data_1ZRT # _model_server_result.job_id Im2o0d7wAjl_-BW5VU8ZtA _model_server_result.datetime_utc '2025-04-29 02:16:23' _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 1zrt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":501}' # _entry.id 1ZRT # _exptl.entry_id 1ZRT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 4 _entity.src_method man _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 113.57 _cell.angle_gamma 90 _cell.entry_id 1ZRT _cell.length_a 95.633 _cell.length_b 154.36 _cell.length_c 103.057 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1ZRT _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_and_software_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,Q,R,S,T,U _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 ? 4 G N N ? 4 H N N ? 4 N N N ? 4 O 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 disulf ? disulf1 B SG CYS 144 D CYS 144 1_555 B SG CYS 167 D CYS 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? disulf ? disulf2 C SG CYS 138 E CYS 138 1_555 C SG CYS 155 E CYS 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 E SG CYS 144 Q CYS 144 1_555 E SG CYS 167 Q CYS 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? disulf ? disulf4 F SG CYS 138 R CYS 138 1_555 F SG CYS 155 R CYS 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 B SG CYS 34 D CYS 34 1_555 L CAB HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.796 ? covale ? covale2 B SG CYS 37 D CYS 37 1_555 L CAC HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.804 ? covale ? covale3 E SG CYS 34 Q CYS 34 1_555 S CAB HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.896 ? covale ? covale4 E SG CYS 37 Q CYS 37 1_555 S CAC HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc1 A NE2 HIS 97 C HIS 97 1_555 G FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? metalc ? metalc2 A NE2 HIS 111 C HIS 111 1_555 H FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc3 A NE2 HIS 198 C HIS 198 1_555 G FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc4 A NE2 HIS 212 C HIS 212 1_555 H FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc5 B NE2 HIS 38 D HIS 38 1_555 L FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? metalc ? metalc6 B SD MET 183 D MET 183 1_555 L FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc7 C SG CYS 133 E CYS 133 1_555 M FE1 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc8 C ND1 HIS 135 E HIS 135 1_555 M FE2 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc9 C SG CYS 153 E CYS 153 1_555 M FE1 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc10 C N HIS 156 E HIS 156 1_555 M FE2 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? metalc ? metalc11 C ND1 HIS 156 E HIS 156 1_555 M FE2 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc12 D NE2 HIS 97 P HIS 97 1_555 N FE HEM . P HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc13 D NE2 HIS 111 P HIS 111 1_555 O FE HEM . P HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc14 D NE2 HIS 198 P HIS 198 1_555 N FE HEM . P HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? metalc ? metalc15 D NE2 HIS 212 P HIS 212 1_555 O FE HEM . P HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc16 E NE2 HIS 38 Q HIS 38 1_555 S FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? metalc ? metalc17 E SD MET 183 Q MET 183 1_555 S FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc18 F SG CYS 133 R CYS 133 1_555 U FE1 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc19 F ND1 HIS 135 R HIS 135 1_555 U FE2 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc20 F SG CYS 153 R CYS 153 1_555 U FE1 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc21 F N HIS 156 R HIS 156 1_555 U FE2 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc22 F ND1 HIS 156 R HIS 156 1_555 U FE2 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? # _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 217 n n CHA C4D HEM doub 218 n n CHA HHA HEM sing 219 n n CHB C4A HEM sing 220 n n CHB C1B HEM doub 221 n n CHB HHB HEM sing 222 n n CHC C4B HEM sing 223 n n CHC C1C HEM doub 224 n n CHC HHC HEM sing 225 n n CHD C4C HEM doub 226 n n CHD C1D HEM sing 227 n n CHD HHD HEM sing 228 n n C1A C2A HEM doub 229 n y C1A NA HEM sing 230 n y C2A C3A HEM sing 231 n y C2A CAA HEM sing 232 n n C3A C4A HEM doub 233 n y C3A CMA HEM sing 234 n n C4A NA HEM sing 235 n y CMA HMA HEM sing 236 n n CMA HMAA HEM sing 237 n n CMA HMAB HEM sing 238 n n CAA CBA HEM sing 239 n n CAA HAA HEM sing 240 n n CAA HAAA HEM sing 241 n n CBA CGA HEM sing 242 n n CBA HBA HEM sing 243 n n CBA HBAA HEM sing 244 n n CGA O1A HEM doub 245 n n CGA O2A HEM sing 246 n n C1B C2B HEM sing 247 n n C1B NB HEM sing 248 n n C2B C3B HEM doub 249 n n C2B CMB HEM sing 250 n n C3B C4B HEM sing 251 n n C3B CAB HEM sing 252 n n C4B NB HEM doub 253 n n CMB HMB HEM sing 254 n n CMB HMBA HEM sing 255 n n CMB HMBB HEM sing 256 n n CAB CBB HEM doub 257 n n CAB HAB HEM sing 258 n n CBB HBB HEM sing 259 n n CBB HBBA HEM sing 260 n n C1C C2C HEM sing 261 n y C1C NC HEM sing 262 n y C2C C3C HEM doub 263 n y C2C CMC HEM sing 264 n n C3C C4C HEM sing 265 n y C3C CAC HEM sing 266 n n C4C NC HEM sing 267 n y CMC HMC HEM sing 268 n n CMC HMCA HEM sing 269 n n CMC HMCB HEM sing 270 n n CAC CBC HEM doub 271 n n CAC HAC HEM sing 272 n n CBC HBC HEM sing 273 n n CBC HBCA HEM sing 274 n n C1D C2D HEM sing 275 n n C1D ND HEM doub 276 n n C2D C3D HEM doub 277 n n C2D CMD HEM sing 278 n n C3D C4D HEM sing 279 n n C3D CAD HEM sing 280 n n C4D ND HEM sing 281 n n CMD HMD HEM sing 282 n n CMD HMDA HEM sing 283 n n CMD HMDB HEM sing 284 n n CAD CBD HEM sing 285 n n CAD HAD HEM sing 286 n n CAD HADA HEM sing 287 n n CBD CGD HEM sing 288 n n CBD HBD HEM sing 289 n n CBD HBDA HEM sing 290 n n CGD O1D HEM doub 291 n n CGD O2D HEM sing 292 n n O2A H2A HEM sing 293 n n O2D H2D HEM sing 294 n n FE NA HEM sing 295 n n FE NB HEM sing 296 n n FE NC HEM sing 297 n n FE ND HEM sing 298 n n # _atom_sites.entry_id 1ZRT _atom_sites.fract_transf_matrix[1][1] 0.010457 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004562 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006478 _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] 0.010587 _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 G 4 HEM C 1 501 501 HEM HEM . H 4 HEM C 1 502 502 HEM HEM . I 5 SMA C 1 503 503 SMA SMA . J 6 UNL C 1 504 504 UNL UNK . K 6 UNL C 1 505 505 UNL UNK . L 7 HEC D 1 501 501 HEC HEC . M 8 FES E 1 501 501 FES FES . N 4 HEM P 1 501 501 HEM HEM . O 4 HEM P 1 502 502 HEM HEM . P 5 SMA P 1 503 503 SMA SMA . Q 6 UNL P 1 504 504 UNL UNK . R 6 UNL P 1 505 505 UNL UNK . S 7 HEC Q 1 501 501 HEC HEC . T 9 PG6 Q 1 502 502 PG6 PG6 . U 8 FES R 1 501 501 FES FES . # 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 . . . N 4 -8.565 -8.099 30.894 1 97.63 ? CHA HEM 501 P 1 HETATM 2 C CHB HEM . . . N 4 -5.608 -7.36 34.73 1 97.81 ? CHB HEM 501 P 1 HETATM 3 C CHC HEM . . . N 4 -2.023 -6.118 31.673 1 97.46 ? CHC HEM 501 P 1 HETATM 4 C CHD HEM . . . N 4 -5.294 -5.998 28.002 1 89.51 ? CHD HEM 501 P 1 HETATM 5 C C1A HEM . . . N 4 -8.033 -8.061 32.186 1 100.07 ? C1A HEM 501 P 1 HETATM 6 C C2A HEM . . . N 4 -8.718 -8.549 33.364 1 91.82 ? C2A HEM 501 P 1 HETATM 7 C C3A HEM . . . N 4 -7.906 -8.346 34.399 1 93.17 ? C3A HEM 501 P 1 HETATM 8 C C4A HEM . . . N 4 -6.681 -7.707 33.938 1 88.75 ? C4A HEM 501 P 1 HETATM 9 C CMA HEM . . . N 4 -8.225 -8.719 35.857 1 100.13 ? CMA HEM 501 P 1 HETATM 10 C CAA HEM . . . N 4 -10.089 -9.227 33.391 1 84.02 ? CAA HEM 501 P 1 HETATM 11 C CBA HEM . . . N 4 -9.836 -10.666 32.971 1 89.14 ? CBA HEM 501 P 1 HETATM 12 C CGA HEM . . . N 4 -11.176 -11.316 32.768 1 114.85 ? CGA HEM 501 P 1 HETATM 13 O O1A HEM . . . N 4 -11.361 -12.015 31.728 1 109.97 ? O1A HEM 501 P 1 HETATM 14 O O2A HEM . . . N 4 -12.07 -11.105 33.648 1 129.26 ? O2A HEM 501 P 1 HETATM 15 C C1B HEM . . . N 4 -4.377 -6.951 34.272 1 99.92 ? C1B HEM 501 P 1 HETATM 16 C C2B HEM . . . N 4 -3.249 -6.493 35.068 1 99.12 ? C2B HEM 501 P 1 HETATM 17 C C3B HEM . . . N 4 -2.264 -6.179 34.179 1 88.33 ? C3B HEM 501 P 1 HETATM 18 C C4B HEM . . . N 4 -2.739 -6.376 32.843 1 94.71 ? C4B HEM 501 P 1 HETATM 19 C CMB HEM . . . N 4 -3.324 -6.486 36.63 1 85.55 ? CMB HEM 501 P 1 HETATM 20 C CAB HEM . . . N 4 -0.877 -5.603 34.321 1 91.17 ? CAB HEM 501 P 1 HETATM 21 C CBB HEM . . . N 4 -0.586 -4.735 35.287 1 105.9 ? CBB HEM 501 P 1 HETATM 22 C C1C HEM . . . N 4 -2.644 -5.843 30.437 1 100.38 ? C1C HEM 501 P 1 HETATM 23 C C2C HEM . . . N 4 -2.112 -5.012 29.38 1 91.76 ? C2C HEM 501 P 1 HETATM 24 C C3C HEM . . . N 4 -2.98 -4.994 28.39 1 89.81 ? C3C HEM 501 P 1 HETATM 25 C C4C HEM . . . N 4 -4.16 -5.764 28.752 1 82.74 ? C4C HEM 501 P 1 HETATM 26 C CMC HEM . . . N 4 -0.758 -4.293 29.32 1 84.8 ? CMC HEM 501 P 1 HETATM 27 C CAC HEM . . . N 4 -2.671 -4.168 27.135 1 94.01 ? CAC HEM 501 P 1 HETATM 28 C CBC HEM . . . N 4 -2.97 -4.622 25.918 1 96.61 ? CBC HEM 501 P 1 HETATM 29 C C1D HEM . . . N 4 -6.448 -6.657 28.403 1 99.87 ? C1D HEM 501 P 1 HETATM 30 C C2D HEM . . . N 4 -7.574 -7.127 27.576 1 97.97 ? C2D HEM 501 P 1 HETATM 31 C C3D HEM . . . N 4 -8.458 -7.713 28.407 1 87.47 ? C3D HEM 501 P 1 HETATM 32 C C4D HEM . . . N 4 -7.953 -7.627 29.747 1 89.77 ? C4D HEM 501 P 1 HETATM 33 C CMD HEM . . . N 4 -7.71 -6.987 26.029 1 80.49 ? CMD HEM 501 P 1 HETATM 34 C CAD HEM . . . N 4 -9.791 -8.365 28.072 1 88.65 ? CAD HEM 501 P 1 HETATM 35 C CBD HEM . . . N 4 -9.503 -9.86 27.977 1 83.49 ? CBD HEM 501 P 1 HETATM 36 C CGD HEM . . . N 4 -10.362 -10.568 28.971 1 90.35 ? CGD HEM 501 P 1 HETATM 37 O O1D HEM . . . N 4 -11.124 -9.882 29.683 1 94.01 ? O1D HEM 501 P 1 HETATM 38 O O2D HEM . . . N 4 -10.281 -11.804 29.067 1 83.75 ? O2D HEM 501 P 1 HETATM 39 N NA HEM . . . N 4 -6.781 -7.541 32.575 1 90.01 ? NA HEM 501 P 1 HETATM 40 N NB HEM . . . N 4 -4.048 -6.86 32.93 1 97.66 ? NB HEM 501 P 1 HETATM 41 N NC HEM . . . N 4 -3.911 -6.29 30.001 1 87.44 ? NC HEM 501 P 1 HETATM 42 N ND HEM . . . N 4 -6.725 -6.978 29.721 1 95.32 ? ND HEM 501 P 1 HETATM 43 FE FE HEM . . . N 4 -5.427 -6.908 31.312 1 73.92 ? FE HEM 501 P 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 37 _model_server_stats.query_time_ms 544 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 43 #