data_3VR8 # _model_server_result.job_id k-_ajQMOwoN_j3OhVzlDTA _model_server_result.datetime_utc '2024-11-28 10:05:09' _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 3vr8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":201}' # _entry.id 3VR8 # _exptl.entry_id 3VR8 _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 3VR8 _cell.length_a 123.707 _cell.length_b 129.09 _cell.length_c 221.167 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VR8 _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,X 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.979 ? disulf ? disulf2 E SG CYS 191 E CYS 191 1_555 E SG CYS 193 E CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.931 ? covale ? covale1 A NE2 HIS 79 A HIS 79 1_555 J C8M FAD . A FAD 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.845 ? covale ? covale2 E NE2 HIS 79 E HIS 79 1_555 R C8M FAD . E FAD 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.842 ? metalc ? metalc1 B SG CYS 89 B CYS 89 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc2 B SG CYS 94 B CYS 94 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc3 B SG CYS 97 B CYS 97 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc4 B SG CYS 109 B CYS 109 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? metalc ? metalc5 B SG CYS 182 B CYS 182 1_555 L FE3 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc6 B SG CYS 185 B CYS 185 1_555 L FE1 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc7 B SG CYS 188 B CYS 188 1_555 L FE2 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc8 B SG CYS 192 B CYS 192 1_555 M FE4 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.914 ? metalc ? metalc9 B SG CYS 239 B CYS 239 1_555 M FE1 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc10 B SG CYS 245 B CYS 245 1_555 M FE3 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc11 B SG CYS 249 B CYS 249 1_555 L FE4 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc12 C NE2 HIS 131 C HIS 131 1_555 N FE HEM . C HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc13 N FE HEM . C HEM 201 1_555 D NE2 HIS 95 D HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc14 F SG CYS 89 F CYS 89 1_555 S FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc15 F SG CYS 94 F CYS 94 1_555 S FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc16 F SG CYS 97 F CYS 97 1_555 S FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc17 F SG CYS 109 F CYS 109 1_555 S FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? metalc ? metalc18 F SG CYS 182 F CYS 182 1_555 T FE3 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc19 F SG CYS 185 F CYS 185 1_555 T FE1 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc20 F SG CYS 188 F CYS 188 1_555 T FE2 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc21 F SG CYS 192 F CYS 192 1_555 U FE4 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc22 F SG CYS 239 F CYS 239 1_555 U FE1 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc23 F SG CYS 245 F CYS 245 1_555 U FE3 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc24 F SG CYS 249 F CYS 249 1_555 T FE4 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc25 G NE2 HIS 131 G HIS 131 1_555 V FE HEM . G HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc26 V FE HEM . G HEM 201 1_555 H NE2 HIS 95 H HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? # _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 349 n n CHA C4D HEM doub 350 n n CHA HHA HEM sing 351 n n CHB C4A HEM sing 352 n n CHB C1B HEM doub 353 n n CHB HHB HEM sing 354 n n CHC C4B HEM sing 355 n n CHC C1C HEM doub 356 n n CHC HHC HEM sing 357 n n CHD C4C HEM doub 358 n n CHD C1D HEM sing 359 n n CHD HHD HEM sing 360 n n C1A C2A HEM doub 361 n y C1A NA HEM sing 362 n y C2A C3A HEM sing 363 n y C2A CAA HEM sing 364 n n C3A C4A HEM doub 365 n y C3A CMA HEM sing 366 n n C4A NA HEM sing 367 n y CMA HMA HEM sing 368 n n CMA HMAA HEM sing 369 n n CMA HMAB HEM sing 370 n n CAA CBA HEM sing 371 n n CAA HAA HEM sing 372 n n CAA HAAA HEM sing 373 n n CBA CGA HEM sing 374 n n CBA HBA HEM sing 375 n n CBA HBAA HEM sing 376 n n CGA O1A HEM doub 377 n n CGA O2A HEM sing 378 n n C1B C2B HEM sing 379 n n C1B NB HEM sing 380 n n C2B C3B HEM doub 381 n n C2B CMB HEM sing 382 n n C3B C4B HEM sing 383 n n C3B CAB HEM sing 384 n n C4B NB HEM doub 385 n n CMB HMB HEM sing 386 n n CMB HMBA HEM sing 387 n n CMB HMBB HEM sing 388 n n CAB CBB HEM doub 389 n n CAB HAB HEM sing 390 n n CBB HBB HEM sing 391 n n CBB HBBA HEM sing 392 n n C1C C2C HEM sing 393 n y C1C NC HEM sing 394 n y C2C C3C HEM doub 395 n y C2C CMC HEM sing 396 n n C3C C4C HEM sing 397 n y C3C CAC HEM sing 398 n n C4C NC HEM sing 399 n y CMC HMC HEM sing 400 n n CMC HMCA HEM sing 401 n n CMC HMCB HEM sing 402 n n CAC CBC HEM doub 403 n n CAC HAC HEM sing 404 n n CBC HBC HEM sing 405 n n CBC HBCA HEM sing 406 n n C1D C2D HEM sing 407 n n C1D ND HEM doub 408 n n C2D C3D HEM doub 409 n n C2D CMD HEM sing 410 n n C3D C4D HEM sing 411 n n C3D CAD HEM sing 412 n n C4D ND HEM sing 413 n n CMD HMD HEM sing 414 n n CMD HMDA HEM sing 415 n n CMD HMDB HEM sing 416 n n CAD CBD HEM sing 417 n n CAD HAD HEM sing 418 n n CAD HADA HEM sing 419 n n CBD CGD HEM sing 420 n n CBD HBD HEM sing 421 n n CBD HBDA HEM sing 422 n n CGD O1D HEM doub 423 n n CGD O2D HEM sing 424 n n O2A H2A HEM sing 425 n n O2D H2D HEM sing 426 n n FE NA HEM sing 427 n n FE NB HEM sing 428 n n FE NC HEM sing 429 n n FE ND HEM sing 430 n n # _atom_sites.entry_id 3VR8 _atom_sites.fract_transf_matrix[1][1] 0.008084 _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] 0.007747 _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] 0.004521 _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 1 701 300 MLI MLI . J 6 FAD A 1 702 301 FAD FAD . K 7 FES B 1 301 302 FES FES . L 8 SF4 B 1 302 303 SF4 FS4 . M 9 F3S B 1 303 304 F3S F3S . N 10 HEM C 1 201 305 HEM HEM . O 11 RQX C 1 202 500 RQX RQX . P 12 EPH D 1 201 306 EPH EPH . Q 5 MLI E 1 701 300 MLI MLI . R 6 FAD E 1 702 301 FAD FAD . S 7 FES F 1 301 302 FES FES . T 8 SF4 F 1 302 303 SF4 FS4 . U 9 F3S F 1 303 304 F3S F3S . V 10 HEM G 1 201 305 HEM HEM . W 11 RQX G 1 202 500 RQX RQX . X 12 EPH H 1 201 306 EPH EPH . # 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 -36.557 -12.637 -54.089 1 94.22 ? CHA HEM 201 C 1 HETATM 2 C CHB HEM . . . N 10 -37.886 -8.06 -53.253 1 91.76 ? CHB HEM 201 C 1 HETATM 3 C CHC HEM . . . N 10 -42.47 -9.52 -53.631 1 94.74 ? CHC HEM 201 C 1 HETATM 4 C CHD HEM . . . N 10 -41.13 -14.043 -54.701 1 94.25 ? CHD HEM 201 C 1 HETATM 5 C C1A HEM . . . N 10 -36.539 -11.277 -53.859 1 93.59 ? C1A HEM 201 C 1 HETATM 6 C C2A HEM . . . N 10 -35.322 -10.475 -53.775 1 93.19 ? C2A HEM 201 C 1 HETATM 7 C C3A HEM . . . N 10 -35.687 -9.201 -53.536 1 91.85 ? C3A HEM 201 C 1 HETATM 8 C C4A HEM . . . N 10 -37.13 -9.172 -53.475 1 92.11 ? C4A HEM 201 C 1 HETATM 9 C CMA HEM . . . N 10 -34.79 -7.963 -53.354 1 90.39 ? CMA HEM 201 C 1 HETATM 10 C CAA HEM . . . N 10 -33.894 -11.06 -53.941 1 93.11 ? CAA HEM 201 C 1 HETATM 11 C CBA HEM . . . N 10 -33.755 -12.229 -52.97 1 95.61 ? CBA HEM 201 C 1 HETATM 12 C CGA HEM . . . N 10 -32.375 -12.837 -52.9 1 97.22 ? CGA HEM 201 C 1 HETATM 13 O O1A HEM . . . N 10 -31.708 -13.003 -53.973 1 97.43 ? O1A HEM 201 C 1 HETATM 14 O O2A HEM . . . N 10 -31.983 -13.168 -51.739 1 96.71 ? O2A HEM 201 C 1 HETATM 15 C C1B HEM . . . N 10 -39.249 -8.051 -53.307 1 92.07 ? C1B HEM 201 C 1 HETATM 16 C C2B HEM . . . N 10 -40.096 -6.885 -53.179 1 92.94 ? C2B HEM 201 C 1 HETATM 17 C C3B HEM . . . N 10 -41.35 -7.299 -53.286 1 94.2 ? C3B HEM 201 C 1 HETATM 18 C C4B HEM . . . N 10 -41.347 -8.735 -53.48 1 94 ? C4B HEM 201 C 1 HETATM 19 C CMB HEM . . . N 10 -39.648 -5.422 -52.959 1 92.48 ? CMB HEM 201 C 1 HETATM 20 C CAB HEM . . . N 10 -42.597 -6.397 -53.222 1 96.38 ? CAB HEM 201 C 1 HETATM 21 C CBB HEM . . . N 10 -43.815 -6.953 -53.121 1 98.25 ? CBB HEM 201 C 1 HETATM 22 C C1C HEM . . . N 10 -42.524 -10.874 -53.869 1 95.31 ? C1C HEM 201 C 1 HETATM 23 C C2C HEM . . . N 10 -43.724 -11.715 -53.803 1 95.14 ? C2C HEM 201 C 1 HETATM 24 C C3C HEM . . . N 10 -43.336 -12.968 -54.112 1 95.87 ? C3C HEM 201 C 1 HETATM 25 C C4C HEM . . . N 10 -41.898 -12.958 -54.372 1 94.96 ? C4C HEM 201 C 1 HETATM 26 C CMC HEM . . . N 10 -45.164 -11.264 -53.454 1 91.7 ? CMC HEM 201 C 1 HETATM 27 C CAC HEM . . . N 10 -44.251 -14.215 -54.169 1 96.17 ? CAC HEM 201 C 1 HETATM 28 C CBC HEM . . . N 10 -44.534 -14.775 -55.345 1 96.37 ? CBC HEM 201 C 1 HETATM 29 C C1D HEM . . . N 10 -39.765 -14.133 -54.585 1 93.38 ? C1D HEM 201 C 1 HETATM 30 C C2D HEM . . . N 10 -38.979 -15.341 -54.711 1 92.44 ? C2D HEM 201 C 1 HETATM 31 C C3D HEM . . . N 10 -37.519 -14.933 -54.525 1 92.48 ? C3D HEM 201 C 1 HETATM 32 C C4D HEM . . . N 10 -37.606 -13.491 -54.308 1 93.63 ? C4D HEM 201 C 1 HETATM 33 C CMD HEM . . . N 10 -39.493 -16.762 -54.986 1 91.55 ? CMD HEM 201 C 1 HETATM 34 C CAD HEM . . . N 10 -36.324 -15.946 -54.573 1 92.22 ? CAD HEM 201 C 1 HETATM 35 C CBD HEM . . . N 10 -34.918 -15.513 -54.107 1 91.61 ? CBD HEM 201 C 1 HETATM 36 C CGD HEM . . . N 10 -34.368 -16.087 -52.798 1 90.71 ? CGD HEM 201 C 1 HETATM 37 O O1D HEM . . . N 10 -33.123 -16.299 -52.703 1 89.82 ? O1D HEM 201 C 1 HETATM 38 O O2D HEM . . . N 10 -35.133 -16.308 -51.822 1 90 ? O2D HEM 201 C 1 HETATM 39 N NA HEM . . . N 10 -37.629 -10.449 -53.675 1 93.01 ? NA HEM 201 C 1 HETATM 40 N NB HEM . . . N 10 -40.04 -9.163 -53.494 1 92.92 ? NB HEM 201 C 1 HETATM 41 N NC HEM . . . N 10 -41.43 -11.666 -54.211 1 94.47 ? NC HEM 201 C 1 HETATM 42 N ND HEM . . . N 10 -38.926 -13.064 -54.355 1 93.65 ? ND HEM 201 C 1 HETATM 43 FE FE HEM . . . N 10 -39.517 -11.081 -53.892 1 92.96 ? FE HEM 201 C 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 346 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 43 #