1_555 H FE HEC . A HEC 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc10 A NE2 HIS 206 A HIS 206 1_555 F FE HEC . A HEC 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc11 A NE2 HIS 207 A HIS 207 1_555 G FE HEC . A HEC 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc12 A NE2 HIS 218 A HIS 218 1_555 G FE HEC . A HEC 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc13 A NE2 HIS 233 A HIS 233 1_555 F FE HEC . A HEC 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc14 A NE2 HIS 239 A HIS 239 1_555 I FE HEC . A HEC 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc15 A NE2 HIS 265 A HIS 265 1_555 H FE HEC . A HEC 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc16 A NE2 HIS 276 A HIS 276 1_555 I FE HEC . A HEC 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? # _chem_comp.formula 'C34 H34 Fe N4 O4' _chem_comp.formula_weight 618.503 _chem_comp.id HEC _chem_comp.mon_nstd_flag . _chem_comp.name 'HEME C' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 FE NA HEC sing 129 n n FE NB HEC sing 130 n n FE NC HEC sing 131 n n FE ND HEC sing 132 n n CHA C1A HEC doub 133 n n CHA C4D HEC sing 134 n n CHA HHA HEC sing 135 n n CHB C4A HEC doub 136 n n CHB C1B HEC sing 137 n n CHB HHB HEC sing 138 n n CHC C4B HEC doub 139 n n CHC C1C HEC sing 140 n n CHC HHC HEC sing 141 n n CHD C4C HEC doub 142 n n CHD C1D HEC sing 143 n n CHD HHD HEC sing 144 n n NA C1A HEC sing 145 n y NA C4A HEC sing 146 n y C1A C2A HEC sing 147 n y C2A C3A HEC doub 148 n y C2A CAA HEC sing 149 n n C3A C4A HEC sing 150 n y C3A CMA HEC sing 151 n n CMA HMA1 HEC sing 152 n n CMA HMA2 HEC sing 153 n n CMA HMA3 HEC sing 154 n n CAA CBA HEC sing 155 n n CAA HAA1 HEC sing 156 n n CAA HAA2 HEC sing 157 n n CBA CGA HEC sing 158 n n CBA HBA1 HEC sing 159 n n CBA HBA2 HEC sing 160 n n CGA O1A HEC doub 161 n n CGA O2A HEC sing 162 n n O2A H2A HEC sing 163 n n NB C1B HEC sing 164 n y NB C4B HEC sing 165 n y C1B C2B HEC doub 166 n y C2B C3B HEC sing 167 n y C2B CMB HEC sing 168 n n C3B C4B HEC sing 169 n y C3B CAB HEC doub 170 e n CMB HMB1 HEC sing 171 n n CMB HMB2 HEC sing 172 n n CMB HMB3 HEC sing 173 n n CAB CBB HEC sing 174 n n CAB HAB HEC sing 175 n n CBB HBB1 HEC sing 176 n n CBB HBB2 HEC sing 177 n n CBB HBB3 HEC sing 178 n n NC C1C HEC sing 179 n y NC C4C HEC sing 180 n y C1C C2C HEC doub 181 n y C2C C3C HEC sing 182 n y C2C CMC HEC sing 183 n n C3C C4C HEC sing 184 n y C3C CAC HEC doub 185 e n CMC HMC1 HEC sing 186 n n CMC HMC2 HEC sing 187 n n CMC HMC3 HEC sing 188 n n CAC CBC HEC sing 189 n n CAC HAC HEC sing 190 n n CBC HBC1 HEC sing 191 n n CBC HBC2 HEC sing 192 n n CBC HBC3 HEC sing 193 n n ND C1D HEC sing 194 n y ND C4D HEC sing 195 n y C1D C2D HEC doub 196 n y C2D C3D HEC sing 197 n y C2D CMD HEC sing 198 n n C3D C4D HEC doub 199 n y C3D CAD HEC sing 200 n n CMD HMD1 HEC sing 201 n n CMD HMD2 HEC sing 202 n n CMD HMD3 HEC sing 203 n n CAD CBD HEC sing 204 n n CAD HAD1 HEC sing 205 n n CAD HAD2 HEC sing 206 n n CBD CGD HEC sing 207 n n CBD HBD1 HEC sing 208 n n CBD HBD2 HEC sing 209 n n CGD O1D HEC doub 210 n n CGD O2D HEC sing 211 n n O2D H2D HEC sing 212 n n # _atom_sites.entry_id 8D9M _atom_sites.fract_transf_matrix[1][1] 1 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 1 _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] 1 _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 B 2 HEC A 1 601 601 HEC HEC . C 2 HEC A 1 602 602 HEC HEC . D 2 HEC A 1 603 603 HEC HEC . E 2 HEC A 1 604 604 HEC HEC . F 2 HEC A 1 605 605 HEC HEC . G 2 HEC A 1 606 606 HEC HEC . H 2 HEC A 1 607 607 HEC HEC . I 2 HEC A 1 608 608 HEC HEC . # 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 FE FE HEC . . . B 2 0.833 5.238 26.971 1 115.83 ? FE HEC 601 A 1 HETATM 2 C CHA HEC . . . B 2 2.171 2.137 26.539 1 115.83 ? CHA HEC 601 A 1 HETATM 3 C CHB HEC . . . B 2 2.197 5.422 30.134 1 115.83 ? CHB HEC 601 A 1 HETATM 4 C CHC HEC . . . B 2 -0.546 8.315 27.465 1 115.83 ? CHC HEC 601 A 1 HETATM 5 C CHD HEC . . . B 2 -0.459 5.198 23.808 1 115.83 ? CHD HEC 601 A 1 HETATM 6 N NA HEC . . . B 2 1.946 4.025 28.112 1 115.83 ? NA HEC 601 A 1 HETATM 7 C C1A HEC . . . B 2 2.417 2.783 27.73 1 115.83 ? C1A HEC 601 A 1 HETATM 8 C C2A HEC . . . B 2 3.227 2.261 28.806 1 115.83 ? C2A HEC 601 A 1 HETATM 9 C C3A HEC . . . B 2 3.231 3.158 29.789 1 115.83 ? C3A HEC 601 A 1 HETATM 10 C C4A HEC . . . B 2 2.428 4.29 29.38 1 115.83 ? C4A HEC 601 A 1 HETATM 11 C CMA HEC . . . B 2 3.981 3.018 31.129 1 115.83 ? CMA HEC 601 A 1 HETATM 12 C CAA HEC . . . B 2 3.97 0.907 28.817 1 115.83 ? CAA HEC 601 A 1 HETATM 13 C CBA HEC . . . B 2 5.186 0.991 27.895 1 115.83 ? CBA HEC 601 A 1 HETATM 14 C CGA HEC . . . B 2 6.053 -0.233 28.071 1 115.83 ? CGA HEC 601 A 1 HETATM 15 O O1A HEC . . . B 2 5.568 -1.352 27.77 1 115.83 ? O1A HEC 601 A 1 HETATM 16 O O2A HEC . . . B 2 7.23 -0.106 28.517 1 115.83 ? O2A HEC 601 A 1 HETATM 17 N NB HEC . . . B 2 0.844 6.616 28.516 1 115.83 ? NB HEC 601 A 1 HETATM 18 C C1B HEC . . . B 2 1.44 6.506 29.752 1 115.83 ? C1B HEC 601 A 1 HETATM 19 C C2B HEC . . . B 2 1.133 7.704 30.532 1 115.83 ? C2B HEC 601 A 1 HETATM 20 C C3B HEC . . . B 2 0.359 8.489 29.767 1 115.83 ? C3B HEC 601 A 1 HETATM 21 C C4B HEC . . . B 2 0.179 7.818 28.505 1 115.83 ? C4B HEC 601 A 1 HETATM 22 C CMB HEC . . . B 2 1.591 7.993 31.992 1 115.83 ? CMB HEC 601 A 1 HETATM 23 C CAB HEC . . . B 2 -0.268 9.866 30.096 1 115.83 ? CAB HEC 601 A 1 HETATM 24 C CBB HEC . . . B 2 0.842 10.932 30.129 1 115.83 ? CBB HEC 601 A 1 HETATM 25 N NC HEC . . . B 2 -0.266 6.495 25.859 1 115.83 ? NC HEC 601 A 1 HETATM 26 C C1C HEC . . . B 2 -0.754 7.717 26.257 1 115.83 ? C1C HEC 601 A 1 HETATM 27 C C2C HEC . . . B 2 -1.506 8.308 25.178 1 115.83 ? C2C HEC 601 A 1 HETATM 28 C C3C HEC . . . B 2 -1.518 7.43 24.173 1 115.83 ? C3C HEC 601 A 1 HETATM 29 C C4C HEC . . . B 2 -0.719 6.296 24.577 1 115.83 ? C4C HEC 601 A 1 HETATM 30 C CMC HEC . . . B 2 -2.251 9.659 25.282 1 115.83 ? CMC HEC 601 A 1 HETATM 31 C CAC HEC . . . B 2 -2.206 7.565 22.797 1 115.83 ? CAC HEC 601 A 1 HETATM 32 C CBC HEC . . . B 2 -1.644 8.752 21.985 1 115.83 ? CBC HEC 601 A 1 HETATM 33 N ND HEC . . . B 2 0.867 3.868 25.416 1 115.83 ? ND HEC 601 A 1 HETATM 34 C C1D HEC . . . B 2 0.23 4.082 24.202 1 115.83 ? C1D HEC 601 A 1 HETATM 35 C C2D HEC . . . B 2 0.401 2.926 23.367 1 115.83 ? C2D HEC 601 A 1 HETATM 36 C C3D HEC . . . B 2 1.232 1.936 24.179 1 115.83 ? C3D HEC 601 A 1 HETATM 37 C C4D HEC . . . B 2 1.468 2.611 25.453 1 115.83 ? C4D HEC 601 A 1 HETATM 38 C CMD HEC . . . B 2 -0.143 2.725 21.937 1 115.83 ? CMD HEC 601 A 1 HETATM 39 C CAD HEC . . . B 2 1.621 0.536 23.629 1 115.83 ? CAD HEC 601 A 1 HETATM 40 C CBD HEC . . . B 2 2.72 -0.204 24.379 1 115.83 ? CBD HEC 601 A 1 HETATM 41 C CGD HEC . . . B 2 3.274 -1.298 23.505 1 115.83 ? CGD HEC 601 A 1 HETATM 42 O O1D HEC . . . B 2 2.641 -1.615 22.465 1 115.83 ? O1D HEC 601 A 1 HETATM 43 O O2D HEC . . . B 2 4.343 -1.861 23.852 1 115.83 ? O2D HEC 601 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #