data_4YTM # _model_server_result.job_id ocZwJpEI9QRfu536ntDB7A _model_server_result.datetime_utc '2024-11-28 11:20:59' _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 4ytm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":201}' # _entry.id 4YTM # _exptl.entry_id 4YTM _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 4YTM _cell.length_a 123.654 _cell.length_b 126.426 _cell.length_c 220.873 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YTM _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 1 1 E,F,G,H,Q,R,S,T,U,V,W 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 metalc ? metalc1 B SG CYS 89 B CYS 89 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc2 B SG CYS 94 B CYS 94 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc3 B SG CYS 97 B CYS 97 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc4 B SG CYS 109 B CYS 109 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc5 B SG CYS 182 B CYS 182 1_555 L FE3 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc6 B SG CYS 185 B CYS 185 1_555 L FE1 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? metalc ? metalc7 B SG CYS 188 B CYS 188 1_555 L FE2 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc8 B SG CYS 192 B CYS 192 1_555 M FE4 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc9 B SG CYS 239 B CYS 239 1_555 M FE1 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc10 B SG CYS 245 B CYS 245 1_555 M FE3 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc11 B SG CYS 249 B CYS 249 1_555 L FE4 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc12 C NE2 HIS 131 C HIS 131 1_555 N FE HEM . C HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc13 N FE HEM . C HEM 201 1_555 D NE2 HIS 95 D HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc14 F SG CYS 89 F CYS 89 1_555 S FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc15 F SG CYS 94 F CYS 94 1_555 S FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc16 F SG CYS 97 F CYS 97 1_555 S FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? metalc ? metalc17 F SG CYS 109 F CYS 109 1_555 S FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc18 F SG CYS 182 F CYS 182 1_555 T FE3 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc19 F SG CYS 185 F CYS 185 1_555 T FE1 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc20 F SG CYS 188 F CYS 188 1_555 T FE2 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc21 F SG CYS 192 F CYS 192 1_555 U FE4 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc22 F SG CYS 239 F CYS 239 1_555 U FE1 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc23 F SG CYS 245 F CYS 245 1_555 U FE3 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc24 F SG CYS 249 F CYS 249 1_555 T FE4 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc25 G NE2 HIS 131 G HIS 131 1_555 V FE HEM . G HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc26 V FE HEM . G HEM 201 1_555 H NE2 HIS 95 H HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? # _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 390 n n CHA C4D HEM doub 391 n n CHA HHA HEM sing 392 n n CHB C4A HEM sing 393 n n CHB C1B HEM doub 394 n n CHB HHB HEM sing 395 n n CHC C4B HEM sing 396 n n CHC C1C HEM doub 397 n n CHC HHC HEM sing 398 n n CHD C4C HEM doub 399 n n CHD C1D HEM sing 400 n n CHD HHD HEM sing 401 n n C1A C2A HEM doub 402 n y C1A NA HEM sing 403 n y C2A C3A HEM sing 404 n y C2A CAA HEM sing 405 n n C3A C4A HEM doub 406 n y C3A CMA HEM sing 407 n n C4A NA HEM sing 408 n y CMA HMA HEM sing 409 n n CMA HMAA HEM sing 410 n n CMA HMAB HEM sing 411 n n CAA CBA HEM sing 412 n n CAA HAA HEM sing 413 n n CAA HAAA HEM sing 414 n n CBA CGA HEM sing 415 n n CBA HBA HEM sing 416 n n CBA HBAA HEM sing 417 n n CGA O1A HEM doub 418 n n CGA O2A HEM sing 419 n n C1B C2B HEM sing 420 n n C1B NB HEM sing 421 n n C2B C3B HEM doub 422 n n C2B CMB HEM sing 423 n n C3B C4B HEM sing 424 n n C3B CAB HEM sing 425 n n C4B NB HEM doub 426 n n CMB HMB HEM sing 427 n n CMB HMBA HEM sing 428 n n CMB HMBB HEM sing 429 n n CAB CBB HEM doub 430 n n CAB HAB HEM sing 431 n n CBB HBB HEM sing 432 n n CBB HBBA HEM sing 433 n n C1C C2C HEM sing 434 n y C1C NC HEM sing 435 n y C2C C3C HEM doub 436 n y C2C CMC HEM sing 437 n n C3C C4C HEM sing 438 n y C3C CAC HEM sing 439 n n C4C NC HEM sing 440 n y CMC HMC HEM sing 441 n n CMC HMCA HEM sing 442 n n CMC HMCB HEM sing 443 n n CAC CBC HEM doub 444 n n CAC HAC HEM sing 445 n n CBC HBC HEM sing 446 n n CBC HBCA HEM sing 447 n n C1D C2D HEM sing 448 n n C1D ND HEM doub 449 n n C2D C3D HEM doub 450 n n C2D CMD HEM sing 451 n n C3D C4D HEM sing 452 n n C3D CAD HEM sing 453 n n C4D ND HEM sing 454 n n CMD HMD HEM sing 455 n n CMD HMDA HEM sing 456 n n CMD HMDB HEM sing 457 n n CAD CBD HEM sing 458 n n CAD HAD HEM sing 459 n n CAD HADA HEM sing 460 n n CBD CGD HEM sing 461 n n CBD HBD HEM sing 462 n n CBD HBDA HEM sing 463 n n CGD O1D HEM doub 464 n n CGD O2D HEM sing 465 n n O2A H2A HEM sing 466 n n O2D H2D HEM sing 467 n n FE NA HEM sing 468 n n FE NB HEM sing 469 n n FE NC HEM sing 470 n n FE ND HEM sing 471 n n # _atom_sites.entry_id 4YTM _atom_sites.fract_transf_matrix[1][1] 0.008087 _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] 0.00791 _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] 0.004527 _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 F6A C 1 202 202 F6A F6A . 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 F6A G 1 202 202 F6A F6A . # 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 . . . V 10 -67.433 -53.157 -82.549 1 85.69 ? CHA HEM 201 G 1 HETATM 2 C CHB HEM . . . V 10 -68.667 -57.781 -82.091 1 94.62 ? CHB HEM 201 G 1 HETATM 3 C CHC HEM . . . V 10 -73.347 -56.555 -82.548 1 97.86 ? CHC HEM 201 G 1 HETATM 4 C CHD HEM . . . V 10 -72.088 -51.87 -82.668 1 83.6 ? CHD HEM 201 G 1 HETATM 5 C C1A HEM . . . V 10 -67.386 -54.512 -82.375 1 87.05 ? C1A HEM 201 G 1 HETATM 6 C C2A HEM . . . V 10 -66.195 -55.246 -82.162 1 89.43 ? C2A HEM 201 G 1 HETATM 7 C C3A HEM . . . V 10 -66.539 -56.543 -82.023 1 90.32 ? C3A HEM 201 G 1 HETATM 8 C C4A HEM . . . V 10 -67.941 -56.618 -82.164 1 90.77 ? C4A HEM 201 G 1 HETATM 9 C CMA HEM . . . V 10 -65.588 -57.686 -81.769 1 91.2 ? CMA HEM 201 G 1 HETATM 10 C CAA HEM . . . V 10 -64.79 -54.703 -82.054 1 91.73 ? CAA HEM 201 G 1 HETATM 11 C CBA HEM . . . V 10 -63.931 -54.905 -83.306 1 92.1 ? CBA HEM 201 G 1 HETATM 12 C CGA HEM . . . V 10 -63.067 -53.68 -83.511 1 95.76 ? CGA HEM 201 G 1 HETATM 13 O O1A HEM . . . V 10 -62.438 -53.193 -82.539 1 87.96 ? O1A HEM 201 G 1 HETATM 14 O O2A HEM . . . V 10 -62.987 -53.141 -84.649 1 106.57 ? O2A HEM 201 G 1 HETATM 15 C C1B HEM . . . V 10 -70.061 -57.825 -82.186 1 98.06 ? C1B HEM 201 G 1 HETATM 16 C C2B HEM . . . V 10 -70.76 -59.058 -82.091 1 101.13 ? C2B HEM 201 G 1 HETATM 17 C C3B HEM . . . V 10 -72.086 -58.783 -82.22 1 99.79 ? C3B HEM 201 G 1 HETATM 18 C C4B HEM . . . V 10 -72.171 -57.293 -82.4 1 97.65 ? C4B HEM 201 G 1 HETATM 19 C CMB HEM . . . V 10 -70.151 -60.433 -81.897 1 100.61 ? CMB HEM 201 G 1 HETATM 20 C CAB HEM . . . V 10 -73.105 -59.86 -82.159 1 101.31 ? CAB HEM 201 G 1 HETATM 21 C CBB HEM . . . V 10 -74.417 -59.686 -82.217 1 106.22 ? CBB HEM 201 G 1 HETATM 22 C C1C HEM . . . V 10 -73.428 -55.16 -82.59 1 96.47 ? C1C HEM 201 G 1 HETATM 23 C C2C HEM . . . V 10 -74.622 -54.418 -82.631 1 95.09 ? C2C HEM 201 G 1 HETATM 24 C C3C HEM . . . V 10 -74.303 -53.074 -82.664 1 91.04 ? C3C HEM 201 G 1 HETATM 25 C C4C HEM . . . V 10 -72.863 -52.999 -82.634 1 87.96 ? C4C HEM 201 G 1 HETATM 26 C CMC HEM . . . V 10 -76.033 -54.955 -82.634 1 96.51 ? CMC HEM 201 G 1 HETATM 27 C CAC HEM . . . V 10 -75.383 -52.048 -82.7 1 90.13 ? CAC HEM 201 G 1 HETATM 28 C CBC HEM . . . V 10 -75.223 -50.726 -82.7 1 91.25 ? CBC HEM 201 G 1 HETATM 29 C C1D HEM . . . V 10 -70.699 -51.886 -82.648 1 81.73 ? C1D HEM 201 G 1 HETATM 30 C C2D HEM . . . V 10 -69.916 -50.637 -82.687 1 80.97 ? C2D HEM 201 G 1 HETATM 31 C C3D HEM . . . V 10 -68.619 -50.967 -82.661 1 80.62 ? C3D HEM 201 G 1 HETATM 32 C C4D HEM . . . V 10 -68.616 -52.445 -82.608 1 84.81 ? C4D HEM 201 G 1 HETATM 33 C CMD HEM . . . V 10 -70.401 -49.209 -82.749 1 81.35 ? CMD HEM 201 G 1 HETATM 34 C CAD HEM . . . V 10 -67.531 -49.894 -82.699 1 78.22 ? CAD HEM 201 G 1 HETATM 35 C CBD HEM . . . V 10 -66.029 -50.253 -82.732 1 74.61 ? CBD HEM 201 G 1 HETATM 36 C CGD HEM . . . V 10 -65.494 -50.387 -84.145 1 72.99 ? CGD HEM 201 G 1 HETATM 37 O O1D HEM . . . V 10 -64.259 -50.46 -84.342 1 70.02 ? O1D HEM 201 G 1 HETATM 38 O O2D HEM . . . V 10 -66.257 -50.409 -85.137 1 69.41 ? O2D HEM 201 G 1 HETATM 39 N NA HEM . . . V 10 -68.454 -55.367 -82.382 1 87.89 ? NA HEM 201 G 1 HETATM 40 N NB HEM . . . V 10 -70.919 -56.805 -82.357 1 95.79 ? NB HEM 201 G 1 HETATM 41 N NC HEM . . . V 10 -72.383 -54.283 -82.613 1 89.58 ? NC HEM 201 G 1 HETATM 42 N ND HEM . . . V 10 -69.878 -52.942 -82.592 1 83.66 ? ND HEM 201 G 1 HETATM 43 FE FE HEM . . . V 10 -70.356 -54.771 -82.551 1 83.56 ? FE HEM 201 G 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 252 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 43 #