data_5D5R # _model_server_result.job_id sbKy_aIm1sOMHsQvSERBiw _model_server_result.datetime_utc '2024-11-24 15:41:45' _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 5d5r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 5D5R # _exptl.entry_id 5D5R _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 106.5 _cell.angle_gamma 90 _cell.entry_id 5D5R _cell.length_a 63.6 _cell.length_b 28.8 _cell.length_c 35.6 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5D5R _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NE2 _struct_conn.ptnr1_label_comp_id HIS _struct_conn.ptnr1_label_seq_id 93 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id HIS _struct_conn.ptnr1_auth_seq_id 93 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id FE _struct_conn.ptnr2_label_comp_id HEM _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id HEM _struct_conn.ptnr2_auth_seq_id 201 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id A _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id A _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 2.228 _struct_conn.pdbx_value_order ? # _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 116 n n CHA C4D HEM doub 117 n n CHA HHA HEM sing 118 n n CHB C4A HEM sing 119 n n CHB C1B HEM doub 120 n n CHB HHB HEM sing 121 n n CHC C4B HEM sing 122 n n CHC C1C HEM doub 123 n n CHC HHC HEM sing 124 n n CHD C4C HEM doub 125 n n CHD C1D HEM sing 126 n n CHD HHD HEM sing 127 n n C1A C2A HEM doub 128 n y C1A NA HEM sing 129 n y C2A C3A HEM sing 130 n y C2A CAA HEM sing 131 n n C3A C4A HEM doub 132 n y C3A CMA HEM sing 133 n n C4A NA HEM sing 134 n y CMA HMA HEM sing 135 n n CMA HMAA HEM sing 136 n n CMA HMAB HEM sing 137 n n CAA CBA HEM sing 138 n n CAA HAA HEM sing 139 n n CAA HAAA HEM sing 140 n n CBA CGA HEM sing 141 n n CBA HBA HEM sing 142 n n CBA HBAA HEM sing 143 n n CGA O1A HEM doub 144 n n CGA O2A HEM sing 145 n n C1B C2B HEM sing 146 n n C1B NB HEM sing 147 n n C2B C3B HEM doub 148 n n C2B CMB HEM sing 149 n n C3B C4B HEM sing 150 n n C3B CAB HEM sing 151 n n C4B NB HEM doub 152 n n CMB HMB HEM sing 153 n n CMB HMBA HEM sing 154 n n CMB HMBB HEM sing 155 n n CAB CBB HEM doub 156 n n CAB HAB HEM sing 157 n n CBB HBB HEM sing 158 n n CBB HBBA HEM sing 159 n n C1C C2C HEM sing 160 n y C1C NC HEM sing 161 n y C2C C3C HEM doub 162 n y C2C CMC HEM sing 163 n n C3C C4C HEM sing 164 n y C3C CAC HEM sing 165 n n C4C NC HEM sing 166 n y CMC HMC HEM sing 167 n n CMC HMCA HEM sing 168 n n CMC HMCB HEM sing 169 n n CAC CBC HEM doub 170 n n CAC HAC HEM sing 171 n n CBC HBC HEM sing 172 n n CBC HBCA HEM sing 173 n n C1D C2D HEM sing 174 n n C1D ND HEM doub 175 n n C2D C3D HEM doub 176 n n C2D CMD HEM sing 177 n n C3D C4D HEM sing 178 n n C3D CAD HEM sing 179 n n C4D ND HEM sing 180 n n CMD HMD HEM sing 181 n n CMD HMDA HEM sing 182 n n CMD HMDB HEM sing 183 n n CAD CBD HEM sing 184 n n CAD HAD HEM sing 185 n n CAD HADA HEM sing 186 n n CBD CGD HEM sing 187 n n CBD HBD HEM sing 188 n n CBD HBDA HEM sing 189 n n CGD O1D HEM doub 190 n n CGD O2D HEM sing 191 n n O2A H2A HEM sing 192 n n O2D H2D HEM sing 193 n n FE NA HEM sing 194 n n FE NB HEM sing 195 n n FE NC HEM sing 196 n n FE ND HEM sing 197 n n # _atom_sites.entry_id 5D5R _atom_sites.fract_transf_matrix[1][1] 0.015723 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004657 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.034722 _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] 0.029296 _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 B 2 HEM A 1 201 154 HEM HEM . C 3 HOH A 1 301 17 HOH HOH . C 3 HOH A 2 302 113 HOH HOH . C 3 HOH A 3 303 55 HOH HOH . C 3 HOH A 4 304 118 HOH HOH . C 3 HOH A 5 305 71 HOH HOH . C 3 HOH A 6 306 76 HOH HOH . C 3 HOH A 7 307 26 HOH HOH . C 3 HOH A 8 308 93 HOH HOH . C 3 HOH A 9 309 54 HOH HOH . C 3 HOH A 10 310 95 HOH HOH . C 3 HOH A 11 311 51 HOH HOH . C 3 HOH A 12 312 1 HOH HOH . C 3 HOH A 13 313 46 HOH HOH . C 3 HOH A 14 314 35 HOH HOH . C 3 HOH A 15 315 87 HOH HOH . C 3 HOH A 16 316 72 HOH HOH . C 3 HOH A 17 317 61 HOH HOH . C 3 HOH A 18 318 20 HOH HOH . C 3 HOH A 19 319 43 HOH HOH . C 3 HOH A 20 320 65 HOH HOH . C 3 HOH A 21 321 92 HOH HOH . C 3 HOH A 22 322 89 HOH HOH . C 3 HOH A 23 323 28 HOH HOH . C 3 HOH A 24 324 8 HOH HOH . C 3 HOH A 25 325 31 HOH HOH . C 3 HOH A 26 326 7 HOH HOH . C 3 HOH A 27 327 48 HOH HOH . C 3 HOH A 28 328 106 HOH HOH . C 3 HOH A 29 329 79 HOH HOH . C 3 HOH A 30 330 13 HOH HOH . C 3 HOH A 31 331 39 HOH HOH . C 3 HOH A 32 332 64 HOH HOH . C 3 HOH A 33 333 57 HOH HOH . C 3 HOH A 34 334 78 HOH HOH . C 3 HOH A 35 335 70 HOH HOH . C 3 HOH A 36 336 80 HOH HOH . C 3 HOH A 37 337 100 HOH HOH . C 3 HOH A 38 338 69 HOH HOH . C 3 HOH A 39 339 10 HOH HOH . C 3 HOH A 40 340 3 HOH HOH . C 3 HOH A 41 341 29 HOH HOH . C 3 HOH A 42 342 52 HOH HOH . C 3 HOH A 43 343 67 HOH HOH . C 3 HOH A 44 344 15 HOH HOH . C 3 HOH A 45 345 34 HOH HOH . C 3 HOH A 46 346 27 HOH HOH . C 3 HOH A 47 347 96 HOH HOH . C 3 HOH A 48 348 18 HOH HOH . C 3 HOH A 49 349 115 HOH HOH . C 3 HOH A 50 350 21 HOH HOH . C 3 HOH A 51 351 68 HOH HOH . C 3 HOH A 52 352 41 HOH HOH . C 3 HOH A 53 353 60 HOH HOH . C 3 HOH A 54 354 11 HOH HOH . C 3 HOH A 55 355 36 HOH HOH . C 3 HOH A 56 356 32 HOH HOH . C 3 HOH A 57 357 9 HOH HOH . C 3 HOH A 58 358 73 HOH HOH . C 3 HOH A 59 359 82 HOH HOH . C 3 HOH A 60 360 47 HOH HOH . C 3 HOH A 61 361 104 HOH HOH . C 3 HOH A 62 362 84 HOH HOH . C 3 HOH A 63 363 75 HOH HOH . C 3 HOH A 64 364 111 HOH HOH . C 3 HOH A 65 365 24 HOH HOH . C 3 HOH A 66 366 94 HOH HOH . C 3 HOH A 67 367 2 HOH HOH . C 3 HOH A 68 368 19 HOH HOH . C 3 HOH A 69 369 40 HOH HOH . C 3 HOH A 70 370 45 HOH HOH . C 3 HOH A 71 371 85 HOH HOH . C 3 HOH A 72 372 23 HOH HOH . C 3 HOH A 73 373 4 HOH HOH . C 3 HOH A 74 374 58 HOH HOH . C 3 HOH A 75 375 103 HOH HOH . C 3 HOH A 76 376 25 HOH HOH . C 3 HOH A 77 377 16 HOH HOH . C 3 HOH A 78 378 109 HOH HOH . C 3 HOH A 79 379 53 HOH HOH . C 3 HOH A 80 380 44 HOH HOH . C 3 HOH A 81 381 12 HOH HOH . C 3 HOH A 82 382 77 HOH HOH . C 3 HOH A 83 383 37 HOH HOH . C 3 HOH A 84 384 90 HOH HOH . C 3 HOH A 85 385 6 HOH HOH . C 3 HOH A 86 386 33 HOH HOH . C 3 HOH A 87 387 14 HOH HOH . C 3 HOH A 88 388 119 HOH HOH . C 3 HOH A 89 389 88 HOH HOH . C 3 HOH A 90 390 30 HOH HOH . C 3 HOH A 91 391 107 HOH HOH . C 3 HOH A 92 392 108 HOH HOH . C 3 HOH A 93 393 83 HOH HOH . C 3 HOH A 94 394 22 HOH HOH . C 3 HOH A 95 395 99 HOH HOH . C 3 HOH A 96 396 50 HOH HOH . C 3 HOH A 97 397 49 HOH HOH . C 3 HOH A 98 398 38 HOH HOH . C 3 HOH A 99 399 110 HOH HOH . C 3 HOH A 100 400 117 HOH HOH . C 3 HOH A 101 401 105 HOH HOH . C 3 HOH A 102 402 66 HOH HOH . C 3 HOH A 103 403 116 HOH HOH . C 3 HOH A 104 404 42 HOH HOH . C 3 HOH A 105 405 59 HOH HOH . C 3 HOH A 106 406 56 HOH HOH . C 3 HOH A 107 407 5 HOH HOH . C 3 HOH A 108 408 63 HOH HOH . C 3 HOH A 109 409 97 HOH HOH . C 3 HOH A 110 410 112 HOH HOH . C 3 HOH A 111 411 102 HOH HOH . C 3 HOH A 112 412 74 HOH HOH . C 3 HOH A 113 413 81 HOH HOH . C 3 HOH A 114 414 62 HOH HOH . C 3 HOH A 115 415 86 HOH HOH . C 3 HOH A 116 416 114 HOH HOH . C 3 HOH A 117 417 120 HOH HOH . C 3 HOH A 118 418 91 HOH HOH . C 3 HOH A 119 419 98 HOH HOH . C 3 HOH A 120 420 101 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 HEM . A . B 2 10.674 -32.316 13.155 1 12.62 ? CHA HEM 201 A 1 HETATM 2 C CHB HEM . A . B 2 10.764 -29.246 16.878 1 12.29 ? CHB HEM 201 A 1 HETATM 3 C CHC HEM . A . B 2 12.868 -25.874 14.074 1 12.71 ? CHC HEM 201 A 1 HETATM 4 C CHD HEM . A . B 2 12.943 -29.005 10.38 1 14.45 ? CHD HEM 201 A 1 HETATM 5 C C1A HEM . A . B 2 10.523 -31.78 14.404 1 12.27 ? C1A HEM 201 A 1 HETATM 6 C C2A HEM . A . B 2 9.934 -32.47 15.533 1 11.07 ? C2A HEM 201 A 1 HETATM 7 C C3A HEM . A . B 2 9.956 -31.621 16.563 1 12.54 ? C3A HEM 201 A 1 HETATM 8 C C4A HEM . A . B 2 10.548 -30.369 16.117 1 12.21 ? C4A HEM 201 A 1 HETATM 9 C CMA HEM . A . B 2 9.444 -31.85 17.995 1 13.29 ? CMA HEM 201 A 1 HETATM 10 C CAA HEM . A . B 2 9.414 -33.924 15.519 1 13.51 ? CAA HEM 201 A 1 HETATM 11 C CBA HEM . A . B 2 10.405 -34.787 16.331 1 13.74 ? CBA HEM 201 A 1 HETATM 12 C CGA HEM . A . B 2 11.794 -34.875 15.733 1 15.77 ? CGA HEM 201 A 1 HETATM 13 O O1A HEM . A . B 2 11.911 -35.285 14.549 1 16.02 ? O1A HEM 201 A 1 HETATM 14 O O2A HEM . A . B 2 12.796 -34.571 16.437 1 15.66 ? O2A HEM 201 A 1 HETATM 15 C C1B HEM . A . B 2 11.331 -28.067 16.429 1 12.04 ? C1B HEM 201 A 1 HETATM 16 C C2B HEM . A . B 2 11.465 -26.866 17.215 1 11.76 ? C2B HEM 201 A 1 HETATM 17 C C3B HEM . A . B 2 12.055 -25.937 16.453 1 11.21 ? C3B HEM 201 A 1 HETATM 18 C C4B HEM . A . B 2 12.285 -26.519 15.145 1 12.48 ? C4B HEM 201 A 1 HETATM 19 C CMB HEM . A . B 2 11.025 -26.743 18.694 1 14.07 ? CMB HEM 201 A 1 HETATM 20 C CAB HEM . A . B 2 12.398 -24.476 16.802 1 11.74 ? CAB HEM 201 A 1 HETATM 21 C CBB HEM . A . B 2 11.74 -23.747 17.706 1 18.01 ? CBB HEM 201 A 1 HETATM 22 C C1C HEM . A . B 2 13.048 -26.412 12.823 1 12.09 ? C1C HEM 201 A 1 HETATM 23 C C2C HEM . A . B 2 13.518 -25.718 11.646 1 12.17 ? C2C HEM 201 A 1 HETATM 24 C C3C HEM . A . B 2 13.539 -26.594 10.627 1 11.48 ? C3C HEM 201 A 1 HETATM 25 C C4C HEM . A . B 2 13.066 -27.862 11.122 1 12.73 ? C4C HEM 201 A 1 HETATM 26 C CMC HEM . A . B 2 13.93 -24.232 11.631 1 15.78 ? CMC HEM 201 A 1 HETATM 27 C CAC HEM . A . B 2 13.936 -26.407 9.146 1 16.59 ? CAC HEM 201 A 1 HETATM 28 C CBC HEM . A . B 2 14.134 -25.217 8.582 1 16.96 ? CBC HEM 201 A 1 HETATM 29 C C1D HEM . A . B 2 12.305 -30.15 10.778 1 12.49 ? C1D HEM 201 A 1 HETATM 30 C C2D HEM . A . B 2 12.015 -31.26 9.901 1 13.53 ? C2D HEM 201 A 1 HETATM 31 C C3D HEM . A . B 2 11.326 -32.287 10.77 1 14.62 ? C3D HEM 201 A 1 HETATM 32 C C4D HEM . A . B 2 11.239 -31.683 12.08 1 12.94 ? C4D HEM 201 A 1 HETATM 33 C CMD HEM . A . B 2 12.352 -31.407 8.412 1 15.38 ? CMD HEM 201 A 1 HETATM 34 C CAD HEM . A . B 2 10.77 -33.65 10.33 1 15.45 ? CAD HEM 201 A 1 HETATM 35 C CBD HEM . A . B 2 9.375 -33.351 9.787 1 19.11 ? CBD HEM 201 A 1 HETATM 36 C CGD HEM . A . B 2 8.7 -34.56 9.2 1 23.23 ? CGD HEM 201 A 1 HETATM 37 O O1D HEM . A . B 2 7.792 -35.113 9.864 1 26.56 ? O1D HEM 201 A 1 HETATM 38 O O2D HEM . A . B 2 9.048 -34.957 8.06 1 25.82 ? O2D HEM 201 A 1 HETATM 39 N NA HEM . A . B 2 10.899 -30.512 14.794 1 11.6 ? NA HEM 201 A 1 HETATM 40 N NB HEM . A . B 2 11.841 -27.83 15.161 1 11.26 ? NB HEM 201 A 1 HETATM 41 N NC HEM . A . B 2 12.774 -27.712 12.465 1 11.5 ? NC HEM 201 A 1 HETATM 42 N ND HEM . A . B 2 11.836 -30.427 12.065 1 13.47 ? ND HEM 201 A 1 HETATM 43 FE FE HEM . A . B 2 12.076 -29.216 13.705 1 12.17 ? FE HEM 201 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #