data_8SG5 # _model_server_result.job_id 8Aa5yFQvQz_hIw7yI0b6Uw _model_server_result.datetime_utc '2024-11-28 17:09:30' _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 8sg5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":601}' # _entry.id 8SG5 # _exptl.entry_id 8SG5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _entity.pdbx_number_of_molecules 8 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 92.01 _cell.angle_gamma 90 _cell.entry_id 8SG5 _cell.length_a 104.131 _cell.length_b 200.679 _cell.length_c 110.819 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8SG5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 PISA monomeric 1 author_and_software_defined_assembly 5 PISA monomeric 1 author_and_software_defined_assembly 6 PISA monomeric 1 author_and_software_defined_assembly 7 PISA monomeric 1 author_and_software_defined_assembly 8 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,I,J,K,L,M 1 1 B,N,O,P,Q,R 2 1 C,S,T,U,V,W 3 1 D,X,Y,Z,AA,BA 4 1 E,CA,DA,EA,FA,GA 5 1 F,HA,IA,JA,KA,LA 6 1 G,MA,NA,OA,PA,QA 7 1 H,RA,SA,TA,UA 8 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 ? 2 I N N ? 2 N N N ? 2 S N N ? 2 X N N ? 2 CA N N ? 2 HA N N ? 2 MA N N ? 2 RA 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 A SG CYS 420 A CYS 441 1_555 I FE HEM . A HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc2 I FE HEM . A HEM 601 1_555 J NAN CL6 . A CL6 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.915 ? metalc ? metalc3 B SG CYS 420 B CYS 441 1_555 N FE HEM . B HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc4 N FE HEM . B HEM 601 1_555 O NAN CL6 . B CL6 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? metalc ? metalc5 C SG CYS 420 C CYS 441 1_555 S FE HEM . C HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc6 S FE HEM . C HEM 601 1_555 T NAN CL6 . C CL6 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? metalc ? metalc7 D SG CYS 420 D CYS 441 1_555 X FE HEM . D HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc8 X FE HEM . D HEM 601 1_555 Y NAN CL6 . D CL6 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc9 E SG CYS 420 E CYS 441 1_555 CA FE HEM . E HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc10 CA FE HEM . E HEM 601 1_555 DA NAN CL6 . E CL6 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? metalc ? metalc11 F SG CYS 420 F CYS 441 1_555 HA FE HEM . F HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc12 HA FE HEM . F HEM 601 1_555 IA NAN CL6 . F CL6 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.905 ? metalc ? metalc13 G SG CYS 420 G CYS 441 1_555 MA FE HEM . G HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc14 MA FE HEM . G HEM 601 1_555 NA NAN CL6 . G CL6 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.925 ? metalc ? metalc15 H SG CYS 420 H CYS 441 1_555 RA FE HEM . H HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc16 RA FE HEM . H HEM 601 1_555 SA NAN CL6 . H CL6 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? # _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 275 n n CHA C4D HEM doub 276 n n CHA HHA HEM sing 277 n n CHB C4A HEM sing 278 n n CHB C1B HEM doub 279 n n CHB HHB HEM sing 280 n n CHC C4B HEM sing 281 n n CHC C1C HEM doub 282 n n CHC HHC HEM sing 283 n n CHD C4C HEM doub 284 n n CHD C1D HEM sing 285 n n CHD HHD HEM sing 286 n n C1A C2A HEM doub 287 n y C1A NA HEM sing 288 n y C2A C3A HEM sing 289 n y C2A CAA HEM sing 290 n n C3A C4A HEM doub 291 n y C3A CMA HEM sing 292 n n C4A NA HEM sing 293 n y CMA HMA HEM sing 294 n n CMA HMAA HEM sing 295 n n CMA HMAB HEM sing 296 n n CAA CBA HEM sing 297 n n CAA HAA HEM sing 298 n n CAA HAAA HEM sing 299 n n CBA CGA HEM sing 300 n n CBA HBA HEM sing 301 n n CBA HBAA HEM sing 302 n n CGA O1A HEM doub 303 n n CGA O2A HEM sing 304 n n C1B C2B HEM sing 305 n n C1B NB HEM sing 306 n n C2B C3B HEM doub 307 n n C2B CMB HEM sing 308 n n C3B C4B HEM sing 309 n n C3B CAB HEM sing 310 n n C4B NB HEM doub 311 n n CMB HMB HEM sing 312 n n CMB HMBA HEM sing 313 n n CMB HMBB HEM sing 314 n n CAB CBB HEM doub 315 n n CAB HAB HEM sing 316 n n CBB HBB HEM sing 317 n n CBB HBBA HEM sing 318 n n C1C C2C HEM sing 319 n y C1C NC HEM sing 320 n y C2C C3C HEM doub 321 n y C2C CMC HEM sing 322 n n C3C C4C HEM sing 323 n y C3C CAC HEM sing 324 n n C4C NC HEM sing 325 n y CMC HMC HEM sing 326 n n CMC HMCA HEM sing 327 n n CMC HMCB HEM sing 328 n n CAC CBC HEM doub 329 n n CAC HAC HEM sing 330 n n CBC HBC HEM sing 331 n n CBC HBCA HEM sing 332 n n C1D C2D HEM sing 333 n n C1D ND HEM doub 334 n n C2D C3D HEM doub 335 n n C2D CMD HEM sing 336 n n C3D C4D HEM sing 337 n n C3D CAD HEM sing 338 n n C4D ND HEM sing 339 n n CMD HMD HEM sing 340 n n CMD HMDA HEM sing 341 n n CMD HMDB HEM sing 342 n n CAD CBD HEM sing 343 n n CAD HAD HEM sing 344 n n CAD HADA HEM sing 345 n n CBD CGD HEM sing 346 n n CBD HBD HEM sing 347 n n CBD HBDA HEM sing 348 n n CGD O1D HEM doub 349 n n CGD O2D HEM sing 350 n n O2A H2A HEM sing 351 n n O2D H2D HEM sing 352 n n FE NA HEM sing 353 n n FE NB HEM sing 354 n n FE NC HEM sing 355 n n FE ND HEM sing 356 n n # _atom_sites.entry_id 8SG5 _atom_sites.fract_transf_matrix[1][1] 0.009603 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000337 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004983 _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] 0.009029 _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 2 HEM A 1 601 601 HEM HEM . J 3 CL6 A 1 602 602 CL6 CL6 . K 3 CL6 A 1 603 603 CL6 CL6 . L 3 CL6 A 1 604 604 CL6 CL6 . M 4 CE9 A 1 605 605 CE9 CE9 . N 2 HEM B 1 601 601 HEM HEM . O 3 CL6 B 1 602 602 CL6 CL6 . P 3 CL6 B 1 603 603 CL6 CL6 . Q 3 CL6 B 1 604 604 CL6 CL6 . R 4 CE9 B 1 605 605 CE9 CE9 . S 2 HEM C 1 601 601 HEM HEM . T 3 CL6 C 1 602 602 CL6 CL6 . U 3 CL6 C 1 603 603 CL6 CL6 . V 3 CL6 C 1 604 604 CL6 CL6 . W 4 CE9 C 1 605 605 CE9 CE9 . X 2 HEM D 1 601 601 HEM HEM . Y 3 CL6 D 1 602 602 CL6 CL6 . Z 3 CL6 D 1 603 603 CL6 CL6 . AA 3 CL6 D 1 604 604 CL6 CL6 . BA 4 CE9 D 1 605 605 CE9 CE9 . CA 2 HEM E 1 601 601 HEM HEM . DA 3 CL6 E 1 602 602 CL6 CL6 . EA 3 CL6 E 1 603 603 CL6 CL6 . FA 3 CL6 E 1 604 604 CL6 CL6 . GA 4 CE9 E 1 605 605 CE9 CE9 . HA 2 HEM F 1 601 601 HEM HEM . IA 3 CL6 F 1 602 602 CL6 CL6 . JA 3 CL6 F 1 603 603 CL6 CL6 . KA 3 CL6 F 1 604 604 CL6 CL6 . LA 4 CE9 F 1 605 605 CE9 CE9 . MA 2 HEM G 1 601 601 HEM HEM . NA 3 CL6 G 1 602 602 CL6 CL6 . OA 3 CL6 G 1 603 603 CL6 CL6 . PA 3 CL6 G 1 604 604 CL6 CL6 . QA 4 CE9 G 1 605 605 CE9 CE9 . RA 2 HEM H 1 601 601 HEM HEM . SA 3 CL6 H 1 602 602 CL6 CL6 . TA 3 CL6 H 1 603 603 CL6 CL6 . UA 3 CL6 H 1 604 604 CL6 CL6 . # 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 . . . I 2 38.341 -18.587 7.75 1 60.85 ? CHA HEM 601 A 1 HETATM 2 C CHB HEM . . . I 2 41.497 -20.874 10.637 1 62.27 ? CHB HEM 601 A 1 HETATM 3 C CHC HEM . . . I 2 40.211 -25.159 8.663 1 59.05 ? CHC HEM 601 A 1 HETATM 4 C CHD HEM . . . I 2 37.461 -22.777 5.456 1 63.97 ? CHD HEM 601 A 1 HETATM 5 C C1A HEM . . . I 2 39.263 -18.878 8.726 1 61.57 ? C1A HEM 601 A 1 HETATM 6 C C2A HEM . . . I 2 39.804 -17.916 9.604 1 59.83 ? C2A HEM 601 A 1 HETATM 7 C C3A HEM . . . I 2 40.688 -18.549 10.411 1 60.37 ? C3A HEM 601 A 1 HETATM 8 C C4A HEM . . . I 2 40.711 -19.909 10.041 1 62.17 ? C4A HEM 601 A 1 HETATM 9 C CMA HEM . . . I 2 41.494 -17.908 11.508 1 59.63 ? CMA HEM 601 A 1 HETATM 10 C CAA HEM . . . I 2 39.471 -16.448 9.655 1 59.41 ? CAA HEM 601 A 1 HETATM 11 C CBA HEM . . . I 2 38.213 -16.211 10.492 1 64.26 ? CBA HEM 601 A 1 HETATM 12 C CGA HEM . . . I 2 38.112 -14.752 10.862 1 63.53 ? CGA HEM 601 A 1 HETATM 13 O O1A HEM . . . I 2 37.698 -14.431 11.998 1 63.94 ? O1A HEM 601 A 1 HETATM 14 O O2A HEM . . . I 2 38.43 -13.859 10.04 1 62.28 ? O2A HEM 601 A 1 HETATM 15 C C1B HEM . . . I 2 41.384 -22.234 10.324 1 61.63 ? C1B HEM 601 A 1 HETATM 16 C C2B HEM . . . I 2 42.141 -23.218 11.017 1 61.06 ? C2B HEM 601 A 1 HETATM 17 C C3B HEM . . . I 2 41.803 -24.429 10.486 1 60.94 ? C3B HEM 601 A 1 HETATM 18 C C4B HEM . . . I 2 40.798 -24.148 9.43 1 59.84 ? C4B HEM 601 A 1 HETATM 19 C CMB HEM . . . I 2 43.129 -22.953 12.125 1 58.43 ? CMB HEM 601 A 1 HETATM 20 C CAB HEM . . . I 2 42.327 -25.755 10.867 1 60.8 ? CAB HEM 601 A 1 HETATM 21 C CBB HEM . . . I 2 42.293 -26.182 12.126 1 61.46 ? CBB HEM 601 A 1 HETATM 22 C C1C HEM . . . I 2 39.324 -24.893 7.626 1 64.02 ? C1C HEM 601 A 1 HETATM 23 C C2C HEM . . . I 2 38.677 -25.85 6.819 1 64.24 ? C2C HEM 601 A 1 HETATM 24 C C3C HEM . . . I 2 37.893 -25.157 5.907 1 64.52 ? C3C HEM 601 A 1 HETATM 25 C C4C HEM . . . I 2 38.074 -23.774 6.165 1 63.74 ? C4C HEM 601 A 1 HETATM 26 C CMC HEM . . . I 2 38.806 -27.348 6.928 1 62.18 ? CMC HEM 601 A 1 HETATM 27 C CAC HEM . . . I 2 37.031 -25.717 4.849 1 62.84 ? CAC HEM 601 A 1 HETATM 28 C CBC HEM . . . I 2 35.935 -26.401 5.152 1 69.74 ? CBC HEM 601 A 1 HETATM 29 C C1D HEM . . . I 2 37.508 -21.448 5.867 1 63.45 ? C1D HEM 601 A 1 HETATM 30 C C2D HEM . . . I 2 36.744 -20.428 5.146 1 61.44 ? C2D HEM 601 A 1 HETATM 31 C C3D HEM . . . I 2 36.98 -19.267 5.773 1 61.72 ? C3D HEM 601 A 1 HETATM 32 C C4D HEM . . . I 2 37.891 -19.577 6.886 1 62.77 ? C4D HEM 601 A 1 HETATM 33 C CMD HEM . . . I 2 35.873 -20.644 3.938 1 60.95 ? CMD HEM 601 A 1 HETATM 34 C CAD HEM . . . I 2 36.411 -17.926 5.39 1 60.94 ? CAD HEM 601 A 1 HETATM 35 C CBD HEM . . . I 2 35.082 -17.691 6.105 1 61.29 ? CBD HEM 601 A 1 HETATM 36 C CGD HEM . . . I 2 34.428 -16.464 5.528 1 64.39 ? CGD HEM 601 A 1 HETATM 37 O O1D HEM . . . I 2 33.183 -16.411 5.428 1 67.25 ? O1D HEM 601 A 1 HETATM 38 O O2D HEM . . . I 2 35.128 -15.497 5.155 1 64.93 ? O2D HEM 601 A 1 HETATM 39 N NA HEM . . . I 2 39.849 -20.1 8.99 1 62.16 ? NA HEM 601 A 1 HETATM 40 N NB HEM . . . I 2 40.602 -22.815 9.401 1 61.79 ? NB HEM 601 A 1 HETATM 41 N NC HEM . . . I 2 38.949 -23.643 7.211 1 65.34 ? NC HEM 601 A 1 HETATM 42 N ND HEM . . . I 2 38.174 -20.897 6.897 1 64.56 ? ND HEM 601 A 1 HETATM 43 FE FE HEM . . . I 2 39.294 -21.792 8.107 1 69.64 ? FE HEM 601 A 1 # _model_server_stats.io_time_ms 82 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 501 _model_server_stats.encode_time_ms 22 _model_server_stats.element_count 43 #