data_4YSY # _model_server_result.job_id ZhZZx_YPD5c0YzpnQ58nTg _model_server_result.datetime_utc '2024-11-06 01:25:15' _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 4ysy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":201}' # _entry.id 4YSY # _exptl.entry_id 4YSY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 11 _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 4YSY _cell.length_a 124.12 _cell.length_b 127.66 _cell.length_c 220.736 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YSY _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 1 1 E,F,G,H,Q,R,S,T,U,V,W,X,BA,CA,DA,EA 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 ? 11 O N N ? 11 W 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 E SG CYS 191 E CYS 191 1_555 E SG CYS 193 E CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc1 B SG CYS 89 B CYS 89 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc2 B SG CYS 94 B CYS 94 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? metalc ? metalc3 B SG CYS 97 B CYS 97 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc4 B SG CYS 109 B CYS 109 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc5 B SG CYS 182 B CYS 182 1_555 L FE3 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc6 B SG CYS 185 B CYS 185 1_555 L FE1 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc7 B SG CYS 188 B CYS 188 1_555 L FE2 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc8 B SG CYS 192 B CYS 192 1_555 M FE4 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc9 B SG CYS 239 B CYS 239 1_555 M FE1 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? metalc ? metalc10 B SG CYS 245 B CYS 245 1_555 M FE3 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc11 B SG CYS 249 B CYS 249 1_555 L FE4 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc12 C NE2 HIS 131 C HIS 131 1_555 O FE HEM . C HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc13 O FE HEM . C HEM 201 1_555 D NE2 HIS 95 D HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc14 F SG CYS 89 F CYS 89 1_555 S FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? metalc ? metalc15 F SG CYS 94 F CYS 94 1_555 S FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc16 F SG CYS 97 F CYS 97 1_555 S FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc17 F SG CYS 109 F CYS 109 1_555 S FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc18 F SG CYS 182 F CYS 182 1_555 T FE3 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? metalc ? metalc19 F SG CYS 185 F CYS 185 1_555 T FE1 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc20 F SG CYS 188 F CYS 188 1_555 T FE2 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc21 F SG CYS 192 F CYS 192 1_555 U FE4 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc22 F SG CYS 239 F CYS 239 1_555 U FE1 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc23 F SG CYS 245 F CYS 245 1_555 U FE3 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc24 F SG CYS 249 F CYS 249 1_555 T FE4 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc25 G NE2 HIS 131 G HIS 131 1_555 W FE HEM . G HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc26 W FE HEM . G HEM 201 1_555 H NE2 HIS 95 H HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? # _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 382 n n CHA C4D HEM doub 383 n n CHA HHA HEM sing 384 n n CHB C4A HEM sing 385 n n CHB C1B HEM doub 386 n n CHB HHB HEM sing 387 n n CHC C4B HEM sing 388 n n CHC C1C HEM doub 389 n n CHC HHC HEM sing 390 n n CHD C4C HEM doub 391 n n CHD C1D HEM sing 392 n n CHD HHD HEM sing 393 n n C1A C2A HEM doub 394 n y C1A NA HEM sing 395 n y C2A C3A HEM sing 396 n y C2A CAA HEM sing 397 n n C3A C4A HEM doub 398 n y C3A CMA HEM sing 399 n n C4A NA HEM sing 400 n y CMA HMA HEM sing 401 n n CMA HMAA HEM sing 402 n n CMA HMAB HEM sing 403 n n CAA CBA HEM sing 404 n n CAA HAA HEM sing 405 n n CAA HAAA HEM sing 406 n n CBA CGA HEM sing 407 n n CBA HBA HEM sing 408 n n CBA HBAA HEM sing 409 n n CGA O1A HEM doub 410 n n CGA O2A HEM sing 411 n n C1B C2B HEM sing 412 n n C1B NB HEM sing 413 n n C2B C3B HEM doub 414 n n C2B CMB HEM sing 415 n n C3B C4B HEM sing 416 n n C3B CAB HEM sing 417 n n C4B NB HEM doub 418 n n CMB HMB HEM sing 419 n n CMB HMBA HEM sing 420 n n CMB HMBB HEM sing 421 n n CAB CBB HEM doub 422 n n CAB HAB HEM sing 423 n n CBB HBB HEM sing 424 n n CBB HBBA HEM sing 425 n n C1C C2C HEM sing 426 n y C1C NC HEM sing 427 n y C2C C3C HEM doub 428 n y C2C CMC HEM sing 429 n n C3C C4C HEM sing 430 n y C3C CAC HEM sing 431 n n C4C NC HEM sing 432 n y CMC HMC HEM sing 433 n n CMC HMCA HEM sing 434 n n CMC HMCB HEM sing 435 n n CAC CBC HEM doub 436 n n CAC HAC HEM sing 437 n n CBC HBC HEM sing 438 n n CBC HBCA HEM sing 439 n n C1D C2D HEM sing 440 n n C1D ND HEM doub 441 n n C2D C3D HEM doub 442 n n C2D CMD HEM sing 443 n n C3D C4D HEM sing 444 n n C3D CAD HEM sing 445 n n C4D ND HEM sing 446 n n CMD HMD HEM sing 447 n n CMD HMDA HEM sing 448 n n CMD HMDB HEM sing 449 n n CAD CBD HEM sing 450 n n CAD HAD HEM sing 451 n n CAD HADA HEM sing 452 n n CBD CGD HEM sing 453 n n CBD HBD HEM sing 454 n n CBD HBDA HEM sing 455 n n CGD O1D HEM doub 456 n n CGD O2D HEM sing 457 n n O2A H2A HEM sing 458 n n O2D H2D HEM sing 459 n n FE NA HEM sing 460 n n FE NB HEM sing 461 n n FE NC HEM sing 462 n n FE ND HEM sing 463 n n # _atom_sites.entry_id 4YSY _atom_sites.fract_transf_matrix[1][1] 0.008057 _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] 0.007833 _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] 0.00453 _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 E24 B 1 304 304 E24 E24 . O 11 HEM C 1 201 201 HEM HEM . 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 E24 F 1 304 304 E24 E24 . W 11 HEM G 1 201 201 HEM HEM . 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 . Y 13 HOH A 5 805 805 HOH HOH . Y 13 HOH A 6 806 806 HOH HOH . Y 13 HOH A 7 807 807 HOH HOH . Z 13 HOH B 1 401 401 HOH HOH . Z 13 HOH B 2 402 402 HOH HOH . Z 13 HOH B 3 403 403 HOH HOH . AA 13 HOH C 1 301 301 HOH HOH . BA 13 HOH E 1 801 801 HOH HOH . BA 13 HOH E 2 802 802 HOH HOH . BA 13 HOH E 3 803 803 HOH HOH . BA 13 HOH E 4 804 804 HOH HOH . BA 13 HOH E 5 805 805 HOH HOH . BA 13 HOH E 6 806 806 HOH HOH . BA 13 HOH E 7 807 807 HOH HOH . BA 13 HOH E 8 808 808 HOH HOH . BA 13 HOH E 9 809 809 HOH HOH . BA 13 HOH E 10 810 810 HOH HOH . CA 13 HOH F 1 401 401 HOH HOH . CA 13 HOH F 2 402 402 HOH HOH . DA 13 HOH G 1 301 301 HOH HOH . EA 13 HOH H 1 301 301 HOH HOH . EA 13 HOH H 2 302 302 HOH HOH . EA 13 HOH H 3 303 303 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 . . . O 11 98.637 -12.93 -56.065 1 68.92 ? CHA HEM 201 C 1 HETATM 2 C CHB HEM . . . O 11 99.795 -8.373 -57.012 1 67.9 ? CHB HEM 201 C 1 HETATM 3 C CHC HEM . . . O 11 104.514 -9.451 -56.559 1 66.8 ? CHC HEM 201 C 1 HETATM 4 C CHD HEM . . . O 11 103.32 -14.103 -55.833 1 68.02 ? CHD HEM 201 C 1 HETATM 5 C C1A HEM . . . O 11 98.557 -11.601 -56.318 1 69.34 ? C1A HEM 201 C 1 HETATM 6 C C2A HEM . . . O 11 97.345 -10.887 -56.451 1 70.33 ? C2A HEM 201 C 1 HETATM 7 C C3A HEM . . . O 11 97.684 -9.6 -56.72 1 69.01 ? C3A HEM 201 C 1 HETATM 8 C C4A HEM . . . O 11 99.09 -9.532 -56.767 1 67.82 ? C4A HEM 201 C 1 HETATM 9 C CMA HEM . . . O 11 96.751 -8.43 -56.926 1 69.5 ? CMA HEM 201 C 1 HETATM 10 C CAA HEM . . . O 11 95.944 -11.442 -56.275 1 74.52 ? CAA HEM 201 C 1 HETATM 11 C CBA HEM . . . O 11 95.401 -12.127 -57.535 1 80.22 ? CBA HEM 201 C 1 HETATM 12 C CGA HEM . . . O 11 94.087 -12.848 -57.279 1 81.21 ? CGA HEM 201 C 1 HETATM 13 O O1A HEM . . . O 11 93.625 -13.01 -56.115 1 71.75 ? O1A HEM 201 C 1 HETATM 14 O O2A HEM . . . O 11 93.452 -13.298 -58.267 1 83.92 ? O2A HEM 201 C 1 HETATM 15 C C1B HEM . . . O 11 101.189 -8.271 -56.963 1 66.13 ? C1B HEM 201 C 1 HETATM 16 C C2B HEM . . . O 11 101.863 -7.029 -57.14 1 65.97 ? C2B HEM 201 C 1 HETATM 17 C C3B HEM . . . O 11 103.196 -7.27 -57.026 1 67.88 ? C3B HEM 201 C 1 HETATM 18 C C4B HEM . . . O 11 103.321 -8.742 -56.753 1 67.46 ? C4B HEM 201 C 1 HETATM 19 C CMB HEM . . . O 11 101.255 -5.672 -57.416 1 64.46 ? CMB HEM 201 C 1 HETATM 20 C CAB HEM . . . O 11 104.184 -6.172 -57.144 1 71.21 ? CAB HEM 201 C 1 HETATM 21 C CBB HEM . . . O 11 105.491 -6.293 -56.938 1 76.72 ? CBB HEM 201 C 1 HETATM 22 C C1C HEM . . . O 11 104.606 -10.825 -56.308 1 68.37 ? C1C HEM 201 C 1 HETATM 23 C C2C HEM . . . O 11 105.814 -11.517 -56.149 1 70.32 ? C2C HEM 201 C 1 HETATM 24 C C3C HEM . . . O 11 105.522 -12.855 -55.935 1 68.99 ? C3C HEM 201 C 1 HETATM 25 C C4C HEM . . . O 11 104.082 -12.971 -55.966 1 67.09 ? C4C HEM 201 C 1 HETATM 26 C CMC HEM . . . O 11 107.213 -10.939 -56.181 1 72.46 ? CMC HEM 201 C 1 HETATM 27 C CAC HEM . . . O 11 106.629 -13.827 -55.69 1 69.3 ? CAC HEM 201 C 1 HETATM 28 C CBC HEM . . . O 11 106.502 -15.1 -55.324 1 69.18 ? CBC HEM 201 C 1 HETATM 29 C C1D HEM . . . O 11 101.926 -14.102 -55.857 1 66.69 ? C1D HEM 201 C 1 HETATM 30 C C2D HEM . . . O 11 101.17 -15.345 -55.624 1 65.09 ? C2D HEM 201 C 1 HETATM 31 C C3D HEM . . . O 11 99.861 -15.049 -55.683 1 66.01 ? C3D HEM 201 C 1 HETATM 32 C C4D HEM . . . O 11 99.841 -13.593 -55.942 1 66.61 ? C4D HEM 201 C 1 HETATM 33 C CMD HEM . . . O 11 101.722 -16.723 -55.363 1 65.83 ? CMD HEM 201 C 1 HETATM 34 C CAD HEM . . . O 11 98.759 -16.103 -55.499 1 68.68 ? CAD HEM 201 C 1 HETATM 35 C CBD HEM . . . O 11 97.271 -15.854 -55.895 1 69.89 ? CBD HEM 201 C 1 HETATM 36 C CGD HEM . . . O 11 96.93 -16.018 -57.379 1 72.76 ? CGD HEM 201 C 1 HETATM 37 O O1D HEM . . . O 11 95.93 -15.466 -57.913 1 73.3 ? O1D HEM 201 C 1 HETATM 38 O O2D HEM . . . O 11 97.62 -16.737 -58.126 1 73.84 ? O2D HEM 201 C 1 HETATM 39 N NA HEM . . . O 11 99.619 -10.772 -56.526 1 68.32 ? NA HEM 201 C 1 HETATM 40 N NB HEM . . . O 11 102.073 -9.244 -56.733 1 65.58 ? NB HEM 201 C 1 HETATM 41 N NC HEM . . . O 11 103.576 -11.729 -56.214 1 65.69 ? NC HEM 201 C 1 HETATM 42 N ND HEM . . . O 11 101.09 -13.064 -56.033 1 66.2 ? ND HEM 201 C 1 HETATM 43 FE FE HEM . . . O 11 101.555 -11.255 -56.404 1 63.45 ? FE HEM 201 C 1 # _model_server_stats.io_time_ms 84 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 39 _model_server_stats.query_time_ms 345 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 43 #