data_6Y9B # _model_server_result.job_id SOdPM-sxA7lfr4sjJirxcg _model_server_result.datetime_utc '2024-11-05 05:39:00' _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 6y9b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":401}' # _entry.id 6Y9B # _exptl.entry_id 6Y9B _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 616.487 _entity.id 4 _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 90 _cell.angle_gamma 90 _cell.entry_id 6Y9B _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6Y9B _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details nonameric _pdbx_struct_assembly.oligomeric_count 9 _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,N,O _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation ? _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 J N N ? 4 L N N ? 4 N 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 B SG CYS 23 L CYS 23 1_555 B SG CYS 94 L CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 C SG CYS 22 H CYS 22 1_555 C SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 D SG CYS 22 I CYS 22 1_555 D SG CYS 96 I CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 E SG CYS 22 J CYS 22 1_555 E SG CYS 96 J CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 F SG CYS 23 M CYS 23 1_555 F SG CYS 94 M CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf6 G SG CYS 23 N CYS 23 1_555 G SG CYS 94 N CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc1 A NE2 HIS 177 C HIS 175 1_555 J FE HEM . C HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? metalc ? metalc2 A NE2 HIS 270 C HIS 268 1_555 J FE HEM . C HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? metalc ? metalc3 H NE2 HIS 177 A HIS 175 1_555 L FE HEM . A HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.981 ? metalc ? metalc4 H NE2 HIS 270 A HIS 268 1_555 L FE HEM . A HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc5 I NE2 HIS 177 B HIS 175 1_555 N FE HEM . B HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? metalc ? metalc6 I NE2 HIS 270 B HIS 268 1_555 N FE HEM . B HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? # _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 6Y9B _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 J 4 HEM C 1 401 1073 HEM HEM . K 5 XP4 C 1 402 1101 XP4 UI9 . L 4 HEM A 1 401 1073 HEM HEM . M 5 XP4 A 1 402 1101 XP4 UI9 . N 4 HEM B 1 401 1073 HEM HEM . O 5 XP4 B 1 402 1101 XP4 UI9 . # 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 . . . J 4 142.551 144.824 146.431 1 79.71 ? CHA HEM 401 C 1 HETATM 2 C CHB HEM . . . J 4 147.058 146.535 146.128 1 79.71 ? CHB HEM 401 C 1 HETATM 3 C CHC HEM . . . J 4 147.245 145.168 141.46 1 79.71 ? CHC HEM 401 C 1 HETATM 4 C CHD HEM . . . J 4 142.64 143.72 141.715 1 79.71 ? CHD HEM 401 C 1 HETATM 5 C C1A HEM . . . J 4 143.772 145.37 146.72 1 79.71 ? C1A HEM 401 C 1 HETATM 6 C C2A HEM . . . J 4 144.142 145.821 147.995 1 79.71 ? C2A HEM 401 C 1 HETATM 7 C C3A HEM . . . J 4 145.399 146.306 147.918 1 79.71 ? C3A HEM 401 C 1 HETATM 8 C C4A HEM . . . J 4 145.824 146.154 146.592 1 79.71 ? C4A HEM 401 C 1 HETATM 9 C CMA HEM . . . J 4 146.201 146.889 149.047 1 79.71 ? CMA HEM 401 C 1 HETATM 10 C CAA HEM . . . J 4 143.289 145.79 149.227 1 79.71 ? CAA HEM 401 C 1 HETATM 11 C CBA HEM . . . J 4 142.477 147.085 149.223 1 79.71 ? CBA HEM 401 C 1 HETATM 12 C CGA HEM . . . J 4 141.889 147.342 150.581 1 79.71 ? CGA HEM 401 C 1 HETATM 13 O O1A HEM . . . J 4 140.653 147.484 150.707 1 79.71 ? O1A HEM 401 C 1 HETATM 14 O O2A HEM . . . J 4 142.636 147.42 151.58 1 79.71 ? O2A HEM 401 C 1 HETATM 15 C C1B HEM . . . J 4 147.456 146.274 144.82 1 79.71 ? C1B HEM 401 C 1 HETATM 16 C C2B HEM . . . J 4 148.758 146.602 144.382 1 79.71 ? C2B HEM 401 C 1 HETATM 17 C C3B HEM . . . J 4 148.842 146.231 143.078 1 79.71 ? C3B HEM 401 C 1 HETATM 18 C C4B HEM . . . J 4 147.527 145.657 142.732 1 79.71 ? C4B HEM 401 C 1 HETATM 19 C CMB HEM . . . J 4 149.83 147.24 145.221 1 79.71 ? CMB HEM 401 C 1 HETATM 20 C CAB HEM . . . J 4 149.998 146.358 142.179 1 79.71 ? CAB HEM 401 C 1 HETATM 21 C CBB HEM . . . J 4 150.545 147.538 141.922 1 79.71 ? CBB HEM 401 C 1 HETATM 22 C C1C HEM . . . J 4 146.015 144.629 141.128 1 79.71 ? C1C HEM 401 C 1 HETATM 23 C C2C HEM . . . J 4 145.691 144.048 139.898 1 79.71 ? C2C HEM 401 C 1 HETATM 24 C C3C HEM . . . J 4 144.377 143.637 139.975 1 79.71 ? C3C HEM 401 C 1 HETATM 25 C C4C HEM . . . J 4 143.904 143.975 141.265 1 79.71 ? C4C HEM 401 C 1 HETATM 26 C CMC HEM . . . J 4 146.608 143.897 138.714 1 79.71 ? CMC HEM 401 C 1 HETATM 27 C CAC HEM . . . J 4 143.607 142.967 138.918 1 79.71 ? CAC HEM 401 C 1 HETATM 28 C CBC HEM . . . J 4 143.22 143.65 137.849 1 79.71 ? CBC HEM 401 C 1 HETATM 29 C C1D HEM . . . J 4 142.29 143.91 143.048 1 79.71 ? C1D HEM 401 C 1 HETATM 30 C C2D HEM . . . J 4 140.965 143.53 143.534 1 79.71 ? C2D HEM 401 C 1 HETATM 31 C C3D HEM . . . J 4 140.942 143.835 144.835 1 79.71 ? C3D HEM 401 C 1 HETATM 32 C C4D HEM . . . J 4 142.252 144.397 145.151 1 79.71 ? C4D HEM 401 C 1 HETATM 33 C CMD HEM . . . J 4 139.852 142.921 142.728 1 79.71 ? CMD HEM 401 C 1 HETATM 34 C CAD HEM . . . J 4 139.805 143.64 145.795 1 79.71 ? CAD HEM 401 C 1 HETATM 35 C CBD HEM . . . J 4 138.91 144.874 145.765 1 79.71 ? CBD HEM 401 C 1 HETATM 36 C CGD HEM . . . J 4 137.972 144.824 146.939 1 79.71 ? CGD HEM 401 C 1 HETATM 37 O O1D HEM . . . J 4 136.756 144.607 146.757 1 79.71 ? O1D HEM 401 C 1 HETATM 38 O O2D HEM . . . J 4 138.412 144.993 148.096 1 79.71 ? O2D HEM 401 C 1 HETATM 39 N NA HEM . . . J 4 144.808 145.608 145.858 1 79.71 ? NA HEM 401 C 1 HETATM 40 N NB HEM . . . J 4 146.756 145.715 143.827 1 79.71 ? NB HEM 401 C 1 HETATM 41 N NC HEM . . . J 4 144.92 144.588 141.94 1 79.71 ? NC HEM 401 C 1 HETATM 42 N ND HEM . . . J 4 143.017 144.418 144.053 1 79.71 ? ND HEM 401 C 1 HETATM 43 FE FE HEM . . . J 4 144.768 145.049 143.963 1 79.71 ? FE HEM 401 C 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #