data_4YSZ # _model_server_result.job_id p4ScLWRq3q2S1p5LMsXnhw _model_server_result.datetime_utc '2025-02-17 19:38:14' _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 4ysz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":201}' # _entry.id 4YSZ # _exptl.entry_id 4YSZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 10 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _entity.pdbx_number_of_molecules 2 _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 4YSZ _cell.length_a 123.934 _cell.length_b 126.968 _cell.length_c 219.335 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YSZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,I,J,K,L,M,N,O,P,Y,Z,AA,BA 1 1 E,F,G,H,Q,R,S,T,U,V,W,X,CA,DA 2 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 ? 10 N N N ? 10 V 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 A SG CYS 191 A CYS 191 1_555 A SG CYS 193 A CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf2 E SG CYS 191 E CYS 191 1_555 E SG CYS 193 E CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc1 B SG CYS 89 B CYS 89 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc2 B SG CYS 94 B CYS 94 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc3 B SG CYS 97 B CYS 97 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc4 B SG CYS 109 B CYS 109 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc5 B SG CYS 182 B CYS 182 1_555 L FE3 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc6 B SG CYS 185 B CYS 185 1_555 L FE1 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc7 B SG CYS 188 B CYS 188 1_555 L FE2 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc8 B SG CYS 192 B CYS 192 1_555 M FE4 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc9 B SG CYS 239 B CYS 239 1_555 M FE1 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc10 B SG CYS 245 B CYS 245 1_555 M FE3 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc11 B SG CYS 249 B CYS 249 1_555 L FE4 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc12 C NE2 HIS 131 C HIS 131 1_555 N FE HEM . C HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc13 N FE HEM . C HEM 201 1_555 D NE2 HIS 95 D HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc14 F SG CYS 89 F CYS 89 1_555 S FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc15 F SG CYS 94 F CYS 94 1_555 S FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc16 F SG CYS 97 F CYS 97 1_555 S FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? metalc ? metalc17 F SG CYS 109 F CYS 109 1_555 S FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc18 F SG CYS 182 F CYS 182 1_555 T FE3 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc19 F SG CYS 185 F CYS 185 1_555 T FE1 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc20 F SG CYS 188 F CYS 188 1_555 T FE2 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc21 F SG CYS 192 F CYS 192 1_555 U FE4 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc22 F SG CYS 239 F CYS 239 1_555 U FE1 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc23 F SG CYS 245 F CYS 245 1_555 U FE3 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc24 F SG CYS 249 F CYS 249 1_555 T FE4 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc25 G NE2 HIS 131 G HIS 131 1_555 V FE HEM . G HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc26 V FE HEM . G HEM 201 1_555 H NE2 HIS 95 H HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? # _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 386 n n CHA C4D HEM doub 387 n n CHA HHA HEM sing 388 n n CHB C4A HEM sing 389 n n CHB C1B HEM doub 390 n n CHB HHB HEM sing 391 n n CHC C4B HEM sing 392 n n CHC C1C HEM doub 393 n n CHC HHC HEM sing 394 n n CHD C4C HEM doub 395 n n CHD C1D HEM sing 396 n n CHD HHD HEM sing 397 n n C1A C2A HEM doub 398 n y C1A NA HEM sing 399 n y C2A C3A HEM sing 400 n y C2A CAA HEM sing 401 n n C3A C4A HEM doub 402 n y C3A CMA HEM sing 403 n n C4A NA HEM sing 404 n y CMA HMA HEM sing 405 n n CMA HMAA HEM sing 406 n n CMA HMAB HEM sing 407 n n CAA CBA HEM sing 408 n n CAA HAA HEM sing 409 n n CAA HAAA HEM sing 410 n n CBA CGA HEM sing 411 n n CBA HBA HEM sing 412 n n CBA HBAA HEM sing 413 n n CGA O1A HEM doub 414 n n CGA O2A HEM sing 415 n n C1B C2B HEM sing 416 n n C1B NB HEM sing 417 n n C2B C3B HEM doub 418 n n C2B CMB HEM sing 419 n n C3B C4B HEM sing 420 n n C3B CAB HEM sing 421 n n C4B NB HEM doub 422 n n CMB HMB HEM sing 423 n n CMB HMBA HEM sing 424 n n CMB HMBB HEM sing 425 n n CAB CBB HEM doub 426 n n CAB HAB HEM sing 427 n n CBB HBB HEM sing 428 n n CBB HBBA HEM sing 429 n n C1C C2C HEM sing 430 n y C1C NC HEM sing 431 n y C2C C3C HEM doub 432 n y C2C CMC HEM sing 433 n n C3C C4C HEM sing 434 n y C3C CAC HEM sing 435 n n C4C NC HEM sing 436 n y CMC HMC HEM sing 437 n n CMC HMCA HEM sing 438 n n CMC HMCB HEM sing 439 n n CAC CBC HEM doub 440 n n CAC HAC HEM sing 441 n n CBC HBC HEM sing 442 n n CBC HBCA HEM sing 443 n n C1D C2D HEM sing 444 n n C1D ND HEM doub 445 n n C2D C3D HEM doub 446 n n C2D CMD HEM sing 447 n n C3D C4D HEM sing 448 n n C3D CAD HEM sing 449 n n C4D ND HEM sing 450 n n CMD HMD HEM sing 451 n n CMD HMDA HEM sing 452 n n CMD HMDB HEM sing 453 n n CAD CBD HEM sing 454 n n CAD HAD HEM sing 455 n n CAD HADA HEM sing 456 n n CBD CGD HEM sing 457 n n CBD HBD HEM sing 458 n n CBD HBDA HEM sing 459 n n CGD O1D HEM doub 460 n n CGD O2D HEM sing 461 n n O2A H2A HEM sing 462 n n O2D H2D HEM sing 463 n n FE NA HEM sing 464 n n FE NB HEM sing 465 n n FE NC HEM sing 466 n n FE ND HEM sing 467 n n # _atom_sites.entry_id 4YSZ _atom_sites.fract_transf_matrix[1][1] 0.008069 _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] 0.007876 _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] 0.004559 _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 I 5 MLI A 1 701 701 MLI MLI . J 6 FAD A 1 702 702 FAD FAD . K 7 FES B 1 301 301 FES FES . L 8 SF4 B 1 302 302 SF4 SF4 . M 9 F3S B 1 303 303 F3S F3S . N 10 HEM C 1 201 201 HEM HEM . O 11 12J C 1 202 202 12J 12J . P 12 EPH D 1 201 201 EPH EPH . Q 5 MLI E 1 701 701 MLI MLI . R 6 FAD E 1 702 702 FAD FAD . S 7 FES F 1 301 301 FES FES . T 8 SF4 F 1 302 302 SF4 SF4 . U 9 F3S F 1 303 303 F3S F3S . V 10 HEM G 1 201 201 HEM HEM . W 11 12J G 1 202 202 12J 12J . X 12 EPH H 1 201 201 EPH EPH . Y 13 HOH A 1 801 801 HOH HOH . Y 13 HOH A 2 802 802 HOH HOH . Y 13 HOH A 3 803 803 HOH HOH . Y 13 HOH A 4 804 804 HOH HOH . Z 13 HOH B 1 401 401 HOH HOH . Z 13 HOH B 2 402 402 HOH HOH . AA 13 HOH C 1 301 301 HOH HOH . BA 13 HOH D 1 301 301 HOH HOH . CA 13 HOH E 1 801 801 HOH HOH . CA 13 HOH E 2 802 802 HOH HOH . CA 13 HOH E 3 803 803 HOH HOH . CA 13 HOH E 4 804 804 HOH HOH . CA 13 HOH E 5 805 805 HOH HOH . CA 13 HOH E 6 806 806 HOH HOH . DA 13 HOH H 1 301 301 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 . . . N 10 98.934 13.146 56.089 1 67.59 ? CHA HEM 201 C 1 HETATM 2 C CHB HEM . . . N 10 100.005 8.523 56.743 1 72.04 ? CHB HEM 201 C 1 HETATM 3 C CHC HEM . . . N 10 104.737 9.648 56.94 1 71.5 ? CHC HEM 201 C 1 HETATM 4 C CHD HEM . . . N 10 103.633 14.216 55.723 1 71.83 ? CHD HEM 201 C 1 HETATM 5 C C1A HEM . . . N 10 98.83 11.803 56.252 1 65.87 ? C1A HEM 201 C 1 HETATM 6 C C2A HEM . . . N 10 97.606 11.107 56.351 1 64.18 ? C2A HEM 201 C 1 HETATM 7 C C3A HEM . . . N 10 97.903 9.802 56.532 1 63.12 ? C3A HEM 201 C 1 HETATM 8 C C4A HEM . . . N 10 99.312 9.702 56.544 1 66.74 ? C4A HEM 201 C 1 HETATM 9 C CMA HEM . . . N 10 96.907 8.672 56.671 1 61.25 ? CMA HEM 201 C 1 HETATM 10 C CAA HEM . . . N 10 96.219 11.712 56.248 1 67.91 ? CAA HEM 201 C 1 HETATM 11 C CBA HEM . . . N 10 95.813 12.41 57.556 1 69.86 ? CBA HEM 201 C 1 HETATM 12 C CGA HEM . . . N 10 94.452 13.068 57.458 1 68.07 ? CGA HEM 201 C 1 HETATM 13 O O1A HEM . . . N 10 93.712 12.91 56.442 1 56.97 ? O1A HEM 201 C 1 HETATM 14 O O2A HEM . . . N 10 94.091 13.78 58.438 1 69.27 ? O2A HEM 201 C 1 HETATM 15 C C1B HEM . . . N 10 101.399 8.423 56.874 1 73.99 ? C1B HEM 201 C 1 HETATM 16 C C2B HEM . . . N 10 102.056 7.189 57.142 1 77.57 ? C2B HEM 201 C 1 HETATM 17 C C3B HEM . . . N 10 103.399 7.445 57.217 1 80.84 ? C3B HEM 201 C 1 HETATM 18 C C4B HEM . . . N 10 103.54 8.923 56.977 1 75.39 ? C4B HEM 201 C 1 HETATM 19 C CMB HEM . . . N 10 101.404 5.835 57.329 1 77.24 ? CMB HEM 201 C 1 HETATM 20 C CAB HEM . . . N 10 104.392 6.364 57.475 1 86.71 ? CAB HEM 201 C 1 HETATM 21 C CBB HEM . . . N 10 105.716 6.504 57.492 1 89.37 ? CBB HEM 201 C 1 HETATM 22 C C1C HEM . . . N 10 104.86 10.994 56.597 1 71.2 ? C1C HEM 201 C 1 HETATM 23 C C2C HEM . . . N 10 106.083 11.664 56.438 1 72.67 ? C2C HEM 201 C 1 HETATM 24 C C3C HEM . . . N 10 105.817 12.971 56.086 1 72.57 ? C3C HEM 201 C 1 HETATM 25 C C4C HEM . . . N 10 104.378 13.097 56.012 1 73.61 ? C4C HEM 201 C 1 HETATM 26 C CMC HEM . . . N 10 107.479 11.109 56.61 1 75.15 ? CMC HEM 201 C 1 HETATM 27 C CAC HEM . . . N 10 106.94 13.91 55.824 1 71.85 ? CAC HEM 201 C 1 HETATM 28 C CBC HEM . . . N 10 106.83 15.142 55.342 1 72.22 ? CBC HEM 201 C 1 HETATM 29 C C1D HEM . . . N 10 102.237 14.24 55.758 1 68.09 ? C1D HEM 201 C 1 HETATM 30 C C2D HEM . . . N 10 101.501 15.495 55.519 1 66.41 ? C2D HEM 201 C 1 HETATM 31 C C3D HEM . . . N 10 100.194 15.223 55.62 1 66.51 ? C3D HEM 201 C 1 HETATM 32 C C4D HEM . . . N 10 100.147 13.781 55.936 1 67.34 ? C4D HEM 201 C 1 HETATM 33 C CMD HEM . . . N 10 102.047 16.866 55.21 1 66.2 ? CMD HEM 201 C 1 HETATM 34 C CAD HEM . . . N 10 99.124 16.307 55.462 1 67.12 ? CAD HEM 201 C 1 HETATM 35 C CBD HEM . . . N 10 97.609 16.007 55.663 1 67.45 ? CBD HEM 201 C 1 HETATM 36 C CGD HEM . . . N 10 96.982 16.229 57.052 1 64.7 ? CGD HEM 201 C 1 HETATM 37 O O1D HEM . . . N 10 95.738 16.324 57.126 1 63.12 ? O1D HEM 201 C 1 HETATM 38 O O2D HEM . . . N 10 97.601 16.341 58.142 1 60.1 ? O2D HEM 201 C 1 HETATM 39 N NA HEM . . . N 10 99.868 10.944 56.395 1 66.29 ? NA HEM 201 C 1 HETATM 40 N NB HEM . . . N 10 102.302 9.402 56.782 1 73.17 ? NB HEM 201 C 1 HETATM 41 N NC HEM . . . N 10 103.842 11.884 56.352 1 70.84 ? NC HEM 201 C 1 HETATM 42 N ND HEM . . . N 10 101.385 13.223 56 1 67.62 ? ND HEM 201 C 1 HETATM 43 FE FE HEM . . . N 10 101.813 11.405 56.396 1 64 ? FE HEM 201 C 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #