data_2D2N # _model_server_result.job_id J23mXdKBtmiRCgv-gTNOlg _model_server_result.datetime_utc '2025-09-09 15:33:34' _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 2d2n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":200}' # _entry.id 2D2N # _exptl.entry_id 2D2N _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _entity.pdbx_number_of_molecules 4 _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 120 _cell.entry_id 2D2N _cell.length_a 111.745 _cell.length_b 111.745 _cell.length_c 276.707 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2D2N _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? 24-meric 24 author_defined_assembly 1 PISA,PQS tetrameric 4 software_defined_assembly 2 # 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,J,K,L,M,N,O,P 1 1,2,3,4,5,6 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P 2 1 # 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_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 276.707 5 'crystal symmetry operation' 5_556 x-y,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 276.707 6 'crystal symmetry operation' 6_556 -x,-x+y,-z+1 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 276.707 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 E N N ? 5 H N N ? 5 K N N ? 5 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 A SG CYS 2 A CYS 2 1_555 A SG CYS 130 A CYS 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf2 A SG CYS 121 A CYS 121 1_555 C SG CYS 126 C CYS 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf3 B SG CYS 2 B CYS 2 1_555 B SG CYS 132 B CYS 132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf4 C SG CYS 4 C CYS 4 1_555 C SG CYS 135 C CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf5 D SG CYS 3 D CYS 3 1_555 D SG CYS 133 D CYS 133 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc1 A O PHE 59 A PHE 59 1_555 G HG MMC . A MMC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.469 ? metalc ? metalc2 A SG CYS 63 A CYS 63 1_555 G HG MMC . A MMC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc3 A NE2 HIS 94 A HIS 94 1_555 E FE HEM . A HEM 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc4 E FE HEM . A HEM 200 1_555 F O1 OXY . A OXY 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.797 ? metalc ? metalc5 E FE HEM . A HEM 200 1_555 F O2 OXY . A OXY 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.674 ? metalc ? metalc6 B O GLY 69 B GLY 69 1_555 J HG MMC . B MMC 1500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.511 ? metalc ? metalc7 B SG CYS 73 B CYS 73 1_555 J HG MMC . B MMC 1500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc8 B NE2 HIS 94 B HIS 94 1_555 H FE HEM . B HEM 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc9 H FE HEM . B HEM 200 1_555 I O1 OXY . B OXY 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.793 ? metalc ? metalc10 H FE HEM . B HEM 200 1_555 I O2 OXY . B OXY 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.931 ? metalc ? metalc11 C O PHE 63 C PHE 63 1_555 M HG MMC . C MMC 2500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.236 ? metalc ? metalc12 C N CYS 67 C CYS 67 1_555 M HG MMC . C MMC 2500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.528 ? metalc ? metalc13 C SG CYS 67 C CYS 67 1_555 M HG MMC . C MMC 2500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.715 ? metalc ? metalc14 C NE2 HIS 98 C HIS 98 1_555 K FE HEM . C HEM 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? metalc ? metalc15 K FE HEM . C HEM 200 1_555 L O1 OXY . C OXY 2201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.796 ? metalc ? metalc16 K FE HEM . C HEM 200 1_555 L O2 OXY . C OXY 2201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc17 D SG CYS 85 D CYS 85 1_555 P HG MMC . D MMC 3500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.737 ? metalc ? metalc18 D NE2 HIS 96 D HIS 96 1_555 N FE HEM . D HEM 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc19 N FE HEM . D HEM 200 1_555 O O1 OXY . D OXY 3201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.799 ? metalc ? metalc20 N FE HEM . D HEM 200 1_555 O O2 OXY . D OXY 3201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.896 ? # _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 2D2N _atom_sites.fract_transf_matrix[1][1] 0.008949 _atom_sites.fract_transf_matrix[1][2] 0.005167 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010333 _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] 0.003614 _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 E 5 HEM A 1 200 200 HEM HEM . F 6 OXY A 1 201 201 OXY O2 . G 7 MMC A 1 500 500 MMC HGC . H 5 HEM B 1 200 200 HEM HEM . I 6 OXY B 1 1201 1201 OXY O2 . J 7 MMC B 1 1500 1500 MMC HGC . K 5 HEM C 1 200 200 HEM HEM . L 6 OXY C 1 2201 2201 OXY O2 . M 7 MMC C 1 2500 2500 MMC HGC . N 5 HEM D 1 200 200 HEM HEM . O 6 OXY D 1 3201 3201 OXY O2 . P 7 MMC D 1 3500 3500 MMC HGC . # 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 5 0.9 48.249 133.261 1 70.63 ? CHA HEM 200 A 1 HETATM 2 C CHB HEM . . . E 5 4.014 45.261 131.083 1 70.63 ? CHB HEM 200 A 1 HETATM 3 C CHC HEM . . . E 5 7.506 46.761 134.089 1 70.63 ? CHC HEM 200 A 1 HETATM 4 C CHD HEM . . . E 5 4.214 49.052 136.748 1 70.63 ? CHD HEM 200 A 1 HETATM 5 C C1A HEM . . . E 5 1.46 47.401 132.312 1 70.63 ? C1A HEM 200 A 1 HETATM 6 C C2A HEM . . . E 5 0.789 46.85 131.125 1 70.63 ? C2A HEM 200 A 1 HETATM 7 C C3A HEM . . . E 5 1.738 46.154 130.432 1 70.63 ? C3A HEM 200 A 1 HETATM 8 C C4A HEM . . . E 5 2.904 46.082 131.294 1 70.63 ? C4A HEM 200 A 1 HETATM 9 C CMA HEM . . . E 5 1.65 45.57 129.049 1 70.63 ? CMA HEM 200 A 1 HETATM 10 C CAA HEM . . . E 5 -0.667 47.031 130.778 1 70.63 ? CAA HEM 200 A 1 HETATM 11 C CBA HEM . . . E 5 -0.856 48.164 129.791 1 70.63 ? CBA HEM 200 A 1 HETATM 12 C CGA HEM . . . E 5 -2.15 48.14 128.99 1 70.63 ? CGA HEM 200 A 1 HETATM 13 O O1A HEM . . . E 5 -2.502 47.056 128.416 1 70.63 ? O1A HEM 200 A 1 HETATM 14 O O2A HEM . . . E 5 -2.819 49.219 128.93 1 70.63 ? O2A HEM 200 A 1 HETATM 15 C C1B HEM . . . E 5 5.262 45.419 131.665 1 70.63 ? C1B HEM 200 A 1 HETATM 16 C C2B HEM . . . E 5 6.508 44.806 131.206 1 70.63 ? C2B HEM 200 A 1 HETATM 17 C C3B HEM . . . E 5 7.42 45.052 132.191 1 70.63 ? C3B HEM 200 A 1 HETATM 18 C C4B HEM . . . E 5 6.836 46.046 133.075 1 70.63 ? C4B HEM 200 A 1 HETATM 19 C CMB HEM . . . E 5 6.706 44.063 129.91 1 70.63 ? CMB HEM 200 A 1 HETATM 20 C CAB HEM . . . E 5 8.759 44.446 132.399 1 70.63 ? CAB HEM 200 A 1 HETATM 21 C CBB HEM . . . E 5 9.939 44.933 132.036 1 70.63 ? CBB HEM 200 A 1 HETATM 22 C C1C HEM . . . E 5 6.913 47.354 135.193 1 70.63 ? C1C HEM 200 A 1 HETATM 23 C C2C HEM . . . E 5 7.552 47.622 136.475 1 70.63 ? C2C HEM 200 A 1 HETATM 24 C C3C HEM . . . E 5 6.604 48.245 137.255 1 70.63 ? C3C HEM 200 A 1 HETATM 25 C C4C HEM . . . E 5 5.394 48.388 136.412 1 70.63 ? C4C HEM 200 A 1 HETATM 26 C CMC HEM . . . E 5 8.985 47.252 136.804 1 70.63 ? CMC HEM 200 A 1 HETATM 27 C CAC HEM . . . E 5 6.722 48.719 138.656 1 70.63 ? CAC HEM 200 A 1 HETATM 28 C CBC HEM . . . E 5 7.078 48.009 139.734 1 70.63 ? CBC HEM 200 A 1 HETATM 29 C C1D HEM . . . E 5 2.999 49.072 136.033 1 70.63 ? C1D HEM 200 A 1 HETATM 30 C C2D HEM . . . E 5 1.784 49.737 136.46 1 70.63 ? C2D HEM 200 A 1 HETATM 31 C C3D HEM . . . E 5 0.858 49.558 135.437 1 70.63 ? C3D HEM 200 A 1 HETATM 32 C C4D HEM . . . E 5 1.49 48.722 134.44 1 70.63 ? C4D HEM 200 A 1 HETATM 33 C CMD HEM . . . E 5 1.611 50.477 137.766 1 70.63 ? CMD HEM 200 A 1 HETATM 34 C CAD HEM . . . E 5 -0.522 50.134 135.36 1 70.63 ? CAD HEM 200 A 1 HETATM 35 C CBD HEM . . . E 5 -1.618 49.135 135.77 1 70.63 ? CBD HEM 200 A 1 HETATM 36 C CGD HEM . . . E 5 -2.699 49.882 136.562 1 70.63 ? CGD HEM 200 A 1 HETATM 37 O O1D HEM . . . E 5 -3.723 50.334 135.938 1 70.63 ? O1D HEM 200 A 1 HETATM 38 O O2D HEM . . . E 5 -2.505 50.003 137.831 1 70.63 ? O2D HEM 200 A 1 HETATM 39 N NA HEM . . . E 5 2.75 46.941 132.348 1 70.63 ? NA HEM 200 A 1 HETATM 40 N NB HEM . . . E 5 5.512 46.203 132.77 1 70.63 ? NB HEM 200 A 1 HETATM 41 N NC HEM . . . E 5 5.601 47.763 135.23 1 70.63 ? NC HEM 200 A 1 HETATM 42 N ND HEM . . . E 5 2.779 48.47 134.814 1 70.63 ? ND HEM 200 A 1 HETATM 43 FE FE HEM . . . E 5 4.154 47.444 133.746 1 54.11 ? FE HEM 200 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 252 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #