data_1YCA # _model_server_result.job_id b-envp-jwWq9SyyA1rXU1A _model_server_result.datetime_utc '2024-11-23 21:17:59' _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 1yca # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":154}' # _entry.id 1YCA # _exptl.entry_id 1YCA _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 92.2 _cell.angle_gamma 90 _cell.entry_id 1YCA _cell.length_a 124.2 _cell.length_b 42.5 _cell.length_c 92.1 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YCA _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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,G 1 1 B,E,F,H 2 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 # 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 E 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 93 A HIS 93 1_555 C FE HEM . A HEM 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc2 C FE HEM . A HEM 154 1_555 D C CMO . A CMO 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.789 ? metalc ? metalc3 C FE HEM . A HEM 154 1_555 D O CMO . A CMO 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.006 ? metalc ? metalc4 B NE2 HIS 93 B HIS 93 1_555 E FE HEM . B HEM 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc5 E FE HEM . B HEM 154 1_555 F C CMO . B CMO 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.818 ? metalc ? metalc6 E FE HEM . B HEM 154 1_555 F O CMO . B CMO 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.984 ? # _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 117 n n CHA C4D HEM doub 118 n n CHA HHA HEM sing 119 n n CHB C4A HEM sing 120 n n CHB C1B HEM doub 121 n n CHB HHB HEM sing 122 n n CHC C4B HEM sing 123 n n CHC C1C HEM doub 124 n n CHC HHC HEM sing 125 n n CHD C4C HEM doub 126 n n CHD C1D HEM sing 127 n n CHD HHD HEM sing 128 n n C1A C2A HEM doub 129 n y C1A NA HEM sing 130 n y C2A C3A HEM sing 131 n y C2A CAA HEM sing 132 n n C3A C4A HEM doub 133 n y C3A CMA HEM sing 134 n n C4A NA HEM sing 135 n y CMA HMA HEM sing 136 n n CMA HMAA HEM sing 137 n n CMA HMAB HEM sing 138 n n CAA CBA HEM sing 139 n n CAA HAA HEM sing 140 n n CAA HAAA HEM sing 141 n n CBA CGA HEM sing 142 n n CBA HBA HEM sing 143 n n CBA HBAA HEM sing 144 n n CGA O1A HEM doub 145 n n CGA O2A HEM sing 146 n n C1B C2B HEM sing 147 n n C1B NB HEM sing 148 n n C2B C3B HEM doub 149 n n C2B CMB HEM sing 150 n n C3B C4B HEM sing 151 n n C3B CAB HEM sing 152 n n C4B NB HEM doub 153 n n CMB HMB HEM sing 154 n n CMB HMBA HEM sing 155 n n CMB HMBB HEM sing 156 n n CAB CBB HEM doub 157 n n CAB HAB HEM sing 158 n n CBB HBB HEM sing 159 n n CBB HBBA HEM sing 160 n n C1C C2C HEM sing 161 n y C1C NC HEM sing 162 n y C2C C3C HEM doub 163 n y C2C CMC HEM sing 164 n n C3C C4C HEM sing 165 n y C3C CAC HEM sing 166 n n C4C NC HEM sing 167 n y CMC HMC HEM sing 168 n n CMC HMCA HEM sing 169 n n CMC HMCB HEM sing 170 n n CAC CBC HEM doub 171 n n CAC HAC HEM sing 172 n n CBC HBC HEM sing 173 n n CBC HBCA HEM sing 174 n n C1D C2D HEM sing 175 n n C1D ND HEM doub 176 n n C2D C3D HEM doub 177 n n C2D CMD HEM sing 178 n n C3D C4D HEM sing 179 n n C3D CAD HEM sing 180 n n C4D ND HEM sing 181 n n CMD HMD HEM sing 182 n n CMD HMDA HEM sing 183 n n CMD HMDB HEM sing 184 n n CAD CBD HEM sing 185 n n CAD HAD HEM sing 186 n n CAD HADA HEM sing 187 n n CBD CGD HEM sing 188 n n CBD HBD HEM sing 189 n n CBD HBDA HEM sing 190 n n CGD O1D HEM doub 191 n n CGD O2D HEM sing 192 n n O2A H2A HEM sing 193 n n O2D H2D HEM sing 194 n n FE NA HEM sing 195 n n FE NB HEM sing 196 n n FE NC HEM sing 197 n n FE ND HEM sing 198 n n # _atom_sites.entry_id 1YCA _atom_sites.fract_transf_matrix[1][1] 0.008052 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000309 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.023529 _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] 0.010866 _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 1 154 154 HEM HEM . D 3 CMO A 1 155 154 CMO HEM . E 2 HEM B 1 154 154 HEM HEM . F 3 CMO B 1 155 154 CMO HEM . G 4 HOH A 1 156 1 HOH HOH . G 4 HOH A 2 157 2 HOH HOH . G 4 HOH A 3 158 3 HOH HOH . G 4 HOH A 4 159 4 HOH HOH . G 4 HOH A 5 160 11 HOH HOH . G 4 HOH A 6 161 1 HOH HOH . G 4 HOH A 7 162 2 HOH HOH . G 4 HOH A 8 163 3 HOH HOH . G 4 HOH A 9 164 4 HOH HOH . G 4 HOH A 10 165 5 HOH HOH . G 4 HOH A 11 166 6 HOH HOH . G 4 HOH A 12 167 7 HOH HOH . G 4 HOH A 13 168 8 HOH HOH . G 4 HOH A 14 169 9 HOH HOH . G 4 HOH A 15 170 10 HOH HOH . G 4 HOH A 16 171 11 HOH HOH . G 4 HOH A 17 172 12 HOH HOH . G 4 HOH A 18 173 13 HOH HOH . G 4 HOH A 19 174 14 HOH HOH . G 4 HOH A 20 175 15 HOH HOH . G 4 HOH A 21 176 16 HOH HOH . G 4 HOH A 22 177 17 HOH HOH . G 4 HOH A 23 178 18 HOH HOH . G 4 HOH A 24 179 19 HOH HOH . G 4 HOH A 25 180 20 HOH HOH . G 4 HOH A 26 181 21 HOH HOH . G 4 HOH A 27 182 22 HOH HOH . G 4 HOH A 28 183 23 HOH HOH . G 4 HOH A 29 184 24 HOH HOH . G 4 HOH A 30 185 25 HOH HOH . G 4 HOH A 31 186 26 HOH HOH . G 4 HOH A 32 187 27 HOH HOH . G 4 HOH A 33 188 28 HOH HOH . G 4 HOH A 34 189 29 HOH HOH . G 4 HOH A 35 190 30 HOH HOH . G 4 HOH A 36 191 31 HOH HOH . G 4 HOH A 37 192 32 HOH HOH . G 4 HOH A 38 193 33 HOH HOH . G 4 HOH A 39 194 34 HOH HOH . G 4 HOH A 40 195 35 HOH HOH . G 4 HOH A 41 196 36 HOH HOH . G 4 HOH A 42 197 37 HOH HOH . G 4 HOH A 43 198 38 HOH HOH . G 4 HOH A 44 199 39 HOH HOH . G 4 HOH A 45 200 40 HOH HOH . G 4 HOH A 46 201 41 HOH HOH . G 4 HOH A 47 202 42 HOH HOH . G 4 HOH A 48 203 43 HOH HOH . G 4 HOH A 49 204 44 HOH HOH . H 4 HOH B 1 156 5 HOH HOH . H 4 HOH B 2 157 6 HOH HOH . H 4 HOH B 3 158 7 HOH HOH . H 4 HOH B 4 159 8 HOH HOH . H 4 HOH B 5 160 9 HOH HOH . H 4 HOH B 6 161 10 HOH HOH . H 4 HOH B 7 162 12 HOH HOH . H 4 HOH B 8 163 1 HOH HOH . H 4 HOH B 9 164 2 HOH HOH . H 4 HOH B 10 165 3 HOH HOH . H 4 HOH B 11 166 4 HOH HOH . H 4 HOH B 12 167 5 HOH HOH . H 4 HOH B 13 168 6 HOH HOH . H 4 HOH B 14 169 7 HOH HOH . H 4 HOH B 15 170 8 HOH HOH . H 4 HOH B 16 171 9 HOH HOH . H 4 HOH B 17 172 10 HOH HOH . H 4 HOH B 18 173 11 HOH HOH . H 4 HOH B 19 174 12 HOH HOH . H 4 HOH B 20 175 13 HOH HOH . H 4 HOH B 21 176 14 HOH HOH . H 4 HOH B 22 177 15 HOH HOH . H 4 HOH B 23 178 16 HOH HOH . H 4 HOH B 24 179 17 HOH HOH . H 4 HOH B 25 180 18 HOH HOH . H 4 HOH B 26 181 19 HOH HOH . H 4 HOH B 27 182 20 HOH HOH . H 4 HOH B 28 183 21 HOH HOH . H 4 HOH B 29 184 22 HOH HOH . H 4 HOH B 30 185 23 HOH HOH . H 4 HOH B 31 186 24 HOH HOH . H 4 HOH B 32 187 25 HOH HOH . H 4 HOH B 33 188 26 HOH HOH . H 4 HOH B 34 189 27 HOH HOH . H 4 HOH B 35 190 28 HOH HOH . H 4 HOH B 36 191 29 HOH HOH . H 4 HOH B 37 192 30 HOH HOH . H 4 HOH B 38 193 31 HOH HOH . H 4 HOH B 39 194 32 HOH HOH . H 4 HOH B 40 195 33 HOH HOH . H 4 HOH B 41 196 34 HOH HOH . H 4 HOH B 42 197 35 HOH HOH . H 4 HOH B 43 198 36 HOH HOH . H 4 HOH B 44 199 37 HOH HOH . H 4 HOH B 45 200 38 HOH HOH . H 4 HOH B 46 201 39 HOH HOH . H 4 HOH B 47 202 40 HOH HOH . H 4 HOH B 48 203 41 HOH HOH . H 4 HOH B 49 204 42 HOH HOH . H 4 HOH B 50 205 43 HOH HOH . H 4 HOH B 51 206 44 HOH HOH . H 4 HOH B 52 207 45 HOH HOH . H 4 HOH B 53 208 46 HOH HOH . H 4 HOH B 54 209 47 HOH HOH . H 4 HOH B 55 210 48 HOH HOH . H 4 HOH B 56 211 49 HOH HOH . H 4 HOH B 57 212 50 HOH HOH . H 4 HOH B 58 213 51 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 2 42.244 -19.03 52.055 1 14.7 ? CHA HEM 154 A 1 HETATM 2 C CHB HEM . . . C 2 45.07 -18.686 48.138 1 12.72 ? CHB HEM 154 A 1 HETATM 3 C CHC HEM . . . C 2 44.95 -13.847 48.613 1 14.21 ? CHC HEM 154 A 1 HETATM 4 C CHD HEM . . . C 2 42.217 -14.248 52.606 1 15.13 ? CHD HEM 154 A 1 HETATM 5 C C1A HEM . . . C 2 43.032 -19.379 50.978 1 14.53 ? C1A HEM 154 A 1 HETATM 6 C C2A HEM . . . C 2 43.379 -20.738 50.532 1 14.12 ? C2A HEM 154 A 1 HETATM 7 C C3A HEM . . . C 2 44.156 -20.593 49.425 1 13.57 ? C3A HEM 154 A 1 HETATM 8 C C4A HEM . . . C 2 44.312 -19.173 49.163 1 13.67 ? C4A HEM 154 A 1 HETATM 9 C CMA HEM . . . C 2 44.787 -21.697 48.548 1 12.88 ? CMA HEM 154 A 1 HETATM 10 C CAA HEM . . . C 2 42.855 -22.059 51.145 1 14.37 ? CAA HEM 154 A 1 HETATM 11 C CBA HEM . . . C 2 41.577 -22.584 50.391 1 15.95 ? CBA HEM 154 A 1 HETATM 12 C CGA HEM . . . C 2 40.527 -21.598 50.05 1 17.77 ? CGA HEM 154 A 1 HETATM 13 O O1A HEM . . . C 2 39.688 -20.92 50.789 1 20.28 ? O1A HEM 154 A 1 HETATM 14 O O2A HEM . . . C 2 40.333 -21.259 48.851 1 19.01 ? O2A HEM 154 A 1 HETATM 15 C C1B HEM . . . C 2 45.237 -17.332 47.948 1 13.36 ? C1B HEM 154 A 1 HETATM 16 C C2B HEM . . . C 2 45.961 -16.748 46.816 1 13.27 ? C2B HEM 154 A 1 HETATM 17 C C3B HEM . . . C 2 45.956 -15.436 46.963 1 12.94 ? C3B HEM 154 A 1 HETATM 18 C C4B HEM . . . C 2 45.193 -15.13 48.134 1 13.18 ? C4B HEM 154 A 1 HETATM 19 C CMB HEM . . . C 2 46.689 -17.625 45.724 1 12.81 ? CMB HEM 154 A 1 HETATM 20 C CAB HEM . . . C 2 46.628 -14.387 46.033 1 12.93 ? CAB HEM 154 A 1 HETATM 21 C CBB HEM . . . C 2 47.978 -14.326 45.91 1 13.07 ? CBB HEM 154 A 1 HETATM 22 C C1C HEM . . . C 2 44.176 -13.528 49.712 1 15.44 ? C1C HEM 154 A 1 HETATM 23 C C2C HEM . . . C 2 44.064 -12.226 50.329 1 15.27 ? C2C HEM 154 A 1 HETATM 24 C C3C HEM . . . C 2 43.337 -12.374 51.442 1 15.1 ? C3C HEM 154 A 1 HETATM 25 C C4C HEM . . . C 2 42.979 -13.765 51.579 1 15.42 ? C4C HEM 154 A 1 HETATM 26 C CMC HEM . . . C 2 44.715 -10.941 49.746 1 15.24 ? CMC HEM 154 A 1 HETATM 27 C CAC HEM . . . C 2 42.884 -11.399 52.545 1 15.5 ? CAC HEM 154 A 1 HETATM 28 C CBC HEM . . . C 2 43.284 -10.156 52.418 1 16.52 ? CBC HEM 154 A 1 HETATM 29 C C1D HEM . . . C 2 42.019 -15.589 52.792 1 15.14 ? C1D HEM 154 A 1 HETATM 30 C C2D HEM . . . C 2 41.357 -16.121 53.977 1 15.77 ? C2D HEM 154 A 1 HETATM 31 C C3D HEM . . . C 2 41.377 -17.449 53.845 1 16.42 ? C3D HEM 154 A 1 HETATM 32 C C4D HEM . . . C 2 42.028 -17.778 52.584 1 15.52 ? C4D HEM 154 A 1 HETATM 33 C CMD HEM . . . C 2 40.825 -15.215 55.125 1 15.08 ? CMD HEM 154 A 1 HETATM 34 C CAD HEM . . . C 2 40.882 -18.508 54.833 1 18.13 ? CAD HEM 154 A 1 HETATM 35 C CBD HEM . . . C 2 42.006 -18.992 55.731 1 21.59 ? CBD HEM 154 A 1 HETATM 36 C CGD HEM . . . C 2 41.604 -19.749 56.967 1 23.6 ? CGD HEM 154 A 1 HETATM 37 O O1D HEM . . . C 2 41.243 -19.073 57.983 1 26.08 ? O1D HEM 154 A 1 HETATM 38 O O2D HEM . . . C 2 41.675 -20.982 57.008 1 24.71 ? O2D HEM 154 A 1 HETATM 39 N NA HEM . . . C 2 43.646 -18.435 50.155 1 13.64 ? NA HEM 154 A 1 HETATM 40 N NB HEM . . . C 2 44.735 -16.291 48.706 1 13.87 ? NB HEM 154 A 1 HETATM 41 N NC HEM . . . C 2 43.51 -14.497 50.505 1 15.53 ? NC HEM 154 A 1 HETATM 42 N ND HEM . . . C 2 42.397 -16.61 51.954 1 14.82 ? ND HEM 154 A 1 HETATM 43 FE FE HEM . . . C 2 43.652 -16.493 50.391 1 14.92 ? FE HEM 154 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #