data_5DUO # _model_server_result.job_id 3x6ndCxIuDjHW4CbJM-5zg _model_server_result.datetime_utc '2024-11-25 10:26:55' _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 5duo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":208}' # _entry.id 5DUO # _exptl.entry_id 5DUO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 562.658 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 100.05 _cell.angle_gamma 90 _cell.entry_id 5DUO _cell.length_a 58.388 _cell.length_b 99.191 _cell.length_c 95.326 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DUO _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,V,W 1 1 C,R,S,T,U,X 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 41.752896 0 93.863303 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id K _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C34 H34 N4 O4' _chem_comp.formula_weight 562.658 _chem_comp.id PP9 _chem_comp.mon_nstd_flag . _chem_comp.name 'PROTOPORPHYRIN IX' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 PP9 sing 307 n y CHA C4D PP9 doub 308 z y CHA HHA PP9 sing 309 n n CHB C4A PP9 sing 310 n y CHB C1B PP9 doub 311 z y CHB HHB PP9 sing 312 n n CHC C4B PP9 sing 313 n y CHC C1C PP9 doub 314 z y CHC HHC PP9 sing 315 n n CHD C4C PP9 doub 316 z y CHD C1D PP9 sing 317 n y CHD HHD PP9 sing 318 n n NA C1A PP9 sing 319 n y NA C4A PP9 sing 320 n y NA HNA PP9 sing 321 n n C1A C2A PP9 doub 322 n y C2A C3A PP9 sing 323 n y C2A CAA PP9 sing 324 n n C3A C4A PP9 doub 325 n y C3A CMA PP9 sing 326 n n CMA HMA1 PP9 sing 327 n n CMA HMA2 PP9 sing 328 n n CMA HMA3 PP9 sing 329 n n CAA CBA PP9 sing 330 n n CAA HAA1 PP9 sing 331 n n CAA HAA2 PP9 sing 332 n n CBA CGA PP9 sing 333 n n CBA HBA1 PP9 sing 334 n n CBA HBA2 PP9 sing 335 n n CGA O1A PP9 doub 336 n n CGA O2A PP9 sing 337 n n O2A H2A PP9 sing 338 n n NB C1B PP9 sing 339 n y NB C4B PP9 doub 340 n y C1B C2B PP9 sing 341 n n C2B C3B PP9 doub 342 n n C2B CMB PP9 sing 343 n n C3B C4B PP9 sing 344 n n C3B CAB PP9 sing 345 n n CMB HMB1 PP9 sing 346 n n CMB HMB2 PP9 sing 347 n n CMB HMB3 PP9 sing 348 n n CAB CBB PP9 doub 349 n n CAB HAB PP9 sing 350 n n CBB HBB1 PP9 sing 351 n n CBB HBB2 PP9 sing 352 n n NC C1C PP9 sing 353 n y NC C4C PP9 sing 354 n y NC HNC PP9 sing 355 n n C1C C2C PP9 sing 356 n y C2C C3C PP9 doub 357 n y C2C CMC PP9 sing 358 n n C3C C4C PP9 sing 359 n y C3C CAC PP9 sing 360 n n CMC HMC1 PP9 sing 361 n n CMC HMC2 PP9 sing 362 n n CMC HMC3 PP9 sing 363 n n CAC CBC PP9 doub 364 n n CAC HAC PP9 sing 365 n n CBC HBC1 PP9 sing 366 n n CBC HBC2 PP9 sing 367 n n ND C1D PP9 doub 368 n y ND C4D PP9 sing 369 n y C1D C2D PP9 sing 370 n n C2D C3D PP9 doub 371 n n C2D CMD PP9 sing 372 n n C3D C4D PP9 sing 373 n n C3D CAD PP9 sing 374 n n CMD HMD1 PP9 sing 375 n n CMD HMD2 PP9 sing 376 n n CMD HMD3 PP9 sing 377 n n CAD CBD PP9 sing 378 n n CAD HAD1 PP9 sing 379 n n CAD HAD2 PP9 sing 380 n n CBD CGD PP9 sing 381 n n CBD HBD1 PP9 sing 382 n n CBD HBD2 PP9 sing 383 n n CGD O1D PP9 doub 384 n n CGD O2D PP9 sing 385 n n O2D H2D PP9 sing 386 n n # _atom_sites.entry_id 5DUO _atom_sites.fract_transf_matrix[1][1] 0.017127 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003036 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010082 _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] 0.010654 _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 D 2 OLC A 1 201 201 OLC OLC . E 2 OLC A 1 202 203 OLC OLC . F 2 OLC A 1 203 205 OLC OLC . G 2 OLC A 1 204 209 OLC OLC . H 2 OLC A 1 205 218 OLC OLC . I 3 FMT A 1 206 301 FMT FMT . J 3 FMT A 1 207 302 FMT FMT . K 4 PP9 A 1 208 501 PP9 HMX . L 2 OLC B 1 201 210 OLC OLC . M 2 OLC B 1 202 215 OLC OLC . N 2 OLC B 1 203 217 OLC OLC . O 2 OLC B 1 204 219 OLC OLC . P 2 OLC B 1 205 220 OLC OLC . Q 2 OLC B 1 206 412 OLC OLC . R 2 OLC C 1 201 202 OLC OLC . S 2 OLC C 1 202 206 OLC OLC . T 2 OLC C 1 203 211 OLC OLC . U 2 OLC C 1 204 216 OLC OLC . V 5 HOH A 1 301 1064 HOH HOH . V 5 HOH A 2 302 1058 HOH HOH . V 5 HOH A 3 303 1056 HOH HOH . V 5 HOH A 4 304 1038 HOH HOH . V 5 HOH A 5 305 1010 HOH HOH . V 5 HOH A 6 306 1008 HOH HOH . V 5 HOH A 7 307 1045 HOH HOH . V 5 HOH A 8 308 1039 HOH HOH . V 5 HOH A 9 309 1001 HOH HOH . V 5 HOH A 10 310 1011 HOH HOH . V 5 HOH A 11 311 1048 HOH HOH . V 5 HOH A 12 312 1044 HOH HOH . V 5 HOH A 13 313 1040 HOH HOH . V 5 HOH A 14 314 1057 HOH HOH . V 5 HOH A 15 315 1063 HOH HOH . V 5 HOH A 16 316 1037 HOH HOH . V 5 HOH A 17 317 1025 HOH HOH . V 5 HOH A 18 318 1062 HOH HOH . V 5 HOH A 19 319 1046 HOH HOH . V 5 HOH A 20 320 1014 HOH HOH . V 5 HOH A 21 321 1016 HOH HOH . V 5 HOH A 22 322 1018 HOH HOH . V 5 HOH A 23 323 1065 HOH HOH . V 5 HOH A 24 324 1021 HOH HOH . V 5 HOH A 25 325 1066 HOH HOH . V 5 HOH A 26 326 1067 HOH HOH . V 5 HOH A 27 327 1050 HOH HOH . V 5 HOH A 28 328 1059 HOH HOH . W 5 HOH B 1 301 1061 HOH HOH . W 5 HOH B 2 302 1004 HOH HOH . W 5 HOH B 3 303 1007 HOH HOH . W 5 HOH B 4 304 1003 HOH HOH . W 5 HOH B 5 305 1002 HOH HOH . W 5 HOH B 6 306 1012 HOH HOH . W 5 HOH B 7 307 1052 HOH HOH . W 5 HOH B 8 308 1020 HOH HOH . W 5 HOH B 9 309 1019 HOH HOH . W 5 HOH B 10 310 1015 HOH HOH . W 5 HOH B 11 311 1035 HOH HOH . W 5 HOH B 12 312 1026 HOH HOH . W 5 HOH B 13 313 1023 HOH HOH . W 5 HOH B 14 314 1006 HOH HOH . W 5 HOH B 15 315 1042 HOH HOH . X 5 HOH C 1 301 1031 HOH HOH . X 5 HOH C 2 302 1080 HOH HOH . X 5 HOH C 3 303 1041 HOH HOH . X 5 HOH C 4 304 1027 HOH HOH . X 5 HOH C 5 305 1017 HOH HOH . X 5 HOH C 6 306 1005 HOH HOH . X 5 HOH C 7 307 1009 HOH HOH . X 5 HOH C 8 308 1043 HOH HOH . X 5 HOH C 9 309 1022 HOH HOH . X 5 HOH C 10 310 1051 HOH HOH . X 5 HOH C 11 311 1028 HOH HOH . X 5 HOH C 12 312 1024 HOH HOH . X 5 HOH C 13 313 1060 HOH HOH . X 5 HOH C 14 314 1079 HOH HOH . X 5 HOH C 15 315 1069 HOH HOH . X 5 HOH C 16 316 1073 HOH HOH . X 5 HOH C 17 317 1032 HOH HOH . X 5 HOH C 18 318 1074 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 PP9 . . . K 4 5.418 33.639 18.169 0.52 45.93 ? CHA PP9 208 A 1 HETATM 2 C CHB PP9 . . . K 4 8.098 30.163 19.559 0.52 49.78 ? CHB PP9 208 A 1 HETATM 3 C CHC PP9 . . . K 4 6.471 30.809 24.238 0.52 49.44 ? CHC PP9 208 A 1 HETATM 4 C CHD PP9 . . . K 4 5.926 35.282 22.877 0.52 39.45 ? CHD PP9 208 A 1 HETATM 5 N NA PP9 . . . K 4 6.719 31.959 19.074 0.52 50.01 ? NA PP9 208 A 1 HETATM 6 C C1A PP9 . . . K 4 6.194 32.567 17.989 0.52 44.91 ? C1A PP9 208 A 1 HETATM 7 C C2A PP9 . . . K 4 6.606 31.903 16.785 0.52 45.19 ? C2A PP9 208 A 1 HETATM 8 C C3A PP9 . . . K 4 7.407 30.888 17.167 0.52 50.76 ? C3A PP9 208 A 1 HETATM 9 C C4A PP9 . . . K 4 7.432 30.898 18.627 0.52 52.42 ? C4A PP9 208 A 1 HETATM 10 C CMA PP9 . . . K 4 8.08 29.825 16.265 0.52 48.51 ? CMA PP9 208 A 1 HETATM 11 C CAA PP9 . . . K 4 6.191 32.372 15.377 0.52 46.03 ? CAA PP9 208 A 1 HETATM 12 C CBA PP9 . . . K 4 7.268 33.321 14.831 0.52 46.97 ? CBA PP9 208 A 1 HETATM 13 C CGA PP9 . . . K 4 7.204 34.809 15.172 0.52 43.99 ? CGA PP9 208 A 1 HETATM 14 O O1A PP9 . . . K 4 7.546 35.572 14.23 0.52 40.97 ? O1A PP9 208 A 1 HETATM 15 O O2A PP9 . . . K 4 6.858 35.294 16.308 0.52 45.51 ? O2A PP9 208 A 1 HETATM 16 N NB PP9 . . . K 4 7.392 31.03 21.906 0.52 57.39 ? NB PP9 208 A 1 HETATM 17 C C1B PP9 . . . K 4 7.646 30.145 20.865 0.52 51.89 ? C1B PP9 208 A 1 HETATM 18 C C2B PP9 . . . K 4 7.223 28.899 21.3 0.52 51.61 ? C2B PP9 208 A 1 HETATM 19 C C3B PP9 . . . K 4 6.769 28.928 22.55 0.52 53.28 ? C3B PP9 208 A 1 HETATM 20 C C4B PP9 . . . K 4 6.845 30.308 22.99 0.52 50.74 ? C4B PP9 208 A 1 HETATM 21 C CMB PP9 . . . K 4 7.377 27.835 20.236 0.52 60.24 ? CMB PP9 208 A 1 HETATM 22 C CAB PP9 . . . K 4 6.223 27.706 23.314 0.52 60.29 ? CAB PP9 208 A 1 HETATM 23 C CBB PP9 . . . K 4 5.621 27.792 24.504 0.52 59.81 ? CBB PP9 208 A 1 HETATM 24 N NC PP9 . . . K 4 6.192 33 23.356 0.52 49.01 ? NC PP9 208 A 1 HETATM 25 C C1C PP9 . . . K 4 6.304 32.164 24.432 0.52 48.21 ? C1C PP9 208 A 1 HETATM 26 C C2C PP9 . . . K 4 6.177 32.991 25.621 0.52 49.06 ? C2C PP9 208 A 1 HETATM 27 C C3C PP9 . . . K 4 6.017 34.279 25.247 0.52 46.09 ? C3C PP9 208 A 1 HETATM 28 C C4C PP9 . . . K 4 6.003 34.281 23.796 0.52 44.79 ? C4C PP9 208 A 1 HETATM 29 C CMC PP9 . . . K 4 6.2 32.493 27.07 0.52 48.97 ? CMC PP9 208 A 1 HETATM 30 C CAC PP9 . . . K 4 5.862 35.527 26.167 0.52 43.58 ? CAC PP9 208 A 1 HETATM 31 C CBC PP9 . . . K 4 6.5 35.675 27.342 0.52 37.78 ? CBC PP9 208 A 1 HETATM 32 N ND PP9 . . . K 4 6.171 34.225 20.536 0.52 46.37 ? ND PP9 208 A 1 HETATM 33 C C1D PP9 . . . K 4 5.589 34.948 21.58 0.52 40.05 ? C1D PP9 208 A 1 HETATM 34 C C2D PP9 . . . K 4 4.322 35.345 21.134 0.52 39.15 ? C2D PP9 208 A 1 HETATM 35 C C3D PP9 . . . K 4 4.104 34.869 19.733 0.52 41.19 ? C3D PP9 208 A 1 HETATM 36 C C4D PP9 . . . K 4 5.296 34.19 19.419 0.52 46.68 ? C4D PP9 208 A 1 HETATM 37 C CMD PP9 . . . K 4 3.398 36.138 21.992 0.52 44.11 ? CMD PP9 208 A 1 HETATM 38 C CAD PP9 . . . K 4 2.929 35.099 18.8 0.52 42.4 ? CAD PP9 208 A 1 HETATM 39 C CBD PP9 . . . K 4 3.39 36.334 18.046 0.52 43.18 ? CBD PP9 208 A 1 HETATM 40 C CGD PP9 . . . K 4 2.693 37.432 18.773 0.52 38.28 ? CGD PP9 208 A 1 HETATM 41 O O1D PP9 . . . K 4 3.325 38.262 19.494 0.52 37.22 ? O1D PP9 208 A 1 HETATM 42 O O2D PP9 . . . K 4 1.453 37.375 18.631 0.52 41.06 ? O2D PP9 208 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 42 #