data_2AKJ # _model_server_result.job_id VNveSYDFADOLsKSIqW8aVA _model_server_result.datetime_utc '2025-02-05 17:06:40' _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 2akj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":564}' # _entry.id 2AKJ # _exptl.entry_id 2AKJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 916.661 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SIROHEME _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 2AKJ _cell.length_a 128.97 _cell.length_b 128.97 _cell.length_c 120.95 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2AKJ _symmetry.cell_setting tetragonal _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _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,D _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 3 _struct_asym.id C _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 SG CYS 487 A CYS 441 1_555 B FE1 SF4 . A SF4 563 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc2 A SG CYS 493 A CYS 447 1_555 B FE4 SF4 . A SF4 563 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc3 A SG CYS 528 A CYS 482 1_555 B FE2 SF4 . A SF4 563 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc4 A SG CYS 532 A CYS 486 1_555 B FE3 SF4 . A SF4 563 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc5 A SG CYS 532 A CYS 486 1_555 C FE SRM . A SRM 564 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? # _chem_comp.formula 'C42 H44 Fe N4 O16' _chem_comp.formula_weight 916.661 _chem_comp.id SRM _chem_comp.mon_nstd_flag . _chem_comp.name SIROHEME _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 FE NA SRM sing 302 n n FE NB SRM sing 303 n n FE NC SRM sing 304 n n FE ND SRM sing 305 n n CHA C1A SRM doub 306 n n CHA C4D SRM sing 307 n n CHA HHA SRM sing 308 n n CHB C4A SRM sing 309 n n CHB C1B SRM doub 310 n n CHB HHB SRM sing 311 n n CHC C4B SRM sing 312 n n CHC C1C SRM doub 313 n n CHC HHC SRM sing 314 n n CHD C4C SRM doub 315 n n CHD C1D SRM sing 316 n n CHD HHD SRM sing 317 n n NA C1A SRM sing 318 n n NA C4A SRM doub 319 n n C1A C2A SRM sing 320 n n C2A CMA SRM sing 321 n n C2A CDA SRM sing 322 n n C2A C3A SRM sing 323 n n CMA HMA1 SRM sing 324 n n CMA HMA2 SRM sing 325 n n CMA HMA3 SRM sing 326 n n CDA CEA SRM sing 327 n n CDA HDA1 SRM sing 328 n n CDA HDA2 SRM sing 329 n n CEA O3A SRM doub 330 n n CEA O4A SRM sing 331 n n O4A H4A SRM sing 332 n n C3A CAA SRM sing 333 n n C3A C4A SRM sing 334 n n CAA CBA SRM sing 335 n n CAA HAA1 SRM sing 336 n n CAA HAA2 SRM sing 337 n n CBA CCA SRM sing 338 n n CBA HBA1 SRM sing 339 n n CBA HBA2 SRM sing 340 n n CCA O1A SRM doub 341 n n CCA O2A SRM sing 342 n n O2A H2A SRM sing 343 n n NB C1B SRM sing 344 n n NB C4B SRM doub 345 n n C1B C2B SRM sing 346 n n C2B CMB SRM sing 347 n n C2B CDB SRM sing 348 n n C2B C3B SRM sing 349 n n CMB HMB1 SRM sing 350 n n CMB HMB2 SRM sing 351 n n CMB HMB3 SRM sing 352 n n CDB CEB SRM sing 353 n n CDB HDB1 SRM sing 354 n n CDB HDB2 SRM sing 355 n n CEB O3B SRM doub 356 n n CEB O4B SRM sing 357 n n O4B H4B SRM sing 358 n n C3B CAB SRM sing 359 n n C3B C4B SRM sing 360 n n CAB CBB SRM sing 361 n n CAB HAB1 SRM sing 362 n n CAB HAB2 SRM sing 363 n n CBB CCB SRM sing 364 n n CBB HBB1 SRM sing 365 n n CBB HBB2 SRM sing 366 n n CCB O1B SRM doub 367 n n CCB O2B SRM sing 368 n n O2B H2B SRM sing 369 n n NC C1C SRM sing 370 n n NC C4C SRM sing 371 n n C1C C2C SRM sing 372 n n C2C CDC SRM sing 373 n n C2C C3C SRM doub 374 n n CDC CEC SRM sing 375 n n CDC HCD1 SRM sing 376 n n CDC HCD2 SRM sing 377 n n CEC O3C SRM doub 378 n n CEC O4C SRM sing 379 n n O4C H4C SRM sing 380 n n C3C CAC SRM sing 381 n n C3C C4C SRM sing 382 n n CAC CBC SRM sing 383 n n CAC HAC1 SRM sing 384 n n CAC HAC2 SRM sing 385 n n CBC CCC SRM sing 386 n n CBC HBC1 SRM sing 387 n n CBC HBC2 SRM sing 388 n n CCC O1C SRM doub 389 n n CCC O2C SRM sing 390 n n O2C H2C SRM sing 391 n n ND C1D SRM sing 392 n y ND C4D SRM sing 393 n y C1D C2D SRM doub 394 n y C2D CAD SRM sing 395 n n C2D C3D SRM sing 396 n y CAD CBD SRM sing 397 n n CAD HAD1 SRM sing 398 n n CAD HAD2 SRM sing 399 n n CBD CCD SRM sing 400 n n CBD HBD1 SRM sing 401 n n CBD HBD2 SRM sing 402 n n CCD O1D SRM doub 403 n n CCD O2D SRM sing 404 n n O2D H2D SRM sing 405 n n C3D CDD SRM sing 406 n n C3D C4D SRM doub 407 n y CDD CED SRM sing 408 n n CDD HDD1 SRM sing 409 n n CDD HDD2 SRM sing 410 n n CED O3D SRM doub 411 n n CED O4D SRM sing 412 n n O4D H4D SRM sing 413 n n C3A H1 SRM sing 414 n n C3B H2 SRM sing 415 n n # _atom_sites.entry_id 2AKJ _atom_sites.fract_transf_matrix[1][1] 0.007754 _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] 0.007754 _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] 0.008268 _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 SF4 A 1 563 501 SF4 FS4 . C 3 SRM A 1 564 1 SRM SRM . D 4 HOH A 1 5001 5001 HOH HOH . D 4 HOH A 2 5002 5002 HOH HOH . D 4 HOH A 3 5003 5003 HOH HOH . D 4 HOH A 4 5004 5004 HOH HOH . D 4 HOH A 5 5005 5005 HOH HOH . D 4 HOH A 6 5006 5006 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 FE FE SRM . . . C 3 127.265 43.528 44.5 1 35.84 ? FE SRM 564 A 1 HETATM 2 C CHA SRM . . . C 3 127.77 46.361 46.264 1 35.65 ? CHA SRM 564 A 1 HETATM 3 C CHB SRM . . . C 3 128.314 45.058 41.752 1 36.23 ? CHB SRM 564 A 1 HETATM 4 C CHC SRM . . . C 3 126.773 40.66 42.715 1 35.98 ? CHC SRM 564 A 1 HETATM 5 C CHD SRM . . . C 3 126.287 41.933 47.251 1 36.21 ? CHD SRM 564 A 1 HETATM 6 N NA SRM . . . C 3 127.926 45.337 44.111 1 35.99 ? NA SRM 564 A 1 HETATM 7 C C1A SRM . . . C 3 128.052 46.406 44.936 1 35.76 ? C1A SRM 564 A 1 HETATM 8 C C2A SRM . . . C 3 128.497 47.653 44.209 1 35.48 ? C2A SRM 564 A 1 HETATM 9 C CMA SRM . . . C 3 127.29 48.493 43.803 1 34.11 ? CMA SRM 564 A 1 HETATM 10 C CDA SRM . . . C 3 129.499 48.448 45.054 1 36.07 ? CDA SRM 564 A 1 HETATM 11 C CEA SRM . . . C 3 129.547 49.902 44.655 1 37.06 ? CEA SRM 564 A 1 HETATM 12 O O3A SRM . . . C 3 129.125 50.81 45.411 1 37.96 ? O3A SRM 564 A 1 HETATM 13 O O4A SRM . . . C 3 130.007 50.22 43.544 1 38.04 ? O4A SRM 564 A 1 HETATM 14 C C3A SRM . . . C 3 129.164 47 43.057 1 35.55 ? C3A SRM 564 A 1 HETATM 15 C CAA SRM . . . C 3 129.141 47.802 41.775 1 35.85 ? CAA SRM 564 A 1 HETATM 16 C CBA SRM . . . C 3 130.617 47.724 41.377 1 35.53 ? CBA SRM 564 A 1 HETATM 17 C CCA SRM . . . C 3 130.913 48.064 39.925 1 36.45 ? CCA SRM 564 A 1 HETATM 18 O O1A SRM . . . C 3 131.215 49.256 39.619 1 38.5 ? O1A SRM 564 A 1 HETATM 19 O O2A SRM . . . C 3 130.875 47.185 39.021 1 32.08 ? O2A SRM 564 A 1 HETATM 20 C C4A SRM . . . C 3 128.319 45.794 42.907 1 36.06 ? C4A SRM 564 A 1 HETATM 21 N NB SRM . . . C 3 127.506 42.985 42.638 1 35.84 ? NB SRM 564 A 1 HETATM 22 C C1B SRM . . . C 3 127.978 43.734 41.63 1 35.88 ? C1B SRM 564 A 1 HETATM 23 C C2B SRM . . . C 3 128.435 42.864 40.484 1 35.47 ? C2B SRM 564 A 1 HETATM 24 C CMB SRM . . . C 3 128.396 43.607 39.135 1 34.4 ? CMB SRM 564 A 1 HETATM 25 C CDB SRM . . . C 3 129.801 42.196 40.625 1 36.14 ? CDB SRM 564 A 1 HETATM 26 C CEB SRM . . . C 3 130.176 41.568 39.284 1 36.32 ? CEB SRM 564 A 1 HETATM 27 O O3B SRM . . . C 3 131.246 41.881 38.754 1 37.08 ? O3B SRM 564 A 1 HETATM 28 O O4B SRM . . . C 3 129.466 40.756 38.645 1 36.4 ? O4B SRM 564 A 1 HETATM 29 C C3B SRM . . . C 3 127.457 41.78 40.633 1 35.96 ? C3B SRM 564 A 1 HETATM 30 C CAB SRM . . . C 3 126.031 42.293 40.363 1 34.34 ? CAB SRM 564 A 1 HETATM 31 C CBB SRM . . . C 3 125.254 41.932 39.09 1 33.06 ? CBB SRM 564 A 1 HETATM 32 C CCB SRM . . . C 3 123.809 42.422 39.108 1 30.95 ? CCB SRM 564 A 1 HETATM 33 O O1B SRM . . . C 3 123.217 42.692 40.186 1 31.99 ? O1B SRM 564 A 1 HETATM 34 O O2B SRM . . . C 3 123.164 42.562 38.046 1 27.41 ? O2B SRM 564 A 1 HETATM 35 C C4B SRM . . . C 3 127.258 41.773 42.086 1 36.02 ? C4B SRM 564 A 1 HETATM 36 N NC SRM . . . C 3 126.65 41.682 44.893 1 36.15 ? NC SRM 564 A 1 HETATM 37 C C1C SRM . . . C 3 126.5 40.63 44.042 1 35.84 ? C1C SRM 564 A 1 HETATM 38 C C2C SRM . . . C 3 126.018 39.393 44.687 1 35.86 ? C2C SRM 564 A 1 HETATM 39 C CDC SRM . . . C 3 125.766 38.058 44.045 1 36.02 ? CDC SRM 564 A 1 HETATM 40 C CEC SRM . . . C 3 124.318 37.831 43.723 1 37.94 ? CEC SRM 564 A 1 HETATM 41 O O3C SRM . . . C 3 123.455 38.76 43.737 1 37.74 ? O3C SRM 564 A 1 HETATM 42 O O4C SRM . . . C 3 124.001 36.657 43.429 1 39.15 ? O4C SRM 564 A 1 HETATM 43 C C3C SRM . . . C 3 125.853 39.759 46.092 1 36.06 ? C3C SRM 564 A 1 HETATM 44 C CAC SRM . . . C 3 125.401 38.88 47.257 1 36.19 ? CAC SRM 564 A 1 HETATM 45 C CBC SRM . . . C 3 123.951 38.432 47.292 1 38.66 ? CBC SRM 564 A 1 HETATM 46 C CCC SRM . . . C 3 123.374 39.238 48.414 1 39.11 ? CCC SRM 564 A 1 HETATM 47 O O1C SRM . . . C 3 122.979 40.388 48.159 1 41.07 ? O1C SRM 564 A 1 HETATM 48 O O2C SRM . . . C 3 123.313 38.803 49.585 1 38.93 ? O2C SRM 564 A 1 HETATM 49 C C4C SRM . . . C 3 126.289 41.189 46.104 1 36.1 ? C4C SRM 564 A 1 HETATM 50 N ND SRM . . . C 3 127.065 44.041 46.374 1 35.98 ? ND SRM 564 A 1 HETATM 51 C C1D SRM . . . C 3 126.645 43.246 47.383 1 35.94 ? C1D SRM 564 A 1 HETATM 52 C C2D SRM . . . C 3 126.558 43.916 48.701 1 35.77 ? C2D SRM 564 A 1 HETATM 53 C CAD SRM . . . C 3 126.142 43.309 50.035 1 35.87 ? CAD SRM 564 A 1 HETATM 54 C CBD SRM . . . C 3 124.719 43.529 50.578 1 37.26 ? CBD SRM 564 A 1 HETATM 55 C CCD SRM . . . C 3 124.756 43.468 52.111 1 39.91 ? CCD SRM 564 A 1 HETATM 56 O O1D SRM . . . C 3 123.715 43.272 52.813 1 36.87 ? O1D SRM 564 A 1 HETATM 57 O O2D SRM . . . C 3 125.865 43.612 52.72 1 42.45 ? O2D SRM 564 A 1 HETATM 58 C C3D SRM . . . C 3 127.039 45.261 48.37 1 36 ? C3D SRM 564 A 1 HETATM 59 C CDD SRM . . . C 3 127.185 46.452 49.276 1 36.14 ? CDD SRM 564 A 1 HETATM 60 C CED SRM . . . C 3 125.77 46.882 49.61 1 37.92 ? CED SRM 564 A 1 HETATM 61 O O3D SRM . . . C 3 124.771 46.707 48.838 1 37.24 ? O3D SRM 564 A 1 HETATM 62 O O4D SRM . . . C 3 125.596 47.422 50.722 1 39.31 ? O4D SRM 564 A 1 HETATM 63 C C4D SRM . . . C 3 127.311 45.247 46.916 1 35.91 ? C4D SRM 564 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 63 #