data_1RTX # _model_server_result.job_id S-PMLv4QnttFlM93OoLiOA _model_server_result.datetime_utc '2024-11-29 21:22:48' _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 1rtx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":125}' # _entry.id 1RTX # _exptl.entry_id 1RTX _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 1 _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 1RTX _cell.length_a 42.5 _cell.length_b 46 _cell.length_c 61 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1RTX _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 OD1 ASP 14 A ASP 15 3_555 B CD CD . A CD 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? metalc ? metalc2 A OD2 ASP 14 A ASP 15 3_555 B CD CD . A CD 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc3 A OD2 ASP 18 A ASP 19 3_555 B CD CD . A CD 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc4 A ND1 HIS 32 A HIS 33 1_555 B CD CD . A CD 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? metalc ? metalc5 A O HIS 32 A HIS 33 1_555 B CD CD . A CD 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? metalc ? metalc6 A NE2 HIS 45 A HIS 46 1_555 F FE HEM . A HEM 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? metalc ? metalc7 A NE2 HIS 69 A HIS 70 1_555 F FE HEM . A HEM 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc8 A OE1 GLU 71 A GLU 72 4_555 C CD CD . A CD 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? metalc ? metalc9 A OE2 GLU 71 A GLU 72 4_555 C CD CD . A CD 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc10 A ND1 HIS 76 A HIS 77 1_555 B CD CD . A CD 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc11 A OD2 ASP 119 A ASP 120 1_555 C CD CD . A CD 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.656 ? metalc ? metalc12 A OD1 ASP 119 A ASP 120 1_555 C CD CD . A CD 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc13 C CD CD . A CD 127 1_555 G O HOH . A HOH 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc14 C CD CD . A CD 127 1_555 G O HOH . A HOH 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc15 E K K . A K 129 1_555 G O HOH . A HOH 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.413 ? metalc ? metalc16 E K K . A K 129 1_555 G O HOH . A HOH 162 3_545 ? ? ? ? ? ? ? ? ? ? ? ? 3.519 ? metalc ? metalc17 E K K . A K 129 1_555 G O HOH . A HOH 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc18 E K K . A K 129 1_555 G O HOH . A HOH 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? # _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 116 n n CHA C4D HEM doub 117 n n CHA HHA HEM sing 118 n n CHB C4A HEM sing 119 n n CHB C1B HEM doub 120 n n CHB HHB HEM sing 121 n n CHC C4B HEM sing 122 n n CHC C1C HEM doub 123 n n CHC HHC HEM sing 124 n n CHD C4C HEM doub 125 n n CHD C1D HEM sing 126 n n CHD HHD HEM sing 127 n n C1A C2A HEM doub 128 n y C1A NA HEM sing 129 n y C2A C3A HEM sing 130 n y C2A CAA HEM sing 131 n n C3A C4A HEM doub 132 n y C3A CMA HEM sing 133 n n C4A NA HEM sing 134 n y CMA HMA HEM sing 135 n n CMA HMAA HEM sing 136 n n CMA HMAB HEM sing 137 n n CAA CBA HEM sing 138 n n CAA HAA HEM sing 139 n n CAA HAAA HEM sing 140 n n CBA CGA HEM sing 141 n n CBA HBA HEM sing 142 n n CBA HBAA HEM sing 143 n n CGA O1A HEM doub 144 n n CGA O2A HEM sing 145 n n C1B C2B HEM sing 146 n n C1B NB HEM sing 147 n n C2B C3B HEM doub 148 n n C2B CMB HEM sing 149 n n C3B C4B HEM sing 150 n n C3B CAB HEM sing 151 n n C4B NB HEM doub 152 n n CMB HMB HEM sing 153 n n CMB HMBA HEM sing 154 n n CMB HMBB HEM sing 155 n n CAB CBB HEM doub 156 n n CAB HAB HEM sing 157 n n CBB HBB HEM sing 158 n n CBB HBBA HEM sing 159 n n C1C C2C HEM sing 160 n y C1C NC HEM sing 161 n y C2C C3C HEM doub 162 n y C2C CMC HEM sing 163 n n C3C C4C HEM sing 164 n y C3C CAC HEM sing 165 n n C4C NC HEM sing 166 n y CMC HMC HEM sing 167 n n CMC HMCA HEM sing 168 n n CMC HMCB HEM sing 169 n n CAC CBC HEM doub 170 n n CAC HAC HEM sing 171 n n CBC HBC HEM sing 172 n n CBC HBCA HEM sing 173 n n C1D C2D HEM sing 174 n n C1D ND HEM doub 175 n n C2D C3D HEM doub 176 n n C2D CMD HEM sing 177 n n C3D C4D HEM sing 178 n n C3D CAD HEM sing 179 n n C4D ND HEM sing 180 n n CMD HMD HEM sing 181 n n CMD HMDA HEM sing 182 n n CMD HMDB HEM sing 183 n n CAD CBD HEM sing 184 n n CAD HAD HEM sing 185 n n CAD HADA HEM sing 186 n n CBD CGD HEM sing 187 n n CBD HBD HEM sing 188 n n CBD HBDA HEM sing 189 n n CGD O1D HEM doub 190 n n CGD O2D HEM sing 191 n n O2A H2A HEM sing 192 n n O2D H2D HEM sing 193 n n FE NA HEM sing 194 n n FE NB HEM sing 195 n n FE NC HEM sing 196 n n FE ND HEM sing 197 n n # _atom_sites.entry_id 1RTX _atom_sites.fract_transf_matrix[1][1] 0.023529 _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] 0.021739 _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] 0.016393 _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 B 2 CD A 1 126 126 CD CD . C 2 CD A 1 127 127 CD CD . D 3 SO4 A 1 128 128 SO4 SO4 . E 4 K A 1 129 129 K K . F 5 HEM A 1 125 125 HEM HEM . G 6 HOH A 1 130 1 HOH HOH . G 6 HOH A 2 131 2 HOH HOH . G 6 HOH A 3 132 3 HOH HOH . G 6 HOH A 4 133 4 HOH HOH . G 6 HOH A 5 134 5 HOH HOH . G 6 HOH A 6 135 6 HOH HOH . G 6 HOH A 7 136 7 HOH HOH . G 6 HOH A 8 137 8 HOH HOH . G 6 HOH A 9 138 9 HOH HOH . G 6 HOH A 10 139 10 HOH HOH . G 6 HOH A 11 140 11 HOH HOH . G 6 HOH A 12 141 12 HOH HOH . G 6 HOH A 13 142 13 HOH HOH . G 6 HOH A 14 143 14 HOH HOH . G 6 HOH A 15 144 15 HOH HOH . G 6 HOH A 16 145 16 HOH HOH . G 6 HOH A 17 146 17 HOH HOH . G 6 HOH A 18 147 18 HOH HOH . G 6 HOH A 19 148 19 HOH HOH . G 6 HOH A 20 149 20 HOH HOH . G 6 HOH A 21 150 21 HOH HOH . G 6 HOH A 22 151 22 HOH HOH . G 6 HOH A 23 152 23 HOH HOH . G 6 HOH A 24 153 24 HOH HOH . G 6 HOH A 25 154 25 HOH HOH . G 6 HOH A 26 155 26 HOH HOH . G 6 HOH A 27 156 27 HOH HOH . G 6 HOH A 28 157 28 HOH HOH . G 6 HOH A 29 158 29 HOH HOH . G 6 HOH A 30 159 30 HOH HOH . G 6 HOH A 31 160 31 HOH HOH . G 6 HOH A 32 161 32 HOH HOH . G 6 HOH A 33 162 33 HOH HOH . G 6 HOH A 34 163 34 HOH HOH . G 6 HOH A 35 164 35 HOH HOH . G 6 HOH A 36 165 36 HOH HOH . G 6 HOH A 37 166 37 HOH HOH . G 6 HOH A 38 167 38 HOH HOH . G 6 HOH A 39 168 39 HOH HOH . G 6 HOH A 40 169 40 HOH HOH . G 6 HOH A 41 170 41 HOH HOH . G 6 HOH A 42 171 42 HOH HOH . G 6 HOH A 43 172 43 HOH HOH . G 6 HOH A 44 173 44 HOH HOH . G 6 HOH A 45 174 45 HOH HOH . G 6 HOH A 46 175 46 HOH HOH . G 6 HOH A 47 176 47 HOH HOH . G 6 HOH A 48 177 48 HOH HOH . G 6 HOH A 49 178 49 HOH HOH . G 6 HOH A 50 179 50 HOH HOH . G 6 HOH A 51 180 51 HOH HOH . G 6 HOH A 52 181 52 HOH HOH . G 6 HOH A 53 182 53 HOH HOH . G 6 HOH A 54 183 54 HOH HOH . G 6 HOH A 55 184 55 HOH HOH . G 6 HOH A 56 185 56 HOH HOH . G 6 HOH A 57 186 57 HOH HOH . G 6 HOH A 58 187 58 HOH HOH . G 6 HOH A 59 188 59 HOH HOH . G 6 HOH A 60 189 60 HOH HOH . G 6 HOH A 61 190 61 HOH HOH . G 6 HOH A 62 191 62 HOH HOH . G 6 HOH A 63 192 63 HOH HOH . G 6 HOH A 64 193 64 HOH HOH . G 6 HOH A 65 194 65 HOH HOH . G 6 HOH A 66 195 66 HOH HOH . G 6 HOH A 67 196 67 HOH HOH . G 6 HOH A 68 197 68 HOH HOH . G 6 HOH A 69 198 69 HOH HOH . G 6 HOH A 70 199 70 HOH HOH . G 6 HOH A 71 200 71 HOH HOH . G 6 HOH A 72 201 72 HOH HOH . G 6 HOH A 73 202 73 HOH HOH . G 6 HOH A 74 203 74 HOH HOH . G 6 HOH A 75 204 75 HOH HOH . G 6 HOH A 76 205 76 HOH HOH . G 6 HOH A 77 206 77 HOH HOH . G 6 HOH A 78 207 78 HOH HOH . G 6 HOH A 79 208 79 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 5 4.745 6.536 5.982 1 26.98 ? CHA HEM 125 A 1 HETATM 2 C CHB HEM . . . F 5 9.351 5.68 6.515 1 27.23 ? CHB HEM 125 A 1 HETATM 3 C CHC HEM . . . F 5 9.66 9.171 9.665 1 22.29 ? CHC HEM 125 A 1 HETATM 4 C CHD HEM . . . F 5 5.029 9.791 9.402 1 26.19 ? CHD HEM 125 A 1 HETATM 5 C C1A HEM . . . F 5 6.029 5.978 5.785 1 26.55 ? C1A HEM 125 A 1 HETATM 6 C C2A HEM . . . F 5 6.282 4.908 4.851 1 27.24 ? C2A HEM 125 A 1 HETATM 7 C C3A HEM . . . F 5 7.595 4.648 5.006 1 28.23 ? C3A HEM 125 A 1 HETATM 8 C C4A HEM . . . F 5 8.031 5.577 6.036 1 28.35 ? C4A HEM 125 A 1 HETATM 9 C CMA HEM . . . F 5 8.384 3.534 4.343 1 31.5 ? CMA HEM 125 A 1 HETATM 10 C CAA HEM . . . F 5 5.309 4.26 3.902 1 28.37 ? CAA HEM 125 A 1 HETATM 11 C CBA HEM . . . F 5 4.352 3.212 4.465 1 34.34 ? CBA HEM 125 A 1 HETATM 12 C CGA HEM . . . F 5 3.594 2.685 3.294 1 35.49 ? CGA HEM 125 A 1 HETATM 13 O O1A HEM . . . F 5 3.771 3.204 2.15 1 39.61 ? O1A HEM 125 A 1 HETATM 14 O O2A HEM . . . F 5 2.829 1.713 3.486 1 36.8 ? O2A HEM 125 A 1 HETATM 15 C C1B HEM . . . F 5 9.923 6.556 7.466 1 26.72 ? C1B HEM 125 A 1 HETATM 16 C C2B HEM . . . F 5 11.319 6.57 7.852 1 22.32 ? C2B HEM 125 A 1 HETATM 17 C C3B HEM . . . F 5 11.399 7.579 8.73 1 21.49 ? C3B HEM 125 A 1 HETATM 18 C C4B HEM . . . F 5 10.062 8.123 8.798 1 22.16 ? C4B HEM 125 A 1 HETATM 19 C CMB HEM . . . F 5 12.403 5.657 7.34 1 25.42 ? CMB HEM 125 A 1 HETATM 20 C CAB HEM . . . F 5 12.494 8.059 9.47 1 25.31 ? CAB HEM 125 A 1 HETATM 21 C CBB HEM . . . F 5 13.329 7.196 10.202 1 24.89 ? CBB HEM 125 A 1 HETATM 22 C C1C HEM . . . F 5 8.392 9.727 9.908 1 23.94 ? C1C HEM 125 A 1 HETATM 23 C C2C HEM . . . F 5 8.123 10.792 10.855 1 23.3 ? C2C HEM 125 A 1 HETATM 24 C C3C HEM . . . F 5 6.796 10.945 10.814 1 25.04 ? C3C HEM 125 A 1 HETATM 25 C C4C HEM . . . F 5 6.358 9.976 9.833 1 25.79 ? C4C HEM 125 A 1 HETATM 26 C CMC HEM . . . F 5 9.151 11.477 11.693 1 25.62 ? CMC HEM 125 A 1 HETATM 27 C CAC HEM . . . F 5 6.007 11.858 11.511 1 25.62 ? CAC HEM 125 A 1 HETATM 28 C CBC HEM . . . F 5 4.816 11.466 12.073 1 30.23 ? CBC HEM 125 A 1 HETATM 29 C C1D HEM . . . F 5 4.458 8.939 8.414 1 25.53 ? C1D HEM 125 A 1 HETATM 30 C C2D HEM . . . F 5 3.054 8.921 8.003 1 28.34 ? C2D HEM 125 A 1 HETATM 31 C C3D HEM . . . F 5 2.972 7.989 7.017 1 28.55 ? C3D HEM 125 A 1 HETATM 32 C C4D HEM . . . F 5 4.35 7.549 6.878 1 26.3 ? C4D HEM 125 A 1 HETATM 33 C CMD HEM . . . F 5 1.892 9.661 8.622 1 32.64 ? CMD HEM 125 A 1 HETATM 34 C CAD HEM . . . F 5 1.757 7.543 6.221 1 31.9 ? CAD HEM 125 A 1 HETATM 35 C CBD HEM . . . F 5 0.863 6.45 6.82 1 37.27 ? CBD HEM 125 A 1 HETATM 36 C CGD HEM . . . F 5 0.085 5.799 5.692 1 40.42 ? CGD HEM 125 A 1 HETATM 37 O O1D HEM . . . F 5 0.226 4.549 5.495 1 40.94 ? O1D HEM 125 A 1 HETATM 38 O O2D HEM . . . F 5 -0.679 6.524 4.985 1 42.54 ? O2D HEM 125 A 1 HETATM 39 N NA HEM . . . F 5 7.086 6.473 6.546 1 26.61 ? NA HEM 125 A 1 HETATM 40 N NB HEM . . . F 5 9.079 7.477 8.083 1 25.01 ? NB HEM 125 A 1 HETATM 41 N NC HEM . . . F 5 7.32 9.187 9.236 1 23.86 ? NC HEM 125 A 1 HETATM 42 N ND HEM . . . F 5 5.318 8.106 7.716 1 25.54 ? ND HEM 125 A 1 HETATM 43 FE FE HEM . . . F 5 7.207 7.826 7.903 1 24.91 ? FE HEM 125 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #