data_3G93 # _model_server_result.job_id 8dDCDwO5ZnK21IoESEjnMw _model_server_result.datetime_utc '2025-02-17 14:07:16' _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 3g93 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":500}' # _entry.id 3G93 # _exptl.entry_id 3G93 _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 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 90 _cell.entry_id 3G93 _cell.length_a 86.91 _cell.length_b 151.815 _cell.length_c 181.583 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3G93 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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 tetrameric 4 software_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 ? monomeric 1 author_defined_assembly 5 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression C,I,J,O 1 1 D,K,L,P 1 2 A,B,E,F,G,H,M,N 1 3 A,E,F,G,M 2 3 B,H,N 3 3 C,I,J,O 4 3 D,K,L,P 5 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 'crystal symmetry operation' 2_655 -x+3/2,-y,z+1/2 -1 0 0 0 -1 0 0 0 1 130.365 0 90.7915 2 'crystal symmetry operation' 3_645 -x+1,y-1/2,-z+1/2 -1 0 0 0 1 0 0 0 -1 86.91 -75.9075 90.7915 3 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 H N N ? 2 I N N ? 2 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 417 A CYS 436 1_555 E FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc2 G NAD PB2 . A PB2 496 1_555 H FE HEM . B HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc3 E FE HEM . A HEM 500 1_555 F NAD PB2 . A PB2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc4 B SG CYS 417 B CYS 436 1_555 H FE HEM . B HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc5 C SG CYS 417 C CYS 436 1_555 I FE HEM . C HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc6 I FE HEM . C HEM 500 1_555 J NAD PB2 . C PB2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.867 ? metalc ? metalc7 D SG CYS 417 D CYS 436 1_555 K FE HEM . D HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc8 K FE HEM . D HEM 500 1_555 L NAD PB2 . D PB2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? # _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 3G93 _atom_sites.fract_transf_matrix[1][1] 0.011506 _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] 0.006587 _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] 0.005507 _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 2 HEM A 1 500 500 HEM HEM . F 3 PB2 A 1 501 501 PB2 PB2 . G 3 PB2 A 1 496 496 PB2 PB2 . H 2 HEM B 1 500 500 HEM HEM . I 2 HEM C 1 500 500 HEM HEM . J 3 PB2 C 1 501 501 PB2 PB2 . K 2 HEM D 1 500 500 HEM HEM . L 3 PB2 D 1 501 501 PB2 PB2 . M 4 HOH A 1 3 3 HOH HOH . M 4 HOH A 2 8 8 HOH HOH . M 4 HOH A 3 9 9 HOH HOH . M 4 HOH A 4 10 10 HOH HOH . M 4 HOH A 5 14 14 HOH HOH . M 4 HOH A 6 17 17 HOH HOH . M 4 HOH A 7 497 497 HOH HOH . M 4 HOH A 8 498 498 HOH HOH . M 4 HOH A 9 499 499 HOH HOH . N 4 HOH B 1 2 2 HOH HOH . N 4 HOH B 2 5 5 HOH HOH . N 4 HOH B 3 6 6 HOH HOH . N 4 HOH B 4 7 7 HOH HOH . N 4 HOH B 5 18 18 HOH HOH . N 4 HOH B 6 496 496 HOH HOH . N 4 HOH B 7 497 497 HOH HOH . N 4 HOH B 8 498 498 HOH HOH . N 4 HOH B 9 499 499 HOH HOH . O 4 HOH C 1 12 12 HOH HOH . O 4 HOH C 2 13 13 HOH HOH . O 4 HOH C 3 15 15 HOH HOH . O 4 HOH C 4 16 16 HOH HOH . O 4 HOH C 5 496 496 HOH HOH . O 4 HOH C 6 497 497 HOH HOH . O 4 HOH C 7 498 498 HOH HOH . O 4 HOH C 8 499 499 HOH HOH . O 4 HOH C 9 502 502 HOH HOH . O 4 HOH C 10 503 503 HOH HOH . O 4 HOH C 11 504 504 HOH HOH . O 4 HOH C 12 505 505 HOH HOH . O 4 HOH C 13 506 506 HOH HOH . P 4 HOH D 1 1 1 HOH HOH . P 4 HOH D 2 4 4 HOH HOH . P 4 HOH D 3 11 11 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 . . . E 2 38.824 7.185 37.694 1 24.29 ? CHA HEM 500 A 1 HETATM 2 C CHB HEM . . . E 2 41.571 6.632 33.961 1 20.06 ? CHB HEM 500 A 1 HETATM 3 C CHC HEM . . . E 2 38.295 7.981 30.909 1 18.18 ? CHC HEM 500 A 1 HETATM 4 C CHD HEM . . . E 2 35.375 8.31 34.631 1 18.3 ? CHD HEM 500 A 1 HETATM 5 C C1A HEM . . . E 2 39.852 6.944 36.864 1 29.7 ? C1A HEM 500 A 1 HETATM 6 C C2A HEM . . . E 2 41.145 6.53 37.316 1 23.13 ? C2A HEM 500 A 1 HETATM 7 C C3A HEM . . . E 2 41.876 6.376 36.279 1 20.59 ? C3A HEM 500 A 1 HETATM 8 C C4A HEM . . . E 2 41.075 6.699 35.168 1 18.13 ? C4A HEM 500 A 1 HETATM 9 C CMA HEM . . . E 2 43.336 5.95 36.256 1 14.2 ? CMA HEM 500 A 1 HETATM 10 C CAA HEM . . . E 2 41.61 6.303 38.743 1 24.65 ? CAA HEM 500 A 1 HETATM 11 C CBA HEM . . . E 2 41.059 5.014 39.254 1 29.39 ? CBA HEM 500 A 1 HETATM 12 C CGA HEM . . . E 2 41.903 4.659 40.403 1 36.6 ? CGA HEM 500 A 1 HETATM 13 O O1A HEM . . . E 2 41.924 5.404 41.368 1 32.56 ? O1A HEM 500 A 1 HETATM 14 O O2A HEM . . . E 2 42.556 3.623 40.359 1 39.61 ? O2A HEM 500 A 1 HETATM 15 C C1B HEM . . . E 2 40.873 6.949 32.888 1 27.07 ? C1B HEM 500 A 1 HETATM 16 C C2B HEM . . . E 2 41.472 6.798 31.625 1 25.23 ? C2B HEM 500 A 1 HETATM 17 C C3B HEM . . . E 2 40.636 7.153 30.742 1 20.64 ? C3B HEM 500 A 1 HETATM 18 C C4B HEM . . . E 2 39.435 7.533 31.445 1 24.15 ? C4B HEM 500 A 1 HETATM 19 C CMB HEM . . . E 2 42.878 6.302 31.341 1 23.59 ? CMB HEM 500 A 1 HETATM 20 C CAB HEM . . . E 2 41.072 7.076 29.283 1 23.39 ? CAB HEM 500 A 1 HETATM 21 C CBB HEM . . . E 2 40.284 7.404 28.281 1 27.58 ? CBB HEM 500 A 1 HETATM 22 C C1C HEM . . . E 2 37.247 8.148 31.741 1 26.56 ? C1C HEM 500 A 1 HETATM 23 C C2C HEM . . . E 2 35.938 8.487 31.288 1 29.67 ? C2C HEM 500 A 1 HETATM 24 C C3C HEM . . . E 2 35.164 8.558 32.301 1 29.35 ? C3C HEM 500 A 1 HETATM 25 C C4C HEM . . . E 2 35.942 8.283 33.441 1 21.69 ? C4C HEM 500 A 1 HETATM 26 C CMC HEM . . . E 2 35.45 8.709 29.873 1 32.15 ? CMC HEM 500 A 1 HETATM 27 C CAC HEM . . . E 2 33.692 8.896 32.255 1 22.36 ? CAC HEM 500 A 1 HETATM 28 C CBC HEM . . . E 2 32.97 8.62 33.324 1 25.94 ? CBC HEM 500 A 1 HETATM 29 C C1D HEM . . . E 2 36.057 8.035 35.746 1 30.79 ? C1D HEM 500 A 1 HETATM 30 C C2D HEM . . . E 2 35.426 8.053 37.034 1 30.52 ? C2D HEM 500 A 1 HETATM 31 C C3D HEM . . . E 2 36.494 7.692 38 1 18.24 ? C3D HEM 500 A 1 HETATM 32 C C4D HEM . . . E 2 37.639 7.504 37.178 1 26.26 ? C4D HEM 500 A 1 HETATM 33 C CMD HEM . . . E 2 33.97 8.364 37.358 1 22.28 ? CMD HEM 500 A 1 HETATM 34 C CAD HEM . . . E 2 36.307 7.575 39.501 1 22.33 ? CAD HEM 500 A 1 HETATM 35 C CBD HEM . . . E 2 37.409 6.766 40.123 1 43.74 ? CBD HEM 500 A 1 HETATM 36 C CGD HEM . . . E 2 36.922 6.26 41.428 1 29.35 ? CGD HEM 500 A 1 HETATM 37 O O1D HEM . . . E 2 35.795 5.79 41.48 1 23.04 ? O1D HEM 500 A 1 HETATM 38 O O2D HEM . . . E 2 37.663 6.303 42.405 1 16.94 ? O2D HEM 500 A 1 HETATM 39 N NA HEM . . . E 2 39.803 7.067 35.488 1 25.37 ? NA HEM 500 A 1 HETATM 40 N NB HEM . . . E 2 39.586 7.393 32.813 1 28.2 ? NB HEM 500 A 1 HETATM 41 N NC HEM . . . E 2 37.241 8.003 33.12 1 23.89 ? NC HEM 500 A 1 HETATM 42 N ND HEM . . . E 2 37.39 7.7 35.816 1 34.76 ? ND HEM 500 A 1 HETATM 43 FE FE HEM . . . E 2 38.352 7.386 34.264 1 22.57 ? FE HEM 500 A 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 43 #