data_3E67 # _model_server_result.job_id 5-9lJN1lb1KXimyHtCL0mQ _model_server_result.datetime_utc '2024-11-16 08:54:58' _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 3e67 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":901}' # _entry.id 3E67 # _exptl.entry_id 3E67 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _entity.pdbx_number_of_molecules 2 _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 3E67 _cell.length_a 214.093 _cell.length_b 214.093 _cell.length_c 115.828 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3E67 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_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,C,D,E,I 1 1,2 B,F,G,H,J 2 1,3 # 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' 11_655 -x+y+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 214.093 0 57.914 3 'crystal symmetry operation' 9_766 -x+2,-x+y+1,-z+5/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 321.1395 185.409977 193.046667 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 F 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 129 A CYS 194 1_555 C FE HEM . A HEM 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc2 B SG CYS 129 B CYS 194 1_555 F FE HEM . B HEM 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? # _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 178 n n CHA C4D HEM doub 179 n n CHA HHA HEM sing 180 n n CHB C4A HEM sing 181 n n CHB C1B HEM doub 182 n n CHB HHB HEM sing 183 n n CHC C4B HEM sing 184 n n CHC C1C HEM doub 185 n n CHC HHC HEM sing 186 n n CHD C4C HEM doub 187 n n CHD C1D HEM sing 188 n n CHD HHD HEM sing 189 n n C1A C2A HEM doub 190 n y C1A NA HEM sing 191 n y C2A C3A HEM sing 192 n y C2A CAA HEM sing 193 n n C3A C4A HEM doub 194 n y C3A CMA HEM sing 195 n n C4A NA HEM sing 196 n y CMA HMA HEM sing 197 n n CMA HMAA HEM sing 198 n n CMA HMAB HEM sing 199 n n CAA CBA HEM sing 200 n n CAA HAA HEM sing 201 n n CAA HAAA HEM sing 202 n n CBA CGA HEM sing 203 n n CBA HBA HEM sing 204 n n CBA HBAA HEM sing 205 n n CGA O1A HEM doub 206 n n CGA O2A HEM sing 207 n n C1B C2B HEM sing 208 n n C1B NB HEM sing 209 n n C2B C3B HEM doub 210 n n C2B CMB HEM sing 211 n n C3B C4B HEM sing 212 n n C3B CAB HEM sing 213 n n C4B NB HEM doub 214 n n CMB HMB HEM sing 215 n n CMB HMBA HEM sing 216 n n CMB HMBB HEM sing 217 n n CAB CBB HEM doub 218 n n CAB HAB HEM sing 219 n n CBB HBB HEM sing 220 n n CBB HBBA HEM sing 221 n n C1C C2C HEM sing 222 n y C1C NC HEM sing 223 n y C2C C3C HEM doub 224 n y C2C CMC HEM sing 225 n n C3C C4C HEM sing 226 n y C3C CAC HEM sing 227 n n C4C NC HEM sing 228 n y CMC HMC HEM sing 229 n n CMC HMCA HEM sing 230 n n CMC HMCB HEM sing 231 n n CAC CBC HEM doub 232 n n CAC HAC HEM sing 233 n n CBC HBC HEM sing 234 n n CBC HBCA HEM sing 235 n n C1D C2D HEM sing 236 n n C1D ND HEM doub 237 n n C2D C3D HEM doub 238 n n C2D CMD HEM sing 239 n n C3D C4D HEM sing 240 n n C3D CAD HEM sing 241 n n C4D ND HEM sing 242 n n CMD HMD HEM sing 243 n n CMD HMDA HEM sing 244 n n CMD HMDB HEM sing 245 n n CAD CBD HEM sing 246 n n CAD HAD HEM sing 247 n n CAD HADA HEM sing 248 n n CBD CGD HEM sing 249 n n CBD HBD HEM sing 250 n n CBD HBDA HEM sing 251 n n CGD O1D HEM doub 252 n n CGD O2D HEM sing 253 n n O2A H2A HEM sing 254 n n O2D H2D HEM sing 255 n n FE NA HEM sing 256 n n FE NB HEM sing 257 n n FE NC HEM sing 258 n n FE ND HEM sing 259 n n # _atom_sites.entry_id 3E67 _atom_sites.fract_transf_matrix[1][1] 0.004671 _atom_sites.fract_transf_matrix[1][2] 0.002697 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005393 _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] 0.008633 _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 C 2 HEM A 1 901 901 HEM HEM . D 3 H4B A 1 902 902 H4B H4B . E 4 BVF A 1 904 904 BVF BVF . F 2 HEM B 1 901 901 HEM HEM . G 3 H4B B 1 902 902 H4B H4B . H 4 BVF B 1 905 905 BVF BVF . I 5 HOH A 1 905 905 HOH HOH . I 5 HOH A 2 906 906 HOH HOH . I 5 HOH A 3 907 907 HOH HOH . I 5 HOH A 4 908 908 HOH HOH . I 5 HOH A 5 909 909 HOH HOH . I 5 HOH A 6 910 910 HOH HOH . I 5 HOH A 7 911 911 HOH HOH . I 5 HOH A 8 912 912 HOH HOH . I 5 HOH A 9 913 913 HOH HOH . I 5 HOH A 10 914 914 HOH HOH . I 5 HOH A 11 915 915 HOH HOH . I 5 HOH A 12 916 916 HOH HOH . I 5 HOH A 13 917 917 HOH HOH . I 5 HOH A 14 918 918 HOH HOH . I 5 HOH A 15 919 919 HOH HOH . I 5 HOH A 16 920 920 HOH HOH . I 5 HOH A 17 921 921 HOH HOH . I 5 HOH A 18 922 922 HOH HOH . I 5 HOH A 19 923 923 HOH HOH . I 5 HOH A 20 924 924 HOH HOH . I 5 HOH A 21 925 925 HOH HOH . I 5 HOH A 22 926 926 HOH HOH . I 5 HOH A 23 927 927 HOH HOH . I 5 HOH A 24 928 928 HOH HOH . I 5 HOH A 25 929 929 HOH HOH . I 5 HOH A 26 930 930 HOH HOH . I 5 HOH A 27 931 931 HOH HOH . I 5 HOH A 28 932 932 HOH HOH . I 5 HOH A 29 933 933 HOH HOH . I 5 HOH A 30 934 934 HOH HOH . I 5 HOH A 31 935 935 HOH HOH . I 5 HOH A 32 936 936 HOH HOH . I 5 HOH A 33 937 937 HOH HOH . I 5 HOH A 34 938 938 HOH HOH . I 5 HOH A 35 939 939 HOH HOH . I 5 HOH A 36 940 940 HOH HOH . I 5 HOH A 37 941 941 HOH HOH . I 5 HOH A 38 942 942 HOH HOH . I 5 HOH A 39 943 943 HOH HOH . I 5 HOH A 40 944 944 HOH HOH . I 5 HOH A 41 945 945 HOH HOH . I 5 HOH A 42 946 946 HOH HOH . J 5 HOH B 1 906 906 HOH HOH . J 5 HOH B 2 907 907 HOH HOH . J 5 HOH B 3 908 908 HOH HOH . J 5 HOH B 4 909 909 HOH HOH . J 5 HOH B 5 910 910 HOH HOH . J 5 HOH B 6 911 911 HOH HOH . J 5 HOH B 7 912 912 HOH HOH . J 5 HOH B 8 913 913 HOH HOH . J 5 HOH B 9 914 914 HOH HOH . J 5 HOH B 10 915 915 HOH HOH . J 5 HOH B 11 916 916 HOH HOH . J 5 HOH B 12 917 917 HOH HOH . J 5 HOH B 13 918 918 HOH HOH . J 5 HOH B 14 919 919 HOH HOH . J 5 HOH B 15 920 920 HOH HOH . J 5 HOH B 16 921 921 HOH HOH . J 5 HOH B 17 922 922 HOH HOH . J 5 HOH B 18 923 923 HOH HOH . J 5 HOH B 19 924 924 HOH HOH . J 5 HOH B 20 925 925 HOH HOH . J 5 HOH B 21 926 926 HOH HOH . J 5 HOH B 22 927 927 HOH HOH . J 5 HOH B 23 928 928 HOH HOH . J 5 HOH B 24 929 929 HOH HOH . J 5 HOH B 25 930 930 HOH HOH . J 5 HOH B 26 931 931 HOH HOH . J 5 HOH B 27 932 932 HOH HOH . J 5 HOH B 28 933 933 HOH HOH . J 5 HOH B 29 934 934 HOH HOH . J 5 HOH B 30 935 935 HOH HOH . J 5 HOH B 31 936 936 HOH HOH . J 5 HOH B 32 937 937 HOH HOH . J 5 HOH B 33 938 938 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 . . . F 2 131.446 113.385 94.547 1 34.5 ? CHA HEM 901 B 1 HETATM 2 C CHB HEM . . . F 2 128.562 116.211 97.124 1 31.94 ? CHB HEM 901 B 1 HETATM 3 C CHC HEM . . . F 2 125.763 112.495 97.933 1 33.97 ? CHC HEM 901 B 1 HETATM 4 C CHD HEM . . . F 2 128.924 109.514 95.916 1 32.04 ? CHD HEM 901 B 1 HETATM 5 C C1A HEM . . . F 2 130.863 114.531 95.081 1 34.1 ? C1A HEM 901 B 1 HETATM 6 C C2A HEM . . . F 2 131.291 115.909 94.826 1 33.82 ? C2A HEM 901 B 1 HETATM 7 C C3A HEM . . . F 2 130.513 116.671 95.631 1 32.64 ? C3A HEM 901 B 1 HETATM 8 C C4A HEM . . . F 2 129.61 115.804 96.33 1 32.77 ? C4A HEM 901 B 1 HETATM 9 C CMA HEM . . . F 2 130.649 118.157 95.801 1 31 ? CMA HEM 901 B 1 HETATM 10 C CAA HEM . . . F 2 132.353 116.425 93.861 1 33.45 ? CAA HEM 901 B 1 HETATM 11 C CBA HEM . . . F 2 131.651 116.526 92.504 1 35.41 ? CBA HEM 901 B 1 HETATM 12 C CGA HEM . . . F 2 132.576 116.963 91.381 1 35.96 ? CGA HEM 901 B 1 HETATM 13 O O1A HEM . . . F 2 132.366 116.514 90.233 1 35.35 ? O1A HEM 901 B 1 HETATM 14 O O2A HEM . . . F 2 133.507 117.755 91.649 1 35.98 ? O2A HEM 901 B 1 HETATM 15 C C1B HEM . . . F 2 127.549 115.435 97.646 1 33.48 ? C1B HEM 901 B 1 HETATM 16 C C2B HEM . . . F 2 126.469 115.944 98.412 1 34.79 ? C2B HEM 901 B 1 HETATM 17 C C3B HEM . . . F 2 125.641 114.916 98.635 1 34.65 ? C3B HEM 901 B 1 HETATM 18 C C4B HEM . . . F 2 126.247 113.772 98 1 33.33 ? C4B HEM 901 B 1 HETATM 19 C CMB HEM . . . F 2 126.292 117.369 98.933 1 36.29 ? CMB HEM 901 B 1 HETATM 20 C CAB HEM . . . F 2 124.435 115.079 99.31 1 38.45 ? CAB HEM 901 B 1 HETATM 21 C CBB HEM . . . F 2 123.603 114.115 99.901 1 40.31 ? CBB HEM 901 B 1 HETATM 22 C C1C HEM . . . F 2 126.327 111.333 97.397 1 32.11 ? C1C HEM 901 B 1 HETATM 23 C C2C HEM . . . F 2 125.73 110.007 97.407 1 31.2 ? C2C HEM 901 B 1 HETATM 24 C C3C HEM . . . F 2 126.666 109.128 96.92 1 31.66 ? C3C HEM 901 B 1 HETATM 25 C C4C HEM . . . F 2 127.783 109.959 96.579 1 32.81 ? C4C HEM 901 B 1 HETATM 26 C CMC HEM . . . F 2 124.286 109.757 97.8 1 28.56 ? CMC HEM 901 B 1 HETATM 27 C CAC HEM . . . F 2 126.638 107.759 96.74 1 32.18 ? CAC HEM 901 B 1 HETATM 28 C CBC HEM . . . F 2 125.588 106.925 97.089 1 32.8 ? CBC HEM 901 B 1 HETATM 29 C C1D HEM . . . F 2 129.973 110.323 95.421 1 32.88 ? C1D HEM 901 B 1 HETATM 30 C C2D HEM . . . F 2 131.075 109.865 94.588 1 33.75 ? C2D HEM 901 B 1 HETATM 31 C C3D HEM . . . F 2 131.751 110.958 94.179 1 33.86 ? C3D HEM 901 B 1 HETATM 32 C C4D HEM . . . F 2 131.088 112.074 94.764 1 34.18 ? C4D HEM 901 B 1 HETATM 33 C CMD HEM . . . F 2 131.363 108.432 94.153 1 32.4 ? CMD HEM 901 B 1 HETATM 34 C CAD HEM . . . F 2 132.795 111.034 93.103 1 34.68 ? CAD HEM 901 B 1 HETATM 35 C CBD HEM . . . F 2 132.14 111.027 91.73 1 36.65 ? CBD HEM 901 B 1 HETATM 36 C CGD HEM . . . F 2 133.008 111.686 90.675 1 39.8 ? CGD HEM 901 B 1 HETATM 37 O O1D HEM . . . F 2 132.512 112.594 89.976 1 45.43 ? O1D HEM 901 B 1 HETATM 38 O O2D HEM . . . F 2 134.2 111.323 90.567 1 36.01 ? O2D HEM 901 B 1 HETATM 39 N NA HEM . . . F 2 129.833 114.498 95.986 1 33.12 ? NA HEM 901 B 1 HETATM 40 N NB HEM . . . F 2 127.418 114.098 97.421 1 33.03 ? NB HEM 901 B 1 HETATM 41 N NC HEM . . . F 2 127.56 111.289 96.876 1 31.55 ? NC HEM 901 B 1 HETATM 42 N ND HEM . . . F 2 130.028 111.686 95.526 1 32.86 ? ND HEM 901 B 1 HETATM 43 FE FE HEM . . . F 2 128.871 112.867 96.732 1 38.08 ? FE HEM 901 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 51 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #