data_3G93 # _model_server_result.job_id jwaQUbV46bh907VqeU9lNA _model_server_result.datetime_utc '2024-10-18 05:20:17' _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":"H","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 . . . H 2 56.395 34.028 58.308 1 25.44 ? CHA HEM 500 B 1 HETATM 2 C CHB HEM . . . H 2 54.904 38.043 56.447 1 18.52 ? CHB HEM 500 B 1 HETATM 3 C CHC HEM . . . H 2 59.186 39.092 54.947 1 16.28 ? CHC HEM 500 B 1 HETATM 4 C CHD HEM . . . H 2 60.748 35.14 56.825 1 24 ? CHD HEM 500 B 1 HETATM 5 C C1A HEM . . . H 2 55.656 35.063 57.874 1 25.02 ? C1A HEM 500 B 1 HETATM 6 C C2A HEM . . . H 2 54.243 35.123 58.054 1 31.63 ? C2A HEM 500 B 1 HETATM 7 C C3A HEM . . . H 2 53.847 36.233 57.541 1 32.26 ? C3A HEM 500 B 1 HETATM 8 C C4A HEM . . . H 2 54.991 36.879 57.042 1 18.18 ? C4A HEM 500 B 1 HETATM 9 C CMA HEM . . . H 2 52.416 36.764 57.486 1 24.4 ? CMA HEM 500 B 1 HETATM 10 C CAA HEM . . . H 2 53.341 34.084 58.721 1 35.34 ? CAA HEM 500 B 1 HETATM 11 C CBA HEM . . . H 2 53.388 34.03 60.231 1 27.6 ? CBA HEM 500 B 1 HETATM 12 C CGA HEM . . . H 2 52.498 32.886 60.507 1 51.69 ? CGA HEM 500 B 1 HETATM 13 O O1A HEM . . . H 2 52.916 31.762 60.253 1 44.25 ? O1A HEM 500 B 1 HETATM 14 O O2A HEM . . . H 2 51.359 33.078 60.948 1 42.67 ? O2A HEM 500 B 1 HETATM 15 C C1B HEM . . . H 2 55.983 38.606 55.933 1 17.93 ? C1B HEM 500 B 1 HETATM 16 C C2B HEM . . . H 2 55.895 39.915 55.378 1 16.73 ? C2B HEM 500 B 1 HETATM 17 C C3B HEM . . . H 2 57.078 40.187 54.963 1 19 ? C3B HEM 500 B 1 HETATM 18 C C4B HEM . . . H 2 57.909 39.081 55.261 1 20.83 ? C4B HEM 500 B 1 HETATM 19 C CMB HEM . . . H 2 54.672 40.823 55.269 1 7.46 ? CMB HEM 500 B 1 HETATM 20 C CAB HEM . . . H 2 57.511 41.477 54.309 1 18.18 ? CAB HEM 500 B 1 HETATM 21 C CBB HEM . . . H 2 56.612 42.442 54.248 1 27.44 ? CBB HEM 500 B 1 HETATM 22 C C1C HEM . . . H 2 59.903 38.097 55.416 1 19.52 ? C1C HEM 500 B 1 HETATM 23 C C2C HEM . . . H 2 61.319 38.136 55.34 1 20.68 ? C2C HEM 500 B 1 HETATM 24 C C3C HEM . . . H 2 61.736 37.062 55.863 1 26.47 ? C3C HEM 500 B 1 HETATM 25 C C4C HEM . . . H 2 60.595 36.327 56.271 1 22.53 ? C4C HEM 500 B 1 HETATM 26 C CMC HEM . . . H 2 62.228 39.218 54.786 1 23.43 ? CMC HEM 500 B 1 HETATM 27 C CAC HEM . . . H 2 63.196 36.7 56.015 1 41.24 ? CAC HEM 500 B 1 HETATM 28 C CBC HEM . . . H 2 63.494 35.818 56.952 1 35.98 ? CBC HEM 500 B 1 HETATM 29 C C1D HEM . . . H 2 59.701 34.503 57.343 1 28.53 ? C1D HEM 500 B 1 HETATM 30 C C2D HEM . . . H 2 59.849 33.209 57.882 1 24.24 ? C2D HEM 500 B 1 HETATM 31 C C3D HEM . . . H 2 58.485 32.855 58.374 1 23.13 ? C3D HEM 500 B 1 HETATM 32 C C4D HEM . . . H 2 57.693 33.982 58.036 1 20.38 ? C4D HEM 500 B 1 HETATM 33 C CMD HEM . . . H 2 61.134 32.412 57.933 1 19.05 ? CMD HEM 500 B 1 HETATM 34 C CAD HEM . . . H 2 58.074 31.556 59.055 1 30.82 ? CAD HEM 500 B 1 HETATM 35 C CBD HEM . . . H 2 56.809 31.7 59.857 1 44.03 ? CBD HEM 500 B 1 HETATM 36 C CGD HEM . . . H 2 57.033 30.89 61.082 1 52.46 ? CGD HEM 500 B 1 HETATM 37 O O1D HEM . . . H 2 58.194 30.683 61.427 1 51.66 ? O1D HEM 500 B 1 HETATM 38 O O2D HEM . . . H 2 56.077 30.466 61.731 1 54.22 ? O2D HEM 500 B 1 HETATM 39 N NA HEM . . . H 2 56.145 36.185 57.24 1 18.61 ? NA HEM 500 B 1 HETATM 40 N NB HEM . . . H 2 57.246 38.073 55.879 1 19.7 ? NB HEM 500 B 1 HETATM 41 N NC HEM . . . H 2 59.418 36.966 56.003 1 19.6 ? NC HEM 500 B 1 HETATM 42 N ND HEM . . . H 2 58.414 34.996 57.418 1 27.83 ? ND HEM 500 B 1 HETATM 43 FE FE HEM . . . H 2 57.989 36.815 56.603 1 20.11 ? FE HEM 500 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 260 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 43 #