data_1CYF # _model_server_result.job_id bEyh6pYTxxuei53u5XZx8Q _model_server_result.datetime_utc '2025-04-16 11:23:19' _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 1cyf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":296}' # _entry.id 1CYF # _exptl.entry_id 1CYF _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 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 1CYF _cell.length_a 101.33 _cell.length_b 73.88 _cell.length_c 45 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1CYF _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 _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 2 _struct_asym.id B _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 NE2 HIS 177 A HIS 175 1_555 B FE HEM . A HEM 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc2 C O HOH . A HOH 295 1_555 B FE HEM . A HEM 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.799 ? # _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 1CYF _atom_sites.fract_transf_matrix[1][1] 0.009869 _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] 0.013535 _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] 0.022222 _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 HEM A 1 296 296 HEM HEM . C 3 HOH A 1 295 295 HOH HOH . C 3 HOH A 2 302 302 HOH HOH . C 3 HOH A 3 303 303 HOH HOH . C 3 HOH A 4 306 306 HOH HOH . C 3 HOH A 5 307 307 HOH HOH . C 3 HOH A 6 308 308 HOH HOH . C 3 HOH A 7 309 309 HOH HOH . C 3 HOH A 8 311 311 HOH HOH . C 3 HOH A 9 313 313 HOH HOH . C 3 HOH A 10 314 314 HOH HOH . C 3 HOH A 11 315 315 HOH HOH . C 3 HOH A 12 316 316 HOH HOH . C 3 HOH A 13 317 317 HOH HOH . C 3 HOH A 14 321 321 HOH HOH . C 3 HOH A 15 324 324 HOH HOH . C 3 HOH A 16 326 326 HOH HOH . C 3 HOH A 17 329 329 HOH HOH . C 3 HOH A 18 337 337 HOH HOH . C 3 HOH A 19 341 341 HOH HOH . C 3 HOH A 20 342 342 HOH HOH . C 3 HOH A 21 344 344 HOH HOH . C 3 HOH A 22 345 345 HOH HOH . C 3 HOH A 23 348 348 HOH HOH . C 3 HOH A 24 351 351 HOH HOH . C 3 HOH A 25 353 353 HOH HOH . C 3 HOH A 26 355 355 HOH HOH . C 3 HOH A 27 358 358 HOH HOH . C 3 HOH A 28 359 359 HOH HOH . C 3 HOH A 29 360 360 HOH HOH . C 3 HOH A 30 363 363 HOH HOH . C 3 HOH A 31 366 366 HOH HOH . C 3 HOH A 32 368 368 HOH HOH . C 3 HOH A 33 369 369 HOH HOH . C 3 HOH A 34 371 371 HOH HOH . C 3 HOH A 35 372 372 HOH HOH . C 3 HOH A 36 374 374 HOH HOH . C 3 HOH A 37 375 375 HOH HOH . C 3 HOH A 38 376 376 HOH HOH . C 3 HOH A 39 379 379 HOH HOH . C 3 HOH A 40 382 382 HOH HOH . C 3 HOH A 41 383 383 HOH HOH . C 3 HOH A 42 384 384 HOH HOH . C 3 HOH A 43 385 385 HOH HOH . C 3 HOH A 44 386 386 HOH HOH . C 3 HOH A 45 387 387 HOH HOH . C 3 HOH A 46 388 388 HOH HOH . C 3 HOH A 47 391 391 HOH HOH . C 3 HOH A 48 394 394 HOH HOH . C 3 HOH A 49 395 395 HOH HOH . C 3 HOH A 50 397 397 HOH HOH . C 3 HOH A 51 398 398 HOH HOH . C 3 HOH A 52 400 400 HOH HOH . C 3 HOH A 53 401 401 HOH HOH . C 3 HOH A 54 402 402 HOH HOH . C 3 HOH A 55 403 403 HOH HOH . C 3 HOH A 56 405 405 HOH HOH . C 3 HOH A 57 408 408 HOH HOH . C 3 HOH A 58 409 409 HOH HOH . C 3 HOH A 59 410 410 HOH HOH . C 3 HOH A 60 413 413 HOH HOH . C 3 HOH A 61 416 416 HOH HOH . C 3 HOH A 62 417 417 HOH HOH . C 3 HOH A 63 418 418 HOH HOH . C 3 HOH A 64 419 419 HOH HOH . C 3 HOH A 65 420 420 HOH HOH . C 3 HOH A 66 421 421 HOH HOH . C 3 HOH A 67 422 422 HOH HOH . C 3 HOH A 68 425 425 HOH HOH . C 3 HOH A 69 427 427 HOH HOH . C 3 HOH A 70 428 428 HOH HOH . C 3 HOH A 71 431 431 HOH HOH . C 3 HOH A 72 432 432 HOH HOH . C 3 HOH A 73 433 433 HOH HOH . C 3 HOH A 74 434 434 HOH HOH . C 3 HOH A 75 435 435 HOH HOH . C 3 HOH A 76 436 436 HOH HOH . C 3 HOH A 77 437 437 HOH HOH . C 3 HOH A 78 438 438 HOH HOH . C 3 HOH A 79 441 441 HOH HOH . C 3 HOH A 80 442 442 HOH HOH . C 3 HOH A 81 443 443 HOH HOH . C 3 HOH A 82 445 445 HOH HOH . C 3 HOH A 83 452 452 HOH HOH . C 3 HOH A 84 472 472 HOH HOH . C 3 HOH A 85 474 474 HOH HOH . C 3 HOH A 86 477 477 HOH HOH . C 3 HOH A 87 487 487 HOH HOH . C 3 HOH A 88 494 494 HOH HOH . C 3 HOH A 89 500 500 HOH HOH . C 3 HOH A 90 502 502 HOH HOH . C 3 HOH A 91 508 508 HOH HOH . C 3 HOH A 92 512 512 HOH HOH . C 3 HOH A 93 535 535 HOH HOH . C 3 HOH A 94 560 560 HOH HOH . C 3 HOH A 95 561 561 HOH HOH . C 3 HOH A 96 565 565 HOH HOH . C 3 HOH A 97 567 567 HOH HOH . C 3 HOH A 98 573 573 HOH HOH . C 3 HOH A 99 575 575 HOH HOH . C 3 HOH A 100 596 596 HOH HOH . C 3 HOH A 101 648 648 HOH HOH . C 3 HOH A 102 700 700 HOH HOH . C 3 HOH A 103 703 703 HOH HOH . C 3 HOH A 104 704 704 HOH HOH . C 3 HOH A 105 708 708 HOH HOH . C 3 HOH A 106 722 722 HOH HOH . C 3 HOH A 107 725 725 HOH HOH . C 3 HOH A 108 727 727 HOH HOH . C 3 HOH A 109 732 732 HOH HOH . C 3 HOH A 110 736 736 HOH HOH . C 3 HOH A 111 740 740 HOH HOH . C 3 HOH A 112 743 743 HOH HOH . C 3 HOH A 113 746 746 HOH HOH . C 3 HOH A 114 784 784 HOH HOH . C 3 HOH A 115 863 863 HOH HOH . C 3 HOH A 116 864 864 HOH HOH . C 3 HOH A 117 895 895 HOH HOH . C 3 HOH A 118 896 896 HOH HOH . C 3 HOH A 119 965 965 HOH HOH . C 3 HOH A 120 967 967 HOH HOH . C 3 HOH A 121 968 968 HOH HOH . C 3 HOH A 122 969 969 HOH HOH . C 3 HOH A 123 970 970 HOH HOH . C 3 HOH A 124 971 971 HOH HOH . C 3 HOH A 125 972 972 HOH HOH . C 3 HOH A 126 973 973 HOH HOH . C 3 HOH A 127 974 974 HOH HOH . C 3 HOH A 128 975 975 HOH HOH . C 3 HOH A 129 976 976 HOH HOH . C 3 HOH A 130 977 977 HOH HOH . C 3 HOH A 131 978 978 HOH HOH . C 3 HOH A 132 979 979 HOH HOH . C 3 HOH A 133 980 980 HOH HOH . C 3 HOH A 134 981 981 HOH HOH . C 3 HOH A 135 982 982 HOH HOH . C 3 HOH A 136 983 983 HOH HOH . C 3 HOH A 137 984 984 HOH HOH . C 3 HOH A 138 985 985 HOH HOH . C 3 HOH A 139 986 986 HOH HOH . C 3 HOH A 140 987 987 HOH HOH . C 3 HOH A 141 988 988 HOH HOH . C 3 HOH A 142 989 989 HOH HOH . C 3 HOH A 143 990 990 HOH HOH . C 3 HOH A 144 991 991 HOH HOH . C 3 HOH A 145 992 992 HOH HOH . C 3 HOH A 146 993 993 HOH HOH . C 3 HOH A 147 994 994 HOH HOH . C 3 HOH A 148 995 995 HOH HOH . C 3 HOH A 149 996 996 HOH HOH . C 3 HOH A 150 997 997 HOH HOH . C 3 HOH A 151 998 998 HOH HOH . C 3 HOH A 152 999 999 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 . . . B 2 38.65 28.249 9.704 1 15.7 ? CHA HEM 296 A 1 HETATM 2 C CHB HEM . . . B 2 34.649 30.886 8.883 1 18.23 ? CHB HEM 296 A 1 HETATM 3 C CHC HEM . . . B 2 35.028 29.805 4.233 1 15.64 ? CHC HEM 296 A 1 HETATM 4 C CHD HEM . . . B 2 39.143 27.528 5.018 1 12.96 ? CHD HEM 296 A 1 HETATM 5 C C1A HEM . . . B 2 37.489 28.986 9.832 1 17.26 ? C1A HEM 296 A 1 HETATM 6 C C2A HEM . . . B 2 37.026 29.516 11.095 1 17.4 ? C2A HEM 296 A 1 HETATM 7 C C3A HEM . . . B 2 35.924 30.242 10.864 1 14.27 ? C3A HEM 296 A 1 HETATM 8 C C4A HEM . . . B 2 35.653 30.143 9.455 1 15.42 ? C4A HEM 296 A 1 HETATM 9 C CMA HEM . . . B 2 35.378 31.394 11.715 1 12.25 ? CMA HEM 296 A 1 HETATM 10 C CAA HEM . . . B 2 37.815 29.386 12.393 1 16.51 ? CAA HEM 296 A 1 HETATM 11 C CBA HEM . . . B 2 38.881 30.468 12.536 1 17.69 ? CBA HEM 296 A 1 HETATM 12 C CGA HEM . . . B 2 39.557 30.338 13.859 1 21.35 ? CGA HEM 296 A 1 HETATM 13 O O1A HEM . . . B 2 38.803 30.507 14.857 1 22.83 ? O1A HEM 296 A 1 HETATM 14 O O2A HEM . . . B 2 40.766 30.022 13.771 1 17.03 ? O2A HEM 296 A 1 HETATM 15 C C1B HEM . . . B 2 34.285 30.52 7.608 1 22.46 ? C1B HEM 296 A 1 HETATM 16 C C2B HEM . . . B 2 33.172 31.154 6.933 1 25.33 ? C2B HEM 296 A 1 HETATM 17 C C3B HEM . . . B 2 33.313 30.925 5.643 1 23.9 ? C3B HEM 296 A 1 HETATM 18 C C4B HEM . . . B 2 34.61 30.315 5.438 1 20.69 ? C4B HEM 296 A 1 HETATM 19 C CMB HEM . . . B 2 31.982 31.854 7.622 1 29.5 ? CMB HEM 296 A 1 HETATM 20 C CAB HEM . . . B 2 32.223 31.062 4.566 1 27 ? CAB HEM 296 A 1 HETATM 21 C CBB HEM . . . B 2 30.934 30.982 4.9 1 27.03 ? CBB HEM 296 A 1 HETATM 22 C C1C HEM . . . B 2 36.081 28.949 4.05 1 15.77 ? C1C HEM 296 A 1 HETATM 23 C C2C HEM . . . B 2 36.801 28.921 2.785 1 14.24 ? C2C HEM 296 A 1 HETATM 24 C C3C HEM . . . B 2 37.962 28.283 3.016 1 17.45 ? C3C HEM 296 A 1 HETATM 25 C C4C HEM . . . B 2 37.988 27.949 4.422 1 14.02 ? C4C HEM 296 A 1 HETATM 26 C CMC HEM . . . B 2 36.04 29.041 1.465 1 9.82 ? CMC HEM 296 A 1 HETATM 27 C CAC HEM . . . B 2 39.061 27.708 2.089 1 20.16 ? CAC HEM 296 A 1 HETATM 28 C CBC HEM . . . B 2 38.911 27.313 0.828 1 24.06 ? CBC HEM 296 A 1 HETATM 29 C C1D HEM . . . B 2 39.4 27.597 6.358 1 10.09 ? C1D HEM 296 A 1 HETATM 30 C C2D HEM . . . B 2 40.342 26.714 6.997 1 6.94 ? C2D HEM 296 A 1 HETATM 31 C C3D HEM . . . B 2 40.367 27.055 8.283 1 10.74 ? C3D HEM 296 A 1 HETATM 32 C C4D HEM . . . B 2 39.288 28.003 8.509 1 12.02 ? C4D HEM 296 A 1 HETATM 33 C CMD HEM . . . B 2 41.206 25.692 6.251 1 3.29 ? CMD HEM 296 A 1 HETATM 34 C CAD HEM . . . B 2 41.122 26.413 9.428 1 10.68 ? CAD HEM 296 A 1 HETATM 35 C CBD HEM . . . B 2 41.926 27.557 10.039 1 15.44 ? CBD HEM 296 A 1 HETATM 36 C CGD HEM . . . B 2 42.882 27.114 11.081 1 17.36 ? CGD HEM 296 A 1 HETATM 37 O O1D HEM . . . B 2 43.494 28.061 11.645 1 21.14 ? O1D HEM 296 A 1 HETATM 38 O O2D HEM . . . B 2 42.855 25.878 11.283 1 15.88 ? O2D HEM 296 A 1 HETATM 39 N NA HEM . . . B 2 36.741 29.568 8.827 1 16.27 ? NA HEM 296 A 1 HETATM 40 N NB HEM . . . B 2 35.088 29.913 6.67 1 20.54 ? NB HEM 296 A 1 HETATM 41 N NC HEM . . . B 2 36.953 28.579 5.043 1 13.72 ? NC HEM 296 A 1 HETATM 42 N ND HEM . . . B 2 38.729 28.323 7.306 1 11.91 ? ND HEM 296 A 1 HETATM 43 FE FE HEM . . . B 2 36.872 29.01 6.989 1 16.49 ? FE HEM 296 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 43 #