data_1XME # _model_server_result.job_id ygfcke9Bc7HiKa_U6NOW1g _model_server_result.datetime_utc '2025-07-05 00:46:52' _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 1xme # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":800}' # _entry.id 1XME # _exptl.entry_id 1XME _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 6 _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 1XME _cell.length_a 114.902 _cell.length_b 114.902 _cell.length_c 177.064 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XME _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 6 _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 covale ? covale1 A NE2 HIS 239 A HIS 233 1_555 A CE2 TYR 243 A TYR 237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 ? metalc ? metalc1 A NE2 HIS 78 A HIS 72 1_555 F FE HEM . A HEM 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc2 A ND1 HIS 239 A HIS 233 1_555 E CU CU . A CU 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.962 ? metalc ? metalc3 A NE2 HIS 288 A HIS 282 1_555 E CU CU . A CU 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.962 ? metalc ? metalc4 A NE2 HIS 289 A HIS 283 1_555 E CU CU . A CU 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc5 A NE2 HIS 390 A HIS 384 1_555 G FE HAS . A HAS 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? metalc ? metalc6 A NE2 HIS 392 A HIS 386 1_555 F FE HEM . A HEM 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc7 G FE HAS . A HAS 801 1_555 J O HOH . A HOH 867 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? metalc ? metalc8 E CU CU . A CU 803 1_555 J O HOH . A HOH 867 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc9 B ND1 HIS 114 B HIS 114 1_555 I CU2 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc10 B SG CYS 149 B CYS 149 1_555 I CU1 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc11 B SG CYS 149 B CYS 149 1_555 I CU2 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc12 B O GLN 151 B GLN 151 1_555 I CU1 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.752 ? metalc ? metalc13 B SG CYS 153 B CYS 153 1_555 I CU1 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc14 B SG CYS 153 B CYS 153 1_555 I CU2 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc15 B ND1 HIS 157 B HIS 157 1_555 I CU1 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc16 B SD MET 160 B MET 160 1_555 I CU2 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? # _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 330 n n CHA C4D HEM doub 331 n n CHA HHA HEM sing 332 n n CHB C4A HEM sing 333 n n CHB C1B HEM doub 334 n n CHB HHB HEM sing 335 n n CHC C4B HEM sing 336 n n CHC C1C HEM doub 337 n n CHC HHC HEM sing 338 n n CHD C4C HEM doub 339 n n CHD C1D HEM sing 340 n n CHD HHD HEM sing 341 n n C1A C2A HEM doub 342 n y C1A NA HEM sing 343 n y C2A C3A HEM sing 344 n y C2A CAA HEM sing 345 n n C3A C4A HEM doub 346 n y C3A CMA HEM sing 347 n n C4A NA HEM sing 348 n y CMA HMA HEM sing 349 n n CMA HMAA HEM sing 350 n n CMA HMAB HEM sing 351 n n CAA CBA HEM sing 352 n n CAA HAA HEM sing 353 n n CAA HAAA HEM sing 354 n n CBA CGA HEM sing 355 n n CBA HBA HEM sing 356 n n CBA HBAA HEM sing 357 n n CGA O1A HEM doub 358 n n CGA O2A HEM sing 359 n n C1B C2B HEM sing 360 n n C1B NB HEM sing 361 n n C2B C3B HEM doub 362 n n C2B CMB HEM sing 363 n n C3B C4B HEM sing 364 n n C3B CAB HEM sing 365 n n C4B NB HEM doub 366 n n CMB HMB HEM sing 367 n n CMB HMBA HEM sing 368 n n CMB HMBB HEM sing 369 n n CAB CBB HEM doub 370 n n CAB HAB HEM sing 371 n n CBB HBB HEM sing 372 n n CBB HBBA HEM sing 373 n n C1C C2C HEM sing 374 n y C1C NC HEM sing 375 n y C2C C3C HEM doub 376 n y C2C CMC HEM sing 377 n n C3C C4C HEM sing 378 n y C3C CAC HEM sing 379 n n C4C NC HEM sing 380 n y CMC HMC HEM sing 381 n n CMC HMCA HEM sing 382 n n CMC HMCB HEM sing 383 n n CAC CBC HEM doub 384 n n CAC HAC HEM sing 385 n n CBC HBC HEM sing 386 n n CBC HBCA HEM sing 387 n n C1D C2D HEM sing 388 n n C1D ND HEM doub 389 n n C2D C3D HEM doub 390 n n C2D CMD HEM sing 391 n n C3D C4D HEM sing 392 n n C3D CAD HEM sing 393 n n C4D ND HEM sing 394 n n CMD HMD HEM sing 395 n n CMD HMDA HEM sing 396 n n CMD HMDB HEM sing 397 n n CAD CBD HEM sing 398 n n CAD HAD HEM sing 399 n n CAD HADA HEM sing 400 n n CBD CGD HEM sing 401 n n CBD HBD HEM sing 402 n n CBD HBDA HEM sing 403 n n CGD O1D HEM doub 404 n n CGD O2D HEM sing 405 n n O2A H2A HEM sing 406 n n O2D H2D HEM sing 407 n n FE NA HEM sing 408 n n FE NB HEM sing 409 n n FE NC HEM sing 410 n n FE ND HEM sing 411 n n # _atom_sites.entry_id 1XME _atom_sites.fract_transf_matrix[1][1] 0.008703 _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] 0.008703 _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] 0.005648 _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 D 4 BNG A 1 805 805 BNG BNG . E 5 CU A 1 803 803 CU 1CU . F 6 HEM A 1 800 800 HEM HEM . G 7 HAS A 1 801 801 HAS HAS . H 8 GOL A 1 804 804 GOL GOL . I 9 CUA B 1 802 802 CUA CUA . J 10 HOH A 1 806 1 HOH HOH . J 10 HOH A 2 807 2 HOH HOH . J 10 HOH A 3 808 3 HOH HOH . J 10 HOH A 4 809 4 HOH HOH . J 10 HOH A 5 810 5 HOH HOH . J 10 HOH A 6 811 6 HOH HOH . J 10 HOH A 7 812 7 HOH HOH . J 10 HOH A 8 813 9 HOH HOH . J 10 HOH A 9 814 10 HOH HOH . J 10 HOH A 10 815 11 HOH HOH . J 10 HOH A 11 816 13 HOH HOH . J 10 HOH A 12 817 14 HOH HOH . J 10 HOH A 13 818 15 HOH HOH . J 10 HOH A 14 819 16 HOH HOH . J 10 HOH A 15 820 18 HOH HOH . J 10 HOH A 16 821 19 HOH HOH . J 10 HOH A 17 822 20 HOH HOH . J 10 HOH A 18 823 21 HOH HOH . J 10 HOH A 19 824 23 HOH HOH . J 10 HOH A 20 825 24 HOH HOH . J 10 HOH A 21 826 25 HOH HOH . J 10 HOH A 22 827 26 HOH HOH . J 10 HOH A 23 828 27 HOH HOH . J 10 HOH A 24 829 29 HOH HOH . J 10 HOH A 25 830 30 HOH HOH . J 10 HOH A 26 831 31 HOH HOH . J 10 HOH A 27 832 32 HOH HOH . J 10 HOH A 28 833 33 HOH HOH . J 10 HOH A 29 834 34 HOH HOH . J 10 HOH A 30 835 37 HOH HOH . J 10 HOH A 31 836 38 HOH HOH . J 10 HOH A 32 837 39 HOH HOH . J 10 HOH A 33 838 40 HOH HOH . J 10 HOH A 34 839 41 HOH HOH . J 10 HOH A 35 840 44 HOH HOH . J 10 HOH A 36 841 45 HOH HOH . J 10 HOH A 37 842 46 HOH HOH . J 10 HOH A 38 843 47 HOH HOH . J 10 HOH A 39 844 48 HOH HOH . J 10 HOH A 40 845 50 HOH HOH . J 10 HOH A 41 846 52 HOH HOH . J 10 HOH A 42 847 53 HOH HOH . J 10 HOH A 43 848 54 HOH HOH . J 10 HOH A 44 849 55 HOH HOH . J 10 HOH A 45 850 56 HOH HOH . J 10 HOH A 46 851 59 HOH HOH . J 10 HOH A 47 852 60 HOH HOH . J 10 HOH A 48 853 61 HOH HOH . J 10 HOH A 49 854 63 HOH HOH . J 10 HOH A 50 855 64 HOH HOH . J 10 HOH A 51 856 66 HOH HOH . J 10 HOH A 52 857 67 HOH HOH . J 10 HOH A 53 858 68 HOH HOH . J 10 HOH A 54 859 69 HOH HOH . J 10 HOH A 55 860 71 HOH HOH . J 10 HOH A 56 861 72 HOH HOH . J 10 HOH A 57 862 73 HOH HOH . J 10 HOH A 58 863 74 HOH HOH . J 10 HOH A 59 864 75 HOH HOH . J 10 HOH A 60 865 76 HOH HOH . J 10 HOH A 61 866 77 HOH HOH . J 10 HOH A 62 867 803 HOH 1CU . K 10 HOH B 1 803 12 HOH HOH . K 10 HOH B 2 804 17 HOH HOH . K 10 HOH B 3 805 22 HOH HOH . K 10 HOH B 4 806 28 HOH HOH . K 10 HOH B 5 807 35 HOH HOH . K 10 HOH B 6 808 36 HOH HOH . K 10 HOH B 7 809 42 HOH HOH . K 10 HOH B 8 810 43 HOH HOH . K 10 HOH B 9 811 49 HOH HOH . K 10 HOH B 10 812 51 HOH HOH . K 10 HOH B 11 813 57 HOH HOH . K 10 HOH B 12 814 58 HOH HOH . K 10 HOH B 13 815 62 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 6 89.677 35.435 3.987 1 38.41 ? CHA HEM 800 A 1 HETATM 2 C CHB HEM . . . F 6 90.185 39.72 1.785 1 39.6 ? CHB HEM 800 A 1 HETATM 3 C CHC HEM . . . F 6 86.257 41.401 4.091 1 41.07 ? CHC HEM 800 A 1 HETATM 4 C CHD HEM . . . F 6 85.59 37.006 6.061 1 38.56 ? CHD HEM 800 A 1 HETATM 5 C C1A HEM . . . F 6 90.149 36.449 3.161 1 38.71 ? C1A HEM 800 A 1 HETATM 6 C C2A HEM . . . F 6 91.313 36.292 2.179 1 39.42 ? C2A HEM 800 A 1 HETATM 7 C C3A HEM . . . F 6 91.418 37.508 1.549 1 41.24 ? C3A HEM 800 A 1 HETATM 8 C C4A HEM . . . F 6 90.372 38.383 2.126 1 38.45 ? C4A HEM 800 A 1 HETATM 9 C CMA HEM . . . F 6 92.4 37.925 0.448 1 36.63 ? CMA HEM 800 A 1 HETATM 10 C CAA HEM . . . F 6 92.129 35.029 1.974 1 38.84 ? CAA HEM 800 A 1 HETATM 11 C CBA HEM . . . F 6 93.108 34.803 3.129 1 40.83 ? CBA HEM 800 A 1 HETATM 12 C CGA HEM . . . F 6 93.893 33.5 3.013 1 42.44 ? CGA HEM 800 A 1 HETATM 13 O O1A HEM . . . F 6 95.053 33.453 3.494 1 46.06 ? O1A HEM 800 A 1 HETATM 14 O O2A HEM . . . F 6 93.325 32.503 2.494 1 42.99 ? O2A HEM 800 A 1 HETATM 15 C C1B HEM . . . F 6 89.199 40.59 2.258 1 41.09 ? C1B HEM 800 A 1 HETATM 16 C C2B HEM . . . F 6 89.073 42.01 1.9 1 41.01 ? C2B HEM 800 A 1 HETATM 17 C C3B HEM . . . F 6 87.974 42.478 2.567 1 40.84 ? C3B HEM 800 A 1 HETATM 18 C C4B HEM . . . F 6 87.424 41.358 3.317 1 41.49 ? C4B HEM 800 A 1 HETATM 19 C CMB HEM . . . F 6 89.991 42.764 0.97 1 41.47 ? CMB HEM 800 A 1 HETATM 20 C CAB HEM . . . F 6 87.396 43.848 2.542 1 41.4 ? CAB HEM 800 A 1 HETATM 21 C CBB HEM . . . F 6 87.951 44.977 2.955 1 41.76 ? CBB HEM 800 A 1 HETATM 22 C C1C HEM . . . F 6 85.659 40.361 4.798 1 41.34 ? C1C HEM 800 A 1 HETATM 23 C C2C HEM . . . F 6 84.377 40.438 5.482 1 40.95 ? C2C HEM 800 A 1 HETATM 24 C C3C HEM . . . F 6 84.154 39.123 6.058 1 41.51 ? C3C HEM 800 A 1 HETATM 25 C C4C HEM . . . F 6 85.34 38.334 5.683 1 39.81 ? C4C HEM 800 A 1 HETATM 26 C CMC HEM . . . F 6 83.564 41.578 5.542 1 39.44 ? CMC HEM 800 A 1 HETATM 27 C CAC HEM . . . F 6 83.014 38.592 6.875 1 41.26 ? CAC HEM 800 A 1 HETATM 28 C CBC HEM . . . F 6 81.888 39.211 7.244 1 41.53 ? CBC HEM 800 A 1 HETATM 29 C C1D HEM . . . F 6 86.678 36.186 5.732 1 37.09 ? C1D HEM 800 A 1 HETATM 30 C C2D HEM . . . F 6 86.868 34.918 6.207 1 37.8 ? C2D HEM 800 A 1 HETATM 31 C C3D HEM . . . F 6 88.04 34.43 5.638 1 36.53 ? C3D HEM 800 A 1 HETATM 32 C C4D HEM . . . F 6 88.539 35.479 4.791 1 38.31 ? C4D HEM 800 A 1 HETATM 33 C CMD HEM . . . F 6 85.947 34.18 7.179 1 35.92 ? CMD HEM 800 A 1 HETATM 34 C CAD HEM . . . F 6 88.659 33.057 5.857 1 35.71 ? CAD HEM 800 A 1 HETATM 35 C CBD HEM . . . F 6 89.65 33.031 7.027 1 31.91 ? CBD HEM 800 A 1 HETATM 36 C CGD HEM . . . F 6 90.264 31.637 7.201 1 35.21 ? CGD HEM 800 A 1 HETATM 37 O O1D HEM . . . F 6 90.636 31.286 8.348 1 36.64 ? O1D HEM 800 A 1 HETATM 38 O O2D HEM . . . F 6 90.395 30.909 6.175 1 35.22 ? O2D HEM 800 A 1 HETATM 39 N NA HEM . . . F 6 89.614 37.715 3.067 1 39.82 ? NA HEM 800 A 1 HETATM 40 N NB HEM . . . F 6 88.188 40.237 3.128 1 41.08 ? NB HEM 800 A 1 HETATM 41 N NC HEM . . . F 6 86.183 39.096 4.926 1 40.03 ? NC HEM 800 A 1 HETATM 42 N ND HEM . . . F 6 87.697 36.544 4.883 1 38.09 ? ND HEM 800 A 1 HETATM 43 FE FE HEM . . . F 6 87.944 38.403 4.059 1 36.82 ? FE HEM 800 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 255 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #