data_5MJD # _model_server_result.job_id YNee15Rk1wpn8EHUz-sE6Q _model_server_result.datetime_utc '2025-07-27 11:47:24' _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 5mjd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 5MJD # _exptl.entry_id 5MJD _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 90 _cell.angle_gamma 120 _cell.entry_id 5MJD _cell.length_a 87.819 _cell.length_b 87.819 _cell.length_c 113.522 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MJD _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _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,D,E _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 # 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 NE2 HIS 62 A HIS 64 1_555 B FE HEM . A HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc2 A NE2 HIS 94 A HIS 96 1_555 B FE HEM . A HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? # _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 129 n n CHA C4D HEM doub 130 n n CHA HHA HEM sing 131 n n CHB C4A HEM sing 132 n n CHB C1B HEM doub 133 n n CHB HHB HEM sing 134 n n CHC C4B HEM sing 135 n n CHC C1C HEM doub 136 n n CHC HHC HEM sing 137 n n CHD C4C HEM doub 138 n n CHD C1D HEM sing 139 n n CHD HHD HEM sing 140 n n C1A C2A HEM doub 141 n y C1A NA HEM sing 142 n y C2A C3A HEM sing 143 n y C2A CAA HEM sing 144 n n C3A C4A HEM doub 145 n y C3A CMA HEM sing 146 n n C4A NA HEM sing 147 n y CMA HMA HEM sing 148 n n CMA HMAA HEM sing 149 n n CMA HMAB HEM sing 150 n n CAA CBA HEM sing 151 n n CAA HAA HEM sing 152 n n CAA HAAA HEM sing 153 n n CBA CGA HEM sing 154 n n CBA HBA HEM sing 155 n n CBA HBAA HEM sing 156 n n CGA O1A HEM doub 157 n n CGA O2A HEM sing 158 n n C1B C2B HEM sing 159 n n C1B NB HEM sing 160 n n C2B C3B HEM doub 161 n n C2B CMB HEM sing 162 n n C3B C4B HEM sing 163 n n C3B CAB HEM sing 164 n n C4B NB HEM doub 165 n n CMB HMB HEM sing 166 n n CMB HMBA HEM sing 167 n n CMB HMBB HEM sing 168 n n CAB CBB HEM doub 169 n n CAB HAB HEM sing 170 n n CBB HBB HEM sing 171 n n CBB HBBA HEM sing 172 n n C1C C2C HEM sing 173 n y C1C NC HEM sing 174 n y C2C C3C HEM doub 175 n y C2C CMC HEM sing 176 n n C3C C4C HEM sing 177 n y C3C CAC HEM sing 178 n n C4C NC HEM sing 179 n y CMC HMC HEM sing 180 n n CMC HMCA HEM sing 181 n n CMC HMCB HEM sing 182 n n CAC CBC HEM doub 183 n n CAC HAC HEM sing 184 n n CBC HBC HEM sing 185 n n CBC HBCA HEM sing 186 n n C1D C2D HEM sing 187 n n C1D ND HEM doub 188 n n C2D C3D HEM doub 189 n n C2D CMD HEM sing 190 n n C3D C4D HEM sing 191 n n C3D CAD HEM sing 192 n n C4D ND HEM sing 193 n n CMD HMD HEM sing 194 n n CMD HMDA HEM sing 195 n n CMD HMDB HEM sing 196 n n CAD CBD HEM sing 197 n n CAD HAD HEM sing 198 n n CAD HADA HEM sing 199 n n CBD CGD HEM sing 200 n n CBD HBD HEM sing 201 n n CBD HBDA HEM sing 202 n n CGD O1D HEM doub 203 n n CGD O2D HEM sing 204 n n O2A H2A HEM sing 205 n n O2D H2D HEM sing 206 n n FE NA HEM sing 207 n n FE NB HEM sing 208 n n FE NC HEM sing 209 n n FE ND HEM sing 210 n n # _atom_sites.entry_id 5MJD _atom_sites.fract_transf_matrix[1][1] 0.011387 _atom_sites.fract_transf_matrix[1][2] 0.006574 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013149 _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] 0.008809 _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 1 201 160 HEM HEM . C 3 SO4 A 1 202 170 SO4 SO4 . D 4 OXY A 1 203 180 OXY OXY . E 5 HOH A 1 301 243 HOH HOH . E 5 HOH A 2 302 279 HOH HOH . E 5 HOH A 3 303 212 HOH HOH . E 5 HOH A 4 304 219 HOH HOH . E 5 HOH A 5 305 318 HOH HOH . E 5 HOH A 6 306 308 HOH HOH . E 5 HOH A 7 307 327 HOH HOH . E 5 HOH A 8 308 309 HOH HOH . E 5 HOH A 9 309 326 HOH HOH . E 5 HOH A 10 310 220 HOH HOH . E 5 HOH A 11 311 215 HOH HOH . E 5 HOH A 12 312 242 HOH HOH . E 5 HOH A 13 313 231 HOH HOH . E 5 HOH A 14 314 290 HOH HOH . E 5 HOH A 15 315 285 HOH HOH . E 5 HOH A 16 316 239 HOH HOH . E 5 HOH A 17 317 236 HOH HOH . E 5 HOH A 18 318 313 HOH HOH . E 5 HOH A 19 319 272 HOH HOH . E 5 HOH A 20 320 249 HOH HOH . E 5 HOH A 21 321 213 HOH HOH . E 5 HOH A 22 322 274 HOH HOH . E 5 HOH A 23 323 306 HOH HOH . E 5 HOH A 24 324 237 HOH HOH . E 5 HOH A 25 325 312 HOH HOH . E 5 HOH A 26 326 289 HOH HOH . E 5 HOH A 27 327 287 HOH HOH . E 5 HOH A 28 328 258 HOH HOH . E 5 HOH A 29 329 268 HOH HOH . E 5 HOH A 30 330 234 HOH HOH . E 5 HOH A 31 331 282 HOH HOH . E 5 HOH A 32 332 208 HOH HOH . E 5 HOH A 33 333 201 HOH HOH . E 5 HOH A 34 334 207 HOH HOH . E 5 HOH A 35 335 284 HOH HOH . E 5 HOH A 36 336 209 HOH HOH . E 5 HOH A 37 337 256 HOH HOH . E 5 HOH A 38 338 210 HOH HOH . E 5 HOH A 39 339 203 HOH HOH . E 5 HOH A 40 340 206 HOH HOH . E 5 HOH A 41 341 217 HOH HOH . E 5 HOH A 42 342 246 HOH HOH . E 5 HOH A 43 343 295 HOH HOH . E 5 HOH A 44 344 202 HOH HOH . E 5 HOH A 45 345 261 HOH HOH . E 5 HOH A 46 346 291 HOH HOH . E 5 HOH A 47 347 233 HOH HOH . E 5 HOH A 48 348 247 HOH HOH . E 5 HOH A 49 349 230 HOH HOH . E 5 HOH A 50 350 232 HOH HOH . E 5 HOH A 51 351 245 HOH HOH . E 5 HOH A 52 352 250 HOH HOH . E 5 HOH A 53 353 255 HOH HOH . E 5 HOH A 54 354 216 HOH HOH . E 5 HOH A 55 355 244 HOH HOH . E 5 HOH A 56 356 283 HOH HOH . E 5 HOH A 57 357 205 HOH HOH . E 5 HOH A 58 358 265 HOH HOH . E 5 HOH A 59 359 238 HOH HOH . E 5 HOH A 60 360 204 HOH HOH . E 5 HOH A 61 361 252 HOH HOH . E 5 HOH A 62 362 314 HOH HOH . E 5 HOH A 63 363 281 HOH HOH . E 5 HOH A 64 364 218 HOH HOH . E 5 HOH A 65 365 271 HOH HOH . E 5 HOH A 66 366 224 HOH HOH . E 5 HOH A 67 367 323 HOH HOH . E 5 HOH A 68 368 262 HOH HOH . E 5 HOH A 69 369 253 HOH HOH . E 5 HOH A 70 370 299 HOH HOH . E 5 HOH A 71 371 260 HOH HOH . E 5 HOH A 72 372 223 HOH HOH . E 5 HOH A 73 373 270 HOH HOH . E 5 HOH A 74 374 269 HOH HOH . E 5 HOH A 75 375 263 HOH HOH . E 5 HOH A 76 376 240 HOH HOH . E 5 HOH A 77 377 293 HOH HOH . E 5 HOH A 78 378 280 HOH HOH . E 5 HOH A 79 379 226 HOH HOH . E 5 HOH A 80 380 251 HOH HOH . E 5 HOH A 81 381 229 HOH HOH . E 5 HOH A 82 382 322 HOH HOH . E 5 HOH A 83 383 305 HOH HOH . E 5 HOH A 84 384 248 HOH HOH . E 5 HOH A 85 385 214 HOH HOH . E 5 HOH A 86 386 257 HOH HOH . E 5 HOH A 87 387 310 HOH HOH . E 5 HOH A 88 388 241 HOH HOH . E 5 HOH A 89 389 222 HOH HOH . E 5 HOH A 90 390 273 HOH HOH . E 5 HOH A 91 391 296 HOH HOH . E 5 HOH A 92 392 320 HOH HOH . E 5 HOH A 93 393 225 HOH HOH . E 5 HOH A 94 394 304 HOH HOH . E 5 HOH A 95 395 288 HOH HOH . E 5 HOH A 96 396 317 HOH HOH . E 5 HOH A 97 397 275 HOH HOH . E 5 HOH A 98 398 221 HOH HOH . E 5 HOH A 99 399 315 HOH HOH . E 5 HOH A 100 400 302 HOH HOH . E 5 HOH A 101 401 328 HOH HOH . E 5 HOH A 102 402 324 HOH HOH . E 5 HOH A 103 403 277 HOH HOH . E 5 HOH A 104 404 325 HOH HOH . E 5 HOH A 105 405 301 HOH HOH . E 5 HOH A 106 406 300 HOH HOH . E 5 HOH A 107 407 292 HOH HOH . E 5 HOH A 108 408 276 HOH HOH . E 5 HOH A 109 409 259 HOH HOH . E 5 HOH A 110 410 316 HOH HOH . E 5 HOH A 111 411 227 HOH HOH . E 5 HOH A 112 412 319 HOH HOH . E 5 HOH A 113 413 321 HOH HOH . E 5 HOH A 114 414 211 HOH HOH . E 5 HOH A 115 415 228 HOH HOH . E 5 HOH A 116 416 294 HOH HOH . E 5 HOH A 117 417 286 HOH HOH . E 5 HOH A 118 418 303 HOH HOH . E 5 HOH A 119 419 307 HOH HOH . E 5 HOH A 120 420 298 HOH HOH . E 5 HOH A 121 421 278 HOH HOH . E 5 HOH A 122 422 266 HOH HOH . E 5 HOH A 123 423 311 HOH HOH . E 5 HOH A 124 424 235 HOH HOH . E 5 HOH A 125 425 267 HOH HOH . E 5 HOH A 126 426 254 HOH HOH . E 5 HOH A 127 427 264 HOH HOH . E 5 HOH A 128 428 297 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 . . . B 2 19.45 58.056 36.234 1 21.72 ? CHA HEM 201 A 1 HETATM 2 C CHB HEM . . . B 2 14.973 57.201 34.528 1 23.67 ? CHB HEM 201 A 1 HETATM 3 C CHC HEM . . . B 2 15.644 52.411 35.288 1 22.4 ? CHC HEM 201 A 1 HETATM 4 C CHD HEM . . . B 2 20.22 53.316 36.45 1 19.7 ? CHD HEM 201 A 1 HETATM 5 C C1A HEM . . . B 2 18.164 58.199 35.749 1 21.31 ? C1A HEM 201 A 1 HETATM 6 C C2A HEM . . . B 2 17.605 59.458 35.446 1 23.57 ? C2A HEM 201 A 1 HETATM 7 C C3A HEM . . . B 2 16.37 59.229 34.907 1 24.26 ? C3A HEM 201 A 1 HETATM 8 C C4A HEM . . . B 2 16.157 57.84 34.936 1 23.04 ? C4A HEM 201 A 1 HETATM 9 C CMA HEM . . . B 2 15.396 60.297 34.501 1 27.36 ? CMA HEM 201 A 1 HETATM 10 C CAA HEM . . . B 2 18.209 60.836 35.58 1 24.73 ? CAA HEM 201 A 1 HETATM 11 C CBA HEM . . . B 2 18.732 61.305 34.224 1 23.36 ? CBA HEM 201 A 1 HETATM 12 C CGA HEM . . . B 2 19.879 60.449 33.748 1 27.43 ? CGA HEM 201 A 1 HETATM 13 O O1A HEM . . . B 2 20.978 60.299 34.369 1 25.82 ? O1A HEM 201 A 1 HETATM 14 O O2A HEM . . . B 2 19.772 59.875 32.679 1 22.92 ? O2A HEM 201 A 1 HETATM 15 C C1B HEM . . . B 2 14.766 55.834 34.607 1 23.96 ? C1B HEM 201 A 1 HETATM 16 C C2B HEM . . . B 2 13.498 55.198 34.29 1 24.47 ? C2B HEM 201 A 1 HETATM 17 C C3B HEM . . . B 2 13.688 53.845 34.491 1 25.25 ? C3B HEM 201 A 1 HETATM 18 C C4B HEM . . . B 2 15.053 53.635 34.961 1 22.75 ? C4B HEM 201 A 1 HETATM 19 C CMB HEM . . . B 2 12.232 55.875 33.822 1 27.06 ? CMB HEM 201 A 1 HETATM 20 C CAB HEM . . . B 2 12.746 52.686 34.401 1 22.24 ? CAB HEM 201 A 1 HETATM 21 C CBB HEM . . . B 2 11.462 52.795 34.543 1 29.91 ? CBB HEM 201 A 1 HETATM 22 C C1C HEM . . . B 2 16.967 52.203 35.678 1 22.57 ? C1C HEM 201 A 1 HETATM 23 C C2C HEM . . . B 2 17.549 50.969 36.001 1 25.72 ? C2C HEM 201 A 1 HETATM 24 C C3C HEM . . . B 2 18.885 51.208 36.326 1 23.99 ? C3C HEM 201 A 1 HETATM 25 C C4C HEM . . . B 2 19.062 52.639 36.184 1 21.25 ? C4C HEM 201 A 1 HETATM 26 C CMC HEM . . . B 2 16.812 49.638 35.937 1 28.12 ? CMC HEM 201 A 1 HETATM 27 C CAC HEM . . . B 2 19.946 50.277 36.717 1 26.05 ? CAC HEM 201 A 1 HETATM 28 C CBC HEM . . . B 2 19.832 48.958 36.866 1 31.37 ? CBC HEM 201 A 1 HETATM 29 C C1D HEM . . . B 2 20.33 54.665 36.451 1 18.99 ? C1D HEM 201 A 1 HETATM 30 C C2D HEM . . . B 2 21.591 55.32 36.861 1 20.01 ? C2D HEM 201 A 1 HETATM 31 C C3D HEM . . . B 2 21.349 56.624 36.771 1 19.04 ? C3D HEM 201 A 1 HETATM 32 C C4D HEM . . . B 2 19.967 56.818 36.391 1 21.63 ? C4D HEM 201 A 1 HETATM 33 C CMD HEM . . . B 2 22.835 54.605 37.208 1 20.72 ? CMD HEM 201 A 1 HETATM 34 C CAD HEM . . . B 2 22.328 57.749 37.132 1 21.04 ? CAD HEM 201 A 1 HETATM 35 C CBD HEM . . . B 2 21.922 58.045 38.564 1 25.82 ? CBD HEM 201 A 1 HETATM 36 C CGD HEM . . . B 2 22.773 59.118 39.215 1 30.95 ? CGD HEM 201 A 1 HETATM 37 O O1D HEM . . . B 2 23.575 58.798 40.083 1 36.29 ? O1D HEM 201 A 1 HETATM 38 O O2D HEM . . . B 2 22.648 60.299 38.888 1 35.55 ? O2D HEM 201 A 1 HETATM 39 N NA HEM . . . B 2 17.258 57.146 35.425 1 22.33 ? NA HEM 201 A 1 HETATM 40 N NB HEM . . . B 2 15.604 54.871 34.977 1 20.33 ? NB HEM 201 A 1 HETATM 41 N NC HEM . . . B 2 17.888 53.225 35.835 1 24.54 ? NC HEM 201 A 1 HETATM 42 N ND HEM . . . B 2 19.418 55.6 36.228 1 17.68 ? ND HEM 201 A 1 HETATM 43 FE FE HEM . . . B 2 17.572 55.24 35.606 1 21.7 ? FE HEM 201 A 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 61 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 43 #