data_3VR9 # _model_server_result.job_id ebmygDadEGSzgXsHgBwHlQ _model_server_result.datetime_utc '2024-11-24 16:53:46' _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 3vr9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":201}' # _entry.id 3VR9 # _exptl.entry_id 3VR9 _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 3VR9 _cell.length_a 124.011 _cell.length_b 135.333 _cell.length_c 220.498 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VR9 _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 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 covale ? covale1 A NE2 HIS 79 A HIS 79 1_555 J C8M FAD . A FAD 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.668 ? covale ? covale2 E NE2 HIS 79 E HIS 79 1_555 R C8M FAD . E FAD 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.925 ? metalc ? metalc1 B SG CYS 89 B CYS 89 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc2 B SG CYS 94 B CYS 94 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc3 B SG CYS 97 B CYS 97 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc4 B SG CYS 109 B CYS 109 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc5 B SG CYS 182 B CYS 182 1_555 L FE3 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc6 B SG CYS 185 B CYS 185 1_555 L FE1 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc7 B SG CYS 188 B CYS 188 1_555 L FE4 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc8 B SG CYS 192 B CYS 192 1_555 M FE4 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc9 B SG CYS 239 B CYS 239 1_555 M FE1 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc10 B SG CYS 245 B CYS 245 1_555 M FE3 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc11 B SG CYS 249 B CYS 249 1_555 L FE2 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc12 C NE2 HIS 131 C HIS 131 1_555 N FE HEM . C HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc13 N FE HEM . C HEM 201 1_555 D NE2 HIS 95 D HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc14 F SG CYS 89 F CYS 89 1_555 S FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc15 F SG CYS 94 F CYS 94 1_555 S FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc16 F SG CYS 97 F CYS 97 1_555 S FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc17 F SG CYS 109 F CYS 109 1_555 S FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc18 F SG CYS 182 F CYS 182 1_555 T FE3 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? metalc ? metalc19 F SG CYS 185 F CYS 185 1_555 T FE1 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc20 F SG CYS 188 F CYS 188 1_555 T FE4 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc21 F SG CYS 192 F CYS 192 1_555 U FE4 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc22 F SG CYS 239 F CYS 239 1_555 U FE1 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc23 F SG CYS 245 F CYS 245 1_555 U FE3 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc24 F SG CYS 249 F CYS 249 1_555 T FE2 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc25 G NE2 HIS 131 G HIS 131 1_555 W FE HEM . G HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc26 W FE HEM . G HEM 201 1_555 H NE2 HIS 95 H HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? # _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 389 n n CHA C4D HEM doub 390 n n CHA HHA HEM sing 391 n n CHB C4A HEM sing 392 n n CHB C1B HEM doub 393 n n CHB HHB HEM sing 394 n n CHC C4B HEM sing 395 n n CHC C1C HEM doub 396 n n CHC HHC HEM sing 397 n n CHD C4C HEM doub 398 n n CHD C1D HEM sing 399 n n CHD HHD HEM sing 400 n n C1A C2A HEM doub 401 n y C1A NA HEM sing 402 n y C2A C3A HEM sing 403 n y C2A CAA HEM sing 404 n n C3A C4A HEM doub 405 n y C3A CMA HEM sing 406 n n C4A NA HEM sing 407 n y CMA HMA HEM sing 408 n n CMA HMAA HEM sing 409 n n CMA HMAB HEM sing 410 n n CAA CBA HEM sing 411 n n CAA HAA HEM sing 412 n n CAA HAAA HEM sing 413 n n CBA CGA HEM sing 414 n n CBA HBA HEM sing 415 n n CBA HBAA HEM sing 416 n n CGA O1A HEM doub 417 n n CGA O2A HEM sing 418 n n C1B C2B HEM sing 419 n n C1B NB HEM sing 420 n n C2B C3B HEM doub 421 n n C2B CMB HEM sing 422 n n C3B C4B HEM sing 423 n n C3B CAB HEM sing 424 n n C4B NB HEM doub 425 n n CMB HMB HEM sing 426 n n CMB HMBA HEM sing 427 n n CMB HMBB HEM sing 428 n n CAB CBB HEM doub 429 n n CAB HAB HEM sing 430 n n CBB HBB HEM sing 431 n n CBB HBBA HEM sing 432 n n C1C C2C HEM sing 433 n y C1C NC HEM sing 434 n y C2C C3C HEM doub 435 n y C2C CMC HEM sing 436 n n C3C C4C HEM sing 437 n y C3C CAC HEM sing 438 n n C4C NC HEM sing 439 n y CMC HMC HEM sing 440 n n CMC HMCA HEM sing 441 n n CMC HMCB HEM sing 442 n n CAC CBC HEM doub 443 n n CAC HAC HEM sing 444 n n CBC HBC HEM sing 445 n n CBC HBCA HEM sing 446 n n C1D C2D HEM sing 447 n n C1D ND HEM doub 448 n n C2D C3D HEM doub 449 n n C2D CMD HEM sing 450 n n C3D C4D HEM sing 451 n n C3D CAD HEM sing 452 n n C4D ND HEM sing 453 n n CMD HMD HEM sing 454 n n CMD HMDA HEM sing 455 n n CMD HMDB HEM sing 456 n n CAD CBD HEM sing 457 n n CAD HAD HEM sing 458 n n CAD HADA HEM sing 459 n n CBD CGD HEM sing 460 n n CBD HBD HEM sing 461 n n CBD HBDA HEM sing 462 n n CGD O1D HEM doub 463 n n CGD O2D HEM sing 464 n n O2A H2A HEM sing 465 n n O2D H2D HEM sing 466 n n FE NA HEM sing 467 n n FE NB HEM sing 468 n n FE NC HEM sing 469 n n FE ND HEM sing 470 n n # _atom_sites.entry_id 3VR9 _atom_sites.fract_transf_matrix[1][1] 0.008064 _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] 0.007389 _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] 0.004535 _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 FTN C 1 202 810 FTN FTN . 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 11 FTN F 1 304 810 FTN FTN . W 10 HEM G 1 201 305 HEM HEM . 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 5.069 -9.924 27.975 1 80.7 ? CHA HEM 201 C 1 HETATM 2 C CHB HEM . . . N 10 6.439 -5.307 28.433 1 83.36 ? CHB HEM 201 C 1 HETATM 3 C CHC HEM . . . N 10 11.079 -6.678 28.242 1 84.86 ? CHC HEM 201 C 1 HETATM 4 C CHD HEM . . . N 10 9.687 -11.342 27.736 1 80.09 ? CHD HEM 201 C 1 HETATM 5 C C1A HEM . . . N 10 5.07 -8.563 28.139 1 81.96 ? C1A HEM 201 C 1 HETATM 6 C C2A HEM . . . N 10 3.878 -7.77 28.354 1 82.58 ? C2A HEM 201 C 1 HETATM 7 C C3A HEM . . . N 10 4.261 -6.479 28.5 1 82.42 ? C3A HEM 201 C 1 HETATM 8 C C4A HEM . . . N 10 5.695 -6.442 28.354 1 82.16 ? C4A HEM 201 C 1 HETATM 9 C CMA HEM . . . N 10 3.386 -5.226 28.758 1 80.48 ? CMA HEM 201 C 1 HETATM 10 C CAA HEM . . . N 10 2.453 -8.37 28.463 1 83.27 ? CAA HEM 201 C 1 HETATM 11 C CBA HEM . . . N 10 1.675 -8.631 27.177 1 85.83 ? CBA HEM 201 C 1 HETATM 12 C CGA HEM . . . N 10 0.263 -8.845 27.672 1 88.33 ? CGA HEM 201 C 1 HETATM 13 O O1A HEM . . . N 10 0.061 -9.787 28.492 1 89.86 ? O1A HEM 201 C 1 HETATM 14 O O2A HEM . . . N 10 -0.658 -8.067 27.286 1 89.85 ? O2A HEM 201 C 1 HETATM 15 C C1B HEM . . . N 10 7.816 -5.273 28.43 1 85.11 ? C1B HEM 201 C 1 HETATM 16 C C2B HEM . . . N 10 8.617 -4.061 28.512 1 85.98 ? C2B HEM 201 C 1 HETATM 17 C C3B HEM . . . N 10 9.905 -4.429 28.454 1 87.11 ? C3B HEM 201 C 1 HETATM 18 C C4B HEM . . . N 10 9.965 -5.882 28.339 1 85.6 ? C4B HEM 201 C 1 HETATM 19 C CMB HEM . . . N 10 8.071 -2.609 28.631 1 84.53 ? CMB HEM 201 C 1 HETATM 20 C CAB HEM . . . N 10 11.104 -3.446 28.517 1 90.6 ? CAB HEM 201 C 1 HETATM 21 C CBB HEM . . . N 10 10.977 -2.209 29.05 1 92.11 ? CBB HEM 201 C 1 HETATM 22 C C1C HEM . . . N 10 11.085 -8.043 28.004 1 83.56 ? C1C HEM 201 C 1 HETATM 23 C C2C HEM . . . N 10 12.259 -8.819 27.654 1 83.38 ? C2C HEM 201 C 1 HETATM 24 C C3C HEM . . . N 10 11.864 -10.086 27.525 1 83.98 ? C3C HEM 201 C 1 HETATM 25 C C4C HEM . . . N 10 10.436 -10.182 27.773 1 82.44 ? C4C HEM 201 C 1 HETATM 26 C CMC HEM . . . N 10 13.704 -8.291 27.471 1 81.52 ? CMC HEM 201 C 1 HETATM 27 C CAC HEM . . . N 10 12.786 -11.271 27.171 1 85.85 ? CAC HEM 201 C 1 HETATM 28 C CBC HEM . . . N 10 13.571 -11.797 28.116 1 86.29 ? CBC HEM 201 C 1 HETATM 29 C C1D HEM . . . N 10 8.322 -11.434 27.732 1 78.71 ? C1D HEM 201 C 1 HETATM 30 C C2D HEM . . . N 10 7.52 -12.629 27.554 1 77.96 ? C2D HEM 201 C 1 HETATM 31 C C3D HEM . . . N 10 6.054 -12.188 27.628 1 77.52 ? C3D HEM 201 C 1 HETATM 32 C C4D HEM . . . N 10 6.148 -10.763 27.858 1 79.28 ? C4D HEM 201 C 1 HETATM 33 C CMD HEM . . . N 10 8.015 -14.068 27.326 1 77.52 ? CMD HEM 201 C 1 HETATM 34 C CAD HEM . . . N 10 4.807 -13.105 27.469 1 76 ? CAD HEM 201 C 1 HETATM 35 C CBD HEM . . . N 10 3.43 -12.419 27.475 1 75.96 ? CBD HEM 201 C 1 HETATM 36 C CGD HEM . . . N 10 2.752 -12.316 26.117 1 75.62 ? CGD HEM 201 C 1 HETATM 37 O O1D HEM . . . N 10 1.564 -11.889 26.013 1 74.72 ? O1D HEM 201 C 1 HETATM 38 O O2D HEM . . . N 10 3.405 -12.647 25.103 1 76.61 ? O2D HEM 201 C 1 HETATM 39 N NA HEM . . . N 10 6.172 -7.725 28.133 1 82.27 ? NA HEM 201 C 1 HETATM 40 N NB HEM . . . N 10 8.67 -6.37 28.323 1 84.59 ? NB HEM 201 C 1 HETATM 41 N NC HEM . . . N 10 9.994 -8.908 28.062 1 82.35 ? NC HEM 201 C 1 HETATM 42 N ND HEM . . . N 10 7.482 -10.364 27.917 1 79.94 ? ND HEM 201 C 1 HETATM 43 FE FE HEM . . . N 10 8.109 -8.381 27.983 1 80.82 ? FE HEM 201 C 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 43 #