data_5M6K # _model_server_result.job_id ZdwcS5wJLwBHAstph8yNhw _model_server_result.datetime_utc '2024-11-26 05:44:39' _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 5m6k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 5M6K # _exptl.entry_id 5M6K _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 116.72 _cell.angle_gamma 90 _cell.entry_id 5M6K _cell.length_a 38.26 _cell.length_b 66.645 _cell.length_c 38.494 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5M6K _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,D _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 disulf ? disulf1 A SG CYS 4 A CYS 5 1_555 A SG CYS 123 A CYS 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 41 A CYS 42 1_555 A SG CYS 172 A CYS 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc1 A NE2 HIS 59 A HIS 60 1_555 B FE HEM . A HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc2 B FE HEM . A HEM 201 1_555 C N1 IMD . A IMD 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? # _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 5M6K _atom_sites.fract_transf_matrix[1][1] 0.026137 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.013155 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015005 _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] 0.029083 _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 1 201 186 HEM HEM . C 3 IMD A 1 202 187 IMD IMD . D 4 HOH A 1 301 286 HOH HOH . D 4 HOH A 2 302 305 HOH HOH . D 4 HOH A 3 303 254 HOH HOH . D 4 HOH A 4 304 253 HOH HOH . D 4 HOH A 5 305 272 HOH HOH . D 4 HOH A 6 306 251 HOH HOH . D 4 HOH A 7 307 252 HOH HOH . D 4 HOH A 8 308 239 HOH HOH . D 4 HOH A 9 309 213 HOH HOH . D 4 HOH A 10 310 243 HOH HOH . D 4 HOH A 11 311 203 HOH HOH . D 4 HOH A 12 312 265 HOH HOH . D 4 HOH A 13 313 263 HOH HOH . D 4 HOH A 14 314 276 HOH HOH . D 4 HOH A 15 315 309 HOH HOH . D 4 HOH A 16 316 235 HOH HOH . D 4 HOH A 17 317 207 HOH HOH . D 4 HOH A 18 318 215 HOH HOH . D 4 HOH A 19 319 229 HOH HOH . D 4 HOH A 20 320 230 HOH HOH . D 4 HOH A 21 321 278 HOH HOH . D 4 HOH A 22 322 204 HOH HOH . D 4 HOH A 23 323 267 HOH HOH . D 4 HOH A 24 324 293 HOH HOH . D 4 HOH A 25 325 225 HOH HOH . D 4 HOH A 26 326 299 HOH HOH . D 4 HOH A 27 327 284 HOH HOH . D 4 HOH A 28 328 296 HOH HOH . D 4 HOH A 29 329 202 HOH HOH . D 4 HOH A 30 330 249 HOH HOH . D 4 HOH A 31 331 268 HOH HOH . D 4 HOH A 32 332 246 HOH HOH . D 4 HOH A 33 333 250 HOH HOH . D 4 HOH A 34 334 216 HOH HOH . D 4 HOH A 35 335 238 HOH HOH . D 4 HOH A 36 336 281 HOH HOH . D 4 HOH A 37 337 206 HOH HOH . D 4 HOH A 38 338 226 HOH HOH . D 4 HOH A 39 339 245 HOH HOH . D 4 HOH A 40 340 201 HOH HOH . D 4 HOH A 41 341 275 HOH HOH . D 4 HOH A 42 342 271 HOH HOH . D 4 HOH A 43 343 220 HOH HOH . D 4 HOH A 44 344 319 HOH HOH . D 4 HOH A 45 345 223 HOH HOH . D 4 HOH A 46 346 242 HOH HOH . D 4 HOH A 47 347 232 HOH HOH . D 4 HOH A 48 348 236 HOH HOH . D 4 HOH A 49 349 222 HOH HOH . D 4 HOH A 50 350 214 HOH HOH . D 4 HOH A 51 351 269 HOH HOH . D 4 HOH A 52 352 256 HOH HOH . D 4 HOH A 53 353 228 HOH HOH . D 4 HOH A 54 354 270 HOH HOH . D 4 HOH A 55 355 266 HOH HOH . D 4 HOH A 56 356 261 HOH HOH . D 4 HOH A 57 357 231 HOH HOH . D 4 HOH A 58 358 304 HOH HOH . D 4 HOH A 59 359 208 HOH HOH . D 4 HOH A 60 360 274 HOH HOH . D 4 HOH A 61 361 288 HOH HOH . D 4 HOH A 62 362 241 HOH HOH . D 4 HOH A 63 363 234 HOH HOH . D 4 HOH A 64 364 273 HOH HOH . D 4 HOH A 65 365 264 HOH HOH . D 4 HOH A 66 366 244 HOH HOH . D 4 HOH A 67 367 209 HOH HOH . D 4 HOH A 68 368 217 HOH HOH . D 4 HOH A 69 369 221 HOH HOH . D 4 HOH A 70 370 308 HOH HOH . D 4 HOH A 71 371 237 HOH HOH . D 4 HOH A 72 372 227 HOH HOH . D 4 HOH A 73 373 205 HOH HOH . D 4 HOH A 74 374 255 HOH HOH . D 4 HOH A 75 375 285 HOH HOH . D 4 HOH A 76 376 302 HOH HOH . D 4 HOH A 77 377 301 HOH HOH . D 4 HOH A 78 378 300 HOH HOH . D 4 HOH A 79 379 321 HOH HOH . D 4 HOH A 80 380 287 HOH HOH . D 4 HOH A 81 381 277 HOH HOH . D 4 HOH A 82 382 294 HOH HOH . D 4 HOH A 83 383 212 HOH HOH . D 4 HOH A 84 384 306 HOH HOH . D 4 HOH A 85 385 240 HOH HOH . D 4 HOH A 86 386 320 HOH HOH . D 4 HOH A 87 387 280 HOH HOH . D 4 HOH A 88 388 312 HOH HOH . D 4 HOH A 89 389 210 HOH HOH . D 4 HOH A 90 390 211 HOH HOH . D 4 HOH A 91 391 298 HOH HOH . D 4 HOH A 92 392 292 HOH HOH . D 4 HOH A 93 393 311 HOH HOH . D 4 HOH A 94 394 295 HOH HOH . D 4 HOH A 95 395 224 HOH HOH . D 4 HOH A 96 396 247 HOH HOH . D 4 HOH A 97 397 282 HOH HOH . D 4 HOH A 98 398 315 HOH HOH . D 4 HOH A 99 399 233 HOH HOH . D 4 HOH A 100 400 218 HOH HOH . D 4 HOH A 101 401 316 HOH HOH . D 4 HOH A 102 402 279 HOH HOH . D 4 HOH A 103 403 259 HOH HOH . D 4 HOH A 104 404 257 HOH HOH . D 4 HOH A 105 405 310 HOH HOH . D 4 HOH A 106 406 258 HOH HOH . D 4 HOH A 107 407 307 HOH HOH . D 4 HOH A 108 408 248 HOH HOH . D 4 HOH A 109 409 283 HOH HOH . D 4 HOH A 110 410 260 HOH HOH . D 4 HOH A 111 411 318 HOH HOH . D 4 HOH A 112 412 289 HOH HOH . D 4 HOH A 113 413 303 HOH HOH . D 4 HOH A 114 414 314 HOH HOH . D 4 HOH A 115 415 297 HOH HOH . D 4 HOH A 116 416 313 HOH HOH . D 4 HOH A 117 417 290 HOH HOH . D 4 HOH A 118 418 317 HOH HOH . D 4 HOH A 119 419 262 HOH HOH . D 4 HOH A 120 420 219 HOH HOH . D 4 HOH A 121 421 291 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 -12.217 -9.862 8.373 0.97 20.67 ? CHA HEM 201 A 1 HETATM 2 C CHB HEM . . . B 2 -8.343 -8.516 10.897 0.97 22.31 ? CHB HEM 201 A 1 HETATM 3 C CHC HEM . . . B 2 -9.485 -3.875 10.209 0.97 18.23 ? CHC HEM 201 A 1 HETATM 4 C CHD HEM . . . B 2 -13.767 -5.211 8.334 0.97 17.52 ? CHD HEM 201 A 1 HETATM 5 C C1A HEM . . . B 2 -11.048 -9.905 9.082 0.97 20.93 ? C1A HEM 201 A 1 HETATM 6 C C2A HEM . . . B 2 -10.292 -11.092 9.417 0.97 24.65 ? C2A HEM 201 A 1 HETATM 7 C C3A HEM . . . B 2 -9.213 -10.715 10.109 0.97 24.44 ? C3A HEM 201 A 1 HETATM 8 C C4A HEM . . . B 2 -9.267 -9.281 10.245 0.97 22.1 ? C4A HEM 201 A 1 HETATM 9 C CMA HEM . . . B 2 -8.102 -11.617 10.694 0.97 26.09 ? CMA HEM 201 A 1 HETATM 10 C CAA HEM . . . B 2 -10.665 -12.525 8.995 0.97 30.45 ? CAA HEM 201 A 1 HETATM 11 C CBA HEM . . . B 2 -9.818 -12.804 7.754 0.97 36.07 ? CBA HEM 201 A 1 HETATM 12 C CGA HEM . . . B 2 -10.044 -14.183 7.2 0.97 40.76 ? CGA HEM 201 A 1 HETATM 13 O O1A HEM . . . B 2 -11.159 -14.736 7.386 0.97 40.05 ? O1A HEM 201 A 1 HETATM 14 O O2A HEM . . . B 2 -9.102 -14.717 6.557 0.97 43.96 ? O2A HEM 201 A 1 HETATM 15 C C1B HEM . . . B 2 -8.271 -7.153 10.845 0.97 19.88 ? C1B HEM 201 A 1 HETATM 16 C C2B HEM . . . B 2 -7.13 -6.372 11.247 0.97 20.45 ? C2B HEM 201 A 1 HETATM 17 C C3B HEM . . . B 2 -7.444 -5.082 11.08 0.97 20.23 ? C3B HEM 201 A 1 HETATM 18 C C4B HEM . . . B 2 -8.783 -5.015 10.524 0.97 19.03 ? C4B HEM 201 A 1 HETATM 19 C CMB HEM . . . B 2 -5.835 -6.981 11.821 0.97 21.32 ? CMB HEM 201 A 1 HETATM 20 C CAB HEM . . . B 2 -6.554 -3.847 11.34 0.97 21.45 ? CAB HEM 201 A 1 HETATM 21 C CBB HEM . . . B 2 -5.269 -3.851 10.957 0.97 20.66 ? CBB HEM 201 A 1 HETATM 22 C C1C HEM . . . B 2 -10.782 -3.838 9.733 0.97 17.18 ? C1C HEM 201 A 1 HETATM 23 C C2C HEM . . . B 2 -11.622 -2.663 9.637 0.97 17.75 ? C2C HEM 201 A 1 HETATM 24 C C3C HEM . . . B 2 -12.817 -3.026 9.13 0.97 17.71 ? C3C HEM 201 A 1 HETATM 25 C C4C HEM . . . B 2 -12.75 -4.454 8.871 0.97 18.97 ? C4C HEM 201 A 1 HETATM 26 C CMC HEM . . . B 2 -11.154 -1.268 10.096 0.97 19.98 ? CMC HEM 201 A 1 HETATM 27 C CAC HEM . . . B 2 -14.065 -2.161 8.808 0.97 17.91 ? CAC HEM 201 A 1 HETATM 28 C CBC HEM . . . B 2 -14.014 -0.842 8.547 0.97 20.98 ? CBC HEM 201 A 1 HETATM 29 C C1D HEM . . . B 2 -13.718 -6.564 8.118 0.97 19.02 ? C1D HEM 201 A 1 HETATM 30 C C2D HEM . . . B 2 -14.726 -7.317 7.408 0.97 20.36 ? C2D HEM 201 A 1 HETATM 31 C C3D HEM . . . B 2 -14.233 -8.761 7.43 0.97 22.88 ? C3D HEM 201 A 1 HETATM 32 C C4D HEM . . . B 2 -12.984 -8.742 8.141 0.97 21.8 ? C4D HEM 201 A 1 HETATM 33 C CMD HEM . . . B 2 -16.022 -6.794 6.757 0.97 20.12 ? CMD HEM 201 A 1 HETATM 34 C CAD HEM . . . B 2 -14.909 -10 6.818 0.97 26.42 ? CAD HEM 201 A 1 HETATM 35 C CBD HEM . . . B 2 -14.463 -10.075 5.364 0.97 29.73 ? CBD HEM 201 A 1 HETATM 36 C CGD HEM . . . B 2 -15.025 -11.316 4.724 0.97 34.24 ? CGD HEM 201 A 1 HETATM 37 O O1D HEM . . . B 2 -15.309 -11.274 3.493 0.97 36.49 ? O1D HEM 201 A 1 HETATM 38 O O2D HEM . . . B 2 -15.198 -12.333 5.45 0.97 32.51 ? O2D HEM 201 A 1 HETATM 39 N NA HEM . . . B 2 -10.394 -8.812 9.607 0.97 18.85 ? NA HEM 201 A 1 HETATM 40 N NB HEM . . . B 2 -9.259 -6.301 10.4 0.97 17.42 ? NB HEM 201 A 1 HETATM 41 N NC HEM . . . B 2 -11.503 -4.916 9.254 0.97 17.53 ? NC HEM 201 A 1 HETATM 42 N ND HEM . . . B 2 -12.708 -7.435 8.527 0.97 18.6 ? ND HEM 201 A 1 HETATM 43 FE FE HEM . . . B 2 -10.999 -6.873 9.478 0.97 19.36 ? FE HEM 201 A 1 # _model_server_stats.io_time_ms 45 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 238 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #