data_1YG5 # _model_server_result.job_id mDJEKUAYyA8PZCXRXaSnnA _model_server_result.datetime_utc '2024-12-04 20:45:52' _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 1yg5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":147}' # _entry.id 1YG5 # _exptl.entry_id 1YG5 _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 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 1YG5 _cell.length_a 95.57 _cell.length_b 98.59 _cell.length_c 66.77 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YG5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 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,J,K,L,M,N,O,P _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 G N N ? 3 I N N ? 3 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 NE2 HIS 87 A HIS 87 1_555 E FE HEM . A HEM 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc2 E FE HEM . A HEM 142 1_555 F O1 OXY . A OXY 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.714 ? metalc ? metalc3 B NE2 HIS 92 B HIS 92 1_555 G FE HEM . B HEM 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc4 G FE HEM . B HEM 147 1_555 H O1 OXY . B OXY 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.756 ? metalc ? metalc5 C NE2 HIS 87 C HIS 87 1_555 I FE HEM . C HEM 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc6 I FE HEM . C HEM 142 1_555 J O1 OXY . C OXY 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.719 ? metalc ? metalc7 D NE2 HIS 92 D HIS 92 1_555 K FE HEM . D HEM 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc8 K FE HEM . D HEM 147 1_555 L O1 OXY . D OXY 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.791 ? # _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 1YG5 _atom_sites.fract_transf_matrix[1][1] 0.010464 _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] 0.010143 _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] 0.014977 _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 3 HEM A 1 142 142 HEM HEM . F 4 OXY A 1 150 150 OXY O2 . G 3 HEM B 1 147 147 HEM HEM . H 4 OXY B 1 150 150 OXY O2 . I 3 HEM C 1 142 142 HEM HEM . J 4 OXY C 1 150 150 OXY O2 . K 3 HEM D 1 147 147 HEM HEM . L 4 OXY D 1 150 150 OXY O2 . M 5 HOH A 1 204 204 HOH HOH . M 5 HOH A 2 205 205 HOH HOH . M 5 HOH A 3 215 215 HOH HOH . M 5 HOH A 4 216 216 HOH HOH . M 5 HOH A 5 217 217 HOH HOH . M 5 HOH A 6 220 220 HOH HOH . M 5 HOH A 7 223 223 HOH HOH . M 5 HOH A 8 226 226 HOH HOH . M 5 HOH A 9 233 233 HOH HOH . M 5 HOH A 10 246 246 HOH HOH . M 5 HOH A 11 287 287 HOH HOH . M 5 HOH A 12 291 291 HOH HOH . M 5 HOH A 13 310 310 HOH HOH . M 5 HOH A 14 311 311 HOH HOH . M 5 HOH A 15 312 312 HOH HOH . M 5 HOH A 16 315 315 HOH HOH . M 5 HOH A 17 317 317 HOH HOH . M 5 HOH A 18 319 319 HOH HOH . M 5 HOH A 19 325 325 HOH HOH . M 5 HOH A 20 331 331 HOH HOH . M 5 HOH A 21 332 332 HOH HOH . M 5 HOH A 22 339 339 HOH HOH . M 5 HOH A 23 340 340 HOH HOH . M 5 HOH A 24 343 343 HOH HOH . M 5 HOH A 25 352 352 HOH HOH . M 5 HOH A 26 353 353 HOH HOH . M 5 HOH A 27 355 355 HOH HOH . M 5 HOH A 28 361 361 HOH HOH . M 5 HOH A 29 377 377 HOH HOH . M 5 HOH A 30 382 382 HOH HOH . M 5 HOH A 31 386 386 HOH HOH . M 5 HOH A 32 407 407 HOH HOH . M 5 HOH A 33 429 429 HOH HOH . N 5 HOH B 1 234 234 HOH HOH . N 5 HOH B 2 237 237 HOH HOH . N 5 HOH B 3 239 239 HOH HOH . N 5 HOH B 4 241 241 HOH HOH . N 5 HOH B 5 242 242 HOH HOH . N 5 HOH B 6 244 244 HOH HOH . N 5 HOH B 7 248 248 HOH HOH . N 5 HOH B 8 249 249 HOH HOH . N 5 HOH B 9 251 251 HOH HOH . N 5 HOH B 10 252 252 HOH HOH . N 5 HOH B 11 261 261 HOH HOH . N 5 HOH B 12 262 262 HOH HOH . N 5 HOH B 13 267 267 HOH HOH . N 5 HOH B 14 269 269 HOH HOH . N 5 HOH B 15 275 275 HOH HOH . N 5 HOH B 16 278 278 HOH HOH . N 5 HOH B 17 283 283 HOH HOH . N 5 HOH B 18 289 289 HOH HOH . N 5 HOH B 19 298 298 HOH HOH . N 5 HOH B 20 302 302 HOH HOH . N 5 HOH B 21 313 313 HOH HOH . N 5 HOH B 22 318 318 HOH HOH . N 5 HOH B 23 323 323 HOH HOH . N 5 HOH B 24 335 335 HOH HOH . N 5 HOH B 25 362 362 HOH HOH . N 5 HOH B 26 391 391 HOH HOH . N 5 HOH B 27 402 402 HOH HOH . N 5 HOH B 28 405 405 HOH HOH . N 5 HOH B 29 409 409 HOH HOH . N 5 HOH B 30 414 414 HOH HOH . N 5 HOH B 31 423 423 HOH HOH . O 5 HOH C 1 228 228 HOH HOH . O 5 HOH C 2 243 243 HOH HOH . O 5 HOH C 3 254 254 HOH HOH . O 5 HOH C 4 255 255 HOH HOH . O 5 HOH C 5 257 257 HOH HOH . O 5 HOH C 6 260 260 HOH HOH . O 5 HOH C 7 268 268 HOH HOH . O 5 HOH C 8 309 309 HOH HOH . O 5 HOH C 9 314 314 HOH HOH . O 5 HOH C 10 320 320 HOH HOH . O 5 HOH C 11 321 321 HOH HOH . O 5 HOH C 12 330 330 HOH HOH . O 5 HOH C 13 333 333 HOH HOH . O 5 HOH C 14 337 337 HOH HOH . O 5 HOH C 15 346 346 HOH HOH . O 5 HOH C 16 347 347 HOH HOH . O 5 HOH C 17 363 363 HOH HOH . O 5 HOH C 18 374 374 HOH HOH . O 5 HOH C 19 384 384 HOH HOH . O 5 HOH C 20 408 408 HOH HOH . O 5 HOH C 21 417 417 HOH HOH . O 5 HOH C 22 420 420 HOH HOH . O 5 HOH C 23 425 425 HOH HOH . O 5 HOH C 24 428 428 HOH HOH . O 5 HOH C 25 431 431 HOH HOH . O 5 HOH C 26 436 436 HOH HOH . O 5 HOH C 27 437 437 HOH HOH . P 5 HOH D 1 206 206 HOH HOH . P 5 HOH D 2 207 207 HOH HOH . P 5 HOH D 3 208 208 HOH HOH . P 5 HOH D 4 209 209 HOH HOH . P 5 HOH D 5 210 210 HOH HOH . P 5 HOH D 6 211 211 HOH HOH . P 5 HOH D 7 212 212 HOH HOH . P 5 HOH D 8 272 272 HOH HOH . P 5 HOH D 9 277 277 HOH HOH . P 5 HOH D 10 281 281 HOH HOH . P 5 HOH D 11 282 282 HOH HOH . P 5 HOH D 12 285 285 HOH HOH . P 5 HOH D 13 288 288 HOH HOH . P 5 HOH D 14 293 293 HOH HOH . P 5 HOH D 15 316 316 HOH HOH . P 5 HOH D 16 328 328 HOH HOH . P 5 HOH D 17 388 388 HOH HOH . P 5 HOH D 18 394 394 HOH HOH . P 5 HOH D 19 400 400 HOH HOH . P 5 HOH D 20 415 415 HOH HOH . P 5 HOH D 21 421 421 HOH HOH . P 5 HOH D 22 422 422 HOH HOH . P 5 HOH D 23 438 438 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 . . . K 3 22.044 38.625 -36.277 1 31.02 ? CHA HEM 147 D 1 HETATM 2 C CHB HEM . . . K 3 24.922 34.922 -35.608 1 31.12 ? CHB HEM 147 D 1 HETATM 3 C CHC HEM . . . K 3 22.216 33.385 -32.026 1 29.04 ? CHC HEM 147 D 1 HETATM 4 C CHD HEM . . . K 3 19.048 36.779 -32.946 1 27.36 ? CHD HEM 147 D 1 HETATM 5 C C1A HEM . . . K 3 23.032 37.753 -36.421 1 31.61 ? C1A HEM 147 D 1 HETATM 6 C C2A HEM . . . K 3 24.032 37.785 -37.477 1 33.64 ? C2A HEM 147 D 1 HETATM 7 C C3A HEM . . . K 3 24.773 36.752 -37.235 1 31.21 ? C3A HEM 147 D 1 HETATM 8 C C4A HEM . . . K 3 24.285 36.038 -36.078 1 32.21 ? C4A HEM 147 D 1 HETATM 9 C CMA HEM . . . K 3 25.972 36.413 -38.112 1 29.76 ? CMA HEM 147 D 1 HETATM 10 C CAA HEM . . . K 3 24.37 38.683 -38.738 1 40.43 ? CAA HEM 147 D 1 HETATM 11 C CBA HEM . . . K 3 23.751 40.08 -38.994 1 46.9 ? CBA HEM 147 D 1 HETATM 12 C CGA HEM . . . K 3 24.76 41.127 -39.516 1 48.83 ? CGA HEM 147 D 1 HETATM 13 O O1A HEM . . . K 3 25.957 40.788 -39.774 1 47.08 ? O1A HEM 147 D 1 HETATM 14 O O2A HEM . . . K 3 24.371 42.336 -39.67 1 49.37 ? O2A HEM 147 D 1 HETATM 15 C C1B HEM . . . K 3 24.604 34.163 -34.53 1 29.42 ? C1B HEM 147 D 1 HETATM 16 C C2B HEM . . . K 3 25.31 33.081 -33.852 1 28.98 ? C2B HEM 147 D 1 HETATM 17 C C3B HEM . . . K 3 24.51 32.65 -32.878 1 30.64 ? C3B HEM 147 D 1 HETATM 18 C C4B HEM . . . K 3 23.308 33.479 -32.866 1 30.88 ? C4B HEM 147 D 1 HETATM 19 C CMB HEM . . . K 3 26.646 32.438 -34.168 1 20.8 ? CMB HEM 147 D 1 HETATM 20 C CAB HEM . . . K 3 24.851 31.527 -31.898 1 28.76 ? CAB HEM 147 D 1 HETATM 21 C CBB HEM . . . K 3 26.035 31.598 -31.308 1 29.99 ? CBB HEM 147 D 1 HETATM 22 C C1C HEM . . . K 3 21.09 34.16 -31.995 1 25.35 ? C1C HEM 147 D 1 HETATM 23 C C2C HEM . . . K 3 19.932 33.888 -31.228 1 24.5 ? C2C HEM 147 D 1 HETATM 24 C C3C HEM . . . K 3 19.133 34.923 -31.392 1 25.21 ? C3C HEM 147 D 1 HETATM 25 C C4C HEM . . . K 3 19.631 35.703 -32.425 1 24.4 ? C4C HEM 147 D 1 HETATM 26 C CMC HEM . . . K 3 19.873 32.868 -30.066 1 23.92 ? CMC HEM 147 D 1 HETATM 27 C CAC HEM . . . K 3 17.773 35.151 -30.735 1 25.5 ? CAC HEM 147 D 1 HETATM 28 C CBC HEM . . . K 3 16.831 34.289 -31.103 1 25.25 ? CBC HEM 147 D 1 HETATM 29 C C1D HEM . . . K 3 19.638 37.492 -33.968 1 30.56 ? C1D HEM 147 D 1 HETATM 30 C C2D HEM . . . K 3 18.835 38.417 -34.723 1 30.35 ? C2D HEM 147 D 1 HETATM 31 C C3D HEM . . . K 3 19.707 39.01 -35.785 1 31.21 ? C3D HEM 147 D 1 HETATM 32 C C4D HEM . . . K 3 20.969 38.374 -35.534 1 29.55 ? C4D HEM 147 D 1 HETATM 33 C CMD HEM . . . K 3 17.361 38.765 -34.54 1 29.28 ? CMD HEM 147 D 1 HETATM 34 C CAD HEM . . . K 3 19.345 40.073 -36.842 1 33.9 ? CAD HEM 147 D 1 HETATM 35 C CBD HEM . . . K 3 18.185 39.721 -37.79 1 37.46 ? CBD HEM 147 D 1 HETATM 36 C CGD HEM . . . K 3 18.02 40.903 -38.742 1 40.39 ? CGD HEM 147 D 1 HETATM 37 O O1D HEM . . . K 3 17.256 41.899 -38.453 1 39.52 ? O1D HEM 147 D 1 HETATM 38 O O2D HEM . . . K 3 18.711 40.85 -39.79 1 40.19 ? O2D HEM 147 D 1 HETATM 39 N NA HEM . . . K 3 23.177 36.679 -35.581 1 31.2 ? NA HEM 147 D 1 HETATM 40 N NB HEM . . . K 3 23.431 34.378 -33.893 1 30.38 ? NB HEM 147 D 1 HETATM 41 N NC HEM . . . K 3 20.83 35.223 -32.772 1 27.01 ? NC HEM 147 D 1 HETATM 42 N ND HEM . . . K 3 20.953 37.477 -34.47 1 28.9 ? ND HEM 147 D 1 HETATM 43 FE FE HEM . . . K 3 22.203 35.976 -34.017 1 32.08 ? FE HEM 147 D 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 69 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 43 #