data_3P5Q # _model_server_result.job_id g4TyMS8moSJAAYHZrE8IsQ _model_server_result.datetime_utc '2024-11-05 00:06:15' _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 3p5q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":142}' # _entry.id 3P5Q # _exptl.entry_id 3P5Q _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 3 _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 90 _cell.entry_id 3P5Q _cell.length_a 53.546 _cell.length_b 53.546 _cell.length_c 192.76 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3P5Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 7_555 y,x,-z 0 1 0 1 0 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 ? 3 C N N ? 3 G 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 NE2 HIS 87 A HIS 87 1_555 C FE HEM . A HEM 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc2 C FE HEM . A HEM 142 1_555 H O HOH . A HOH 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc3 B NE2 HIS 92 B HIS 92 1_555 G FE HEM . B HEM 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc4 G FE HEM . B HEM 147 1_555 I O HOH . B HOH 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? # _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 3P5Q _atom_sites.fract_transf_matrix[1][1] 0.018676 _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] 0.018676 _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] 0.005188 _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 3 HEM A 1 142 142 HEM HEM . D 4 MBN A 1 143 1 MBN MBN . E 4 MBN A 1 144 2 MBN MBN . F 4 MBN A 1 145 3 MBN MBN . G 3 HEM B 1 147 147 HEM HEM . H 5 HOH A 1 146 3 HOH HOH . H 5 HOH A 2 147 4 HOH HOH . H 5 HOH A 3 148 5 HOH HOH . H 5 HOH A 4 149 6 HOH HOH . H 5 HOH A 5 150 7 HOH HOH . H 5 HOH A 6 151 8 HOH HOH . H 5 HOH A 7 152 9 HOH HOH . H 5 HOH A 8 153 10 HOH HOH . H 5 HOH A 9 154 12 HOH HOH . H 5 HOH A 10 155 13 HOH HOH . H 5 HOH A 11 156 15 HOH HOH . H 5 HOH A 12 157 18 HOH HOH . H 5 HOH A 13 158 21 HOH HOH . H 5 HOH A 14 159 22 HOH HOH . H 5 HOH A 15 160 23 HOH HOH . H 5 HOH A 16 161 24 HOH HOH . H 5 HOH A 17 162 25 HOH HOH . H 5 HOH A 18 163 26 HOH HOH . H 5 HOH A 19 164 27 HOH HOH . H 5 HOH A 20 165 29 HOH HOH . H 5 HOH A 21 166 30 HOH HOH . H 5 HOH A 22 167 31 HOH HOH . H 5 HOH A 23 168 34 HOH HOH . H 5 HOH A 24 169 35 HOH HOH . H 5 HOH A 25 170 36 HOH HOH . H 5 HOH A 26 171 41 HOH HOH . H 5 HOH A 27 172 42 HOH HOH . H 5 HOH A 28 173 43 HOH HOH . H 5 HOH A 29 174 44 HOH HOH . H 5 HOH A 30 175 47 HOH HOH . H 5 HOH A 31 176 49 HOH HOH . H 5 HOH A 32 177 50 HOH HOH . H 5 HOH A 33 178 52 HOH HOH . H 5 HOH A 34 179 54 HOH HOH . H 5 HOH A 35 180 55 HOH HOH . H 5 HOH A 36 181 57 HOH HOH . H 5 HOH A 37 182 58 HOH HOH . H 5 HOH A 38 183 59 HOH HOH . H 5 HOH A 39 184 60 HOH HOH . H 5 HOH A 40 185 61 HOH HOH . H 5 HOH A 41 186 62 HOH HOH . H 5 HOH A 42 187 66 HOH HOH . H 5 HOH A 43 188 69 HOH HOH . H 5 HOH A 44 189 70 HOH HOH . H 5 HOH A 45 190 71 HOH HOH . H 5 HOH A 46 191 72 HOH HOH . H 5 HOH A 47 192 74 HOH HOH . H 5 HOH A 48 193 76 HOH HOH . H 5 HOH A 49 194 80 HOH HOH . H 5 HOH A 50 195 81 HOH HOH . H 5 HOH A 51 196 82 HOH HOH . H 5 HOH A 52 197 83 HOH HOH . H 5 HOH A 53 198 84 HOH HOH . H 5 HOH A 54 199 85 HOH HOH . H 5 HOH A 55 200 86 HOH HOH . H 5 HOH A 56 201 88 HOH HOH . H 5 HOH A 57 202 89 HOH HOH . H 5 HOH A 58 203 90 HOH HOH . H 5 HOH A 59 204 92 HOH HOH . H 5 HOH A 60 205 93 HOH HOH . H 5 HOH A 61 206 94 HOH HOH . H 5 HOH A 62 207 95 HOH HOH . H 5 HOH A 63 208 100 HOH HOH . H 5 HOH A 64 209 102 HOH HOH . I 5 HOH B 1 148 1 HOH HOH . I 5 HOH B 2 149 2 HOH HOH . I 5 HOH B 3 150 11 HOH HOH . I 5 HOH B 4 151 14 HOH HOH . I 5 HOH B 5 152 16 HOH HOH . I 5 HOH B 6 153 17 HOH HOH . I 5 HOH B 7 154 19 HOH HOH . I 5 HOH B 8 155 20 HOH HOH . I 5 HOH B 9 156 28 HOH HOH . I 5 HOH B 10 157 32 HOH HOH . I 5 HOH B 11 158 33 HOH HOH . I 5 HOH B 12 159 37 HOH HOH . I 5 HOH B 13 160 38 HOH HOH . I 5 HOH B 14 161 39 HOH HOH . I 5 HOH B 15 162 40 HOH HOH . I 5 HOH B 16 163 45 HOH HOH . I 5 HOH B 17 164 46 HOH HOH . I 5 HOH B 18 165 48 HOH HOH . I 5 HOH B 19 166 51 HOH HOH . I 5 HOH B 20 167 53 HOH HOH . I 5 HOH B 21 168 56 HOH HOH . I 5 HOH B 22 169 63 HOH HOH . I 5 HOH B 23 170 64 HOH HOH . I 5 HOH B 24 171 65 HOH HOH . I 5 HOH B 25 172 67 HOH HOH . I 5 HOH B 26 173 68 HOH HOH . I 5 HOH B 27 174 73 HOH HOH . I 5 HOH B 28 175 75 HOH HOH . I 5 HOH B 29 176 77 HOH HOH . I 5 HOH B 30 177 78 HOH HOH . I 5 HOH B 31 178 79 HOH HOH . I 5 HOH B 32 179 87 HOH HOH . I 5 HOH B 33 180 91 HOH HOH . I 5 HOH B 34 181 96 HOH HOH . I 5 HOH B 35 182 97 HOH HOH . I 5 HOH B 36 183 98 HOH HOH . I 5 HOH B 37 184 99 HOH HOH . I 5 HOH B 38 185 101 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 . . . C 3 16.449 1.031 16.865 1 29.62 ? CHA HEM 142 A 1 HETATM 2 C CHB HEM . . . C 3 14.099 5.245 16.163 1 24.65 ? CHB HEM 142 A 1 HETATM 3 C CHC HEM . . . C 3 10.937 3.117 13.157 1 25.69 ? CHC HEM 142 A 1 HETATM 4 C CHD HEM . . . C 3 12.757 -1.184 14.558 1 24.7 ? CHD HEM 142 A 1 HETATM 5 C C1A HEM . . . C 3 16.115 2.373 16.918 1 27.06 ? C1A HEM 142 A 1 HETATM 6 C C2A HEM . . . C 3 16.831 3.416 17.623 1 28.44 ? C2A HEM 142 A 1 HETATM 7 C C3A HEM . . . C 3 16.181 4.578 17.441 1 31.86 ? C3A HEM 142 A 1 HETATM 8 C C4A HEM . . . C 3 15.028 4.317 16.6 1 28.32 ? C4A HEM 142 A 1 HETATM 9 C CMA HEM . . . C 3 16.571 5.97 18.01 1 27.73 ? CMA HEM 142 A 1 HETATM 10 C CAA HEM . . . C 3 18.118 3.205 18.444 1 29.43 ? CAA HEM 142 A 1 HETATM 11 C CBA HEM . . . C 3 17.881 2.427 19.727 1 37.69 ? CBA HEM 142 A 1 HETATM 12 C CGA HEM . . . C 3 19.196 2.22 20.45 1 45.49 ? CGA HEM 142 A 1 HETATM 13 O O1A HEM . . . C 3 19.179 1.622 21.56 1 45.71 ? O1A HEM 142 A 1 HETATM 14 O O2A HEM . . . C 3 20.269 2.641 19.926 1 51.26 ? O2A HEM 142 A 1 HETATM 15 C C1B HEM . . . C 3 13.07 5.063 15.258 1 26.77 ? C1B HEM 142 A 1 HETATM 16 C C2B HEM . . . C 3 12.19 6.094 14.733 1 25.59 ? C2B HEM 142 A 1 HETATM 17 C C3B HEM . . . C 3 11.328 5.512 13.885 1 25.39 ? C3B HEM 142 A 1 HETATM 18 C C4B HEM . . . C 3 11.597 4.081 13.887 1 25.4 ? C4B HEM 142 A 1 HETATM 19 C CMB HEM . . . C 3 12.32 7.6 15.058 1 25.83 ? CMB HEM 142 A 1 HETATM 20 C CAB HEM . . . C 3 10.185 6.146 13.057 1 23.35 ? CAB HEM 142 A 1 HETATM 21 C CBB HEM . . . C 3 9.618 7.288 13.427 1 26.91 ? CBB HEM 142 A 1 HETATM 22 C C1C HEM . . . C 3 11.132 1.753 13.323 1 24.83 ? C1C HEM 142 A 1 HETATM 23 C C2C HEM . . . C 3 10.263 0.723 12.81 1 25.57 ? C2C HEM 142 A 1 HETATM 24 C C3C HEM . . . C 3 10.772 -0.47 13.188 1 27.12 ? C3C HEM 142 A 1 HETATM 25 C C4C HEM . . . C 3 11.963 -0.22 13.974 1 25.74 ? C4C HEM 142 A 1 HETATM 26 C CMC HEM . . . C 3 9.015 1.03 11.952 1 24.28 ? CMC HEM 142 A 1 HETATM 27 C CAC HEM . . . C 3 10.215 -1.885 12.915 1 25.54 ? CAC HEM 142 A 1 HETATM 28 C CBC HEM . . . C 3 8.896 -2.085 12.987 1 24.33 ? CBC HEM 142 A 1 HETATM 29 C C1D HEM . . . C 3 13.894 -1.018 15.31 1 27.42 ? C1D HEM 142 A 1 HETATM 30 C C2D HEM . . . C 3 14.657 -2.094 15.893 1 28.61 ? C2D HEM 142 A 1 HETATM 31 C C3D HEM . . . C 3 15.826 -1.419 16.613 1 30.27 ? C3D HEM 142 A 1 HETATM 32 C C4D HEM . . . C 3 15.644 0.006 16.401 1 27.88 ? C4D HEM 142 A 1 HETATM 33 C CMD HEM . . . C 3 14.334 -3.601 15.785 1 26.94 ? CMD HEM 142 A 1 HETATM 34 C CAD HEM . . . C 3 16.939 -2.128 17.422 1 28.55 ? CAD HEM 142 A 1 HETATM 35 C CBD HEM . . . C 3 16.368 -2.151 18.831 1 29.56 ? CBD HEM 142 A 1 HETATM 36 C CGD HEM . . . C 3 17.214 -2.978 19.749 1 37.58 ? CGD HEM 142 A 1 HETATM 37 O O1D HEM . . . C 3 17.413 -2.534 20.893 1 38.51 ? O1D HEM 142 A 1 HETATM 38 O O2D HEM . . . C 3 17.676 -4.078 19.353 1 43.54 ? O2D HEM 142 A 1 HETATM 39 N NA HEM . . . C 3 15.029 2.962 16.314 1 28.28 ? NA HEM 142 A 1 HETATM 40 N NB HEM . . . C 3 12.659 3.848 14.723 1 25.25 ? NB HEM 142 A 1 HETATM 41 N NC HEM . . . C 3 12.149 1.145 14.035 1 23.47 ? NC HEM 142 A 1 HETATM 42 N ND HEM . . . C 3 14.509 0.184 15.636 1 29.08 ? ND HEM 142 A 1 HETATM 43 FE FE HEM . . . C 3 13.603 2.046 15.166 1 28.24 ? FE HEM 142 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 347 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 43 #