data_4XMF # _model_server_result.job_id y7e6YVFJjGM-p9QAQoWQrw _model_server_result.datetime_utc '2024-11-22 22:15:20' _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 4xmf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4XMF # _exptl.entry_id 4XMF _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 116.87 _cell.angle_gamma 90 _cell.entry_id 4XMF _cell.length_a 38.338 _cell.length_b 66.722 _cell.length_c 38.825 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XMF _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 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc1 A NE2 HIS 59 A HIS 60 1_555 B FE HEM . A HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc2 B FE HEM . A HEM 201 1_555 C NE2 HSM . A HSM 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? # _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 4XMF _atom_sites.fract_transf_matrix[1][1] 0.026084 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.013214 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014988 _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] 0.028873 _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 HSM A 1 202 187 HSM HSM . D 4 HOH A 1 301 271 HOH HOH . D 4 HOH A 2 302 264 HOH HOH . D 4 HOH A 3 303 278 HOH HOH . D 4 HOH A 4 304 241 HOH HOH . D 4 HOH A 5 305 247 HOH HOH . D 4 HOH A 6 306 314 HOH HOH . D 4 HOH A 7 307 298 HOH HOH . D 4 HOH A 8 308 254 HOH HOH . D 4 HOH A 9 309 301 HOH HOH . D 4 HOH A 10 310 286 HOH HOH . D 4 HOH A 11 311 260 HOH HOH . D 4 HOH A 12 312 240 HOH HOH . D 4 HOH A 13 313 235 HOH HOH . D 4 HOH A 14 314 276 HOH HOH . D 4 HOH A 15 315 273 HOH HOH . D 4 HOH A 16 316 221 HOH HOH . D 4 HOH A 17 317 282 HOH HOH . D 4 HOH A 18 318 228 HOH HOH . D 4 HOH A 19 319 268 HOH HOH . D 4 HOH A 20 320 218 HOH HOH . D 4 HOH A 21 321 296 HOH HOH . D 4 HOH A 22 322 216 HOH HOH . D 4 HOH A 23 323 323 HOH HOH . D 4 HOH A 24 324 219 HOH HOH . D 4 HOH A 25 325 202 HOH HOH . D 4 HOH A 26 326 310 HOH HOH . D 4 HOH A 27 327 222 HOH HOH . D 4 HOH A 28 328 307 HOH HOH . D 4 HOH A 29 329 226 HOH HOH . D 4 HOH A 30 330 242 HOH HOH . D 4 HOH A 31 331 274 HOH HOH . D 4 HOH A 32 332 225 HOH HOH . D 4 HOH A 33 333 292 HOH HOH . D 4 HOH A 34 334 244 HOH HOH . D 4 HOH A 35 335 238 HOH HOH . D 4 HOH A 36 336 265 HOH HOH . D 4 HOH A 37 337 239 HOH HOH . D 4 HOH A 38 338 311 HOH HOH . D 4 HOH A 39 339 267 HOH HOH . D 4 HOH A 40 340 205 HOH HOH . D 4 HOH A 41 341 326 HOH HOH . D 4 HOH A 42 342 266 HOH HOH . D 4 HOH A 43 343 324 HOH HOH . D 4 HOH A 44 344 283 HOH HOH . D 4 HOH A 45 345 270 HOH HOH . D 4 HOH A 46 346 272 HOH HOH . D 4 HOH A 47 347 313 HOH HOH . D 4 HOH A 48 348 291 HOH HOH . D 4 HOH A 49 349 287 HOH HOH . D 4 HOH A 50 350 262 HOH HOH . D 4 HOH A 51 351 289 HOH HOH . D 4 HOH A 52 352 319 HOH HOH . D 4 HOH A 53 353 217 HOH HOH . D 4 HOH A 54 354 201 HOH HOH . D 4 HOH A 55 355 203 HOH HOH . D 4 HOH A 56 356 204 HOH HOH . D 4 HOH A 57 357 206 HOH HOH . D 4 HOH A 58 358 207 HOH HOH . D 4 HOH A 59 359 208 HOH HOH . D 4 HOH A 60 360 209 HOH HOH . D 4 HOH A 61 361 210 HOH HOH . D 4 HOH A 62 362 211 HOH HOH . D 4 HOH A 63 363 212 HOH HOH . D 4 HOH A 64 364 213 HOH HOH . D 4 HOH A 65 365 214 HOH HOH . D 4 HOH A 66 366 215 HOH HOH . D 4 HOH A 67 367 220 HOH HOH . D 4 HOH A 68 368 223 HOH HOH . D 4 HOH A 69 369 224 HOH HOH . D 4 HOH A 70 370 227 HOH HOH . D 4 HOH A 71 371 229 HOH HOH . D 4 HOH A 72 372 230 HOH HOH . D 4 HOH A 73 373 231 HOH HOH . D 4 HOH A 74 374 232 HOH HOH . D 4 HOH A 75 375 233 HOH HOH . D 4 HOH A 76 376 234 HOH HOH . D 4 HOH A 77 377 236 HOH HOH . D 4 HOH A 78 378 237 HOH HOH . D 4 HOH A 79 379 243 HOH HOH . D 4 HOH A 80 380 245 HOH HOH . D 4 HOH A 81 381 246 HOH HOH . D 4 HOH A 82 382 248 HOH HOH . D 4 HOH A 83 383 249 HOH HOH . D 4 HOH A 84 384 250 HOH HOH . D 4 HOH A 85 385 251 HOH HOH . D 4 HOH A 86 386 252 HOH HOH . D 4 HOH A 87 387 253 HOH HOH . D 4 HOH A 88 388 255 HOH HOH . D 4 HOH A 89 389 256 HOH HOH . D 4 HOH A 90 390 257 HOH HOH . D 4 HOH A 91 391 258 HOH HOH . D 4 HOH A 92 392 259 HOH HOH . D 4 HOH A 93 393 261 HOH HOH . D 4 HOH A 94 394 263 HOH HOH . D 4 HOH A 95 395 269 HOH HOH . D 4 HOH A 96 396 275 HOH HOH . D 4 HOH A 97 397 277 HOH HOH . D 4 HOH A 98 398 279 HOH HOH . D 4 HOH A 99 399 280 HOH HOH . D 4 HOH A 100 400 281 HOH HOH . D 4 HOH A 101 401 284 HOH HOH . D 4 HOH A 102 402 285 HOH HOH . D 4 HOH A 103 403 288 HOH HOH . D 4 HOH A 104 404 290 HOH HOH . D 4 HOH A 105 405 293 HOH HOH . D 4 HOH A 106 406 294 HOH HOH . D 4 HOH A 107 407 295 HOH HOH . D 4 HOH A 108 408 297 HOH HOH . D 4 HOH A 109 409 299 HOH HOH . D 4 HOH A 110 410 300 HOH HOH . D 4 HOH A 111 411 302 HOH HOH . D 4 HOH A 112 412 303 HOH HOH . D 4 HOH A 113 413 304 HOH HOH . D 4 HOH A 114 414 305 HOH HOH . D 4 HOH A 115 415 306 HOH HOH . D 4 HOH A 116 416 308 HOH HOH . D 4 HOH A 117 417 309 HOH HOH . D 4 HOH A 118 418 312 HOH HOH . D 4 HOH A 119 419 315 HOH HOH . D 4 HOH A 120 420 316 HOH HOH . D 4 HOH A 121 421 317 HOH HOH . D 4 HOH A 122 422 318 HOH HOH . D 4 HOH A 123 423 320 HOH HOH . D 4 HOH A 124 424 321 HOH HOH . D 4 HOH A 125 425 322 HOH HOH . D 4 HOH A 126 426 325 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 7.16 -9.76 7.859 0.81 26.53 ? CHA HEM 201 A 1 HETATM 2 C CHB HEM . . . B 2 10.896 -8.149 10.477 0.81 25.58 ? CHB HEM 201 A 1 HETATM 3 C CHC HEM . . . B 2 9.001 -3.681 10.465 0.81 19.69 ? CHC HEM 201 A 1 HETATM 4 C CHD HEM . . . B 2 5.091 -5.324 8.102 0.81 22.24 ? CHD HEM 201 A 1 HETATM 5 C C1A HEM . . . B 2 8.295 -9.718 8.627 0.81 28.3 ? C1A HEM 201 A 1 HETATM 6 C C2A HEM . . . B 2 9.054 -10.865 9.071 0.81 31.95 ? C2A HEM 201 A 1 HETATM 7 C C3A HEM . . . B 2 10.089 -10.428 9.788 0.81 30.84 ? C3A HEM 201 A 1 HETATM 8 C C4A HEM . . . B 2 10.021 -8.986 9.828 0.81 27.83 ? C4A HEM 201 A 1 HETATM 9 C CMA HEM . . . B 2 11.169 -11.297 10.465 0.81 33.11 ? CMA HEM 201 A 1 HETATM 10 C CAA HEM . . . B 2 8.722 -12.331 8.74 0.81 35.81 ? CAA HEM 201 A 1 HETATM 11 C CBA HEM . . . B 2 9.38 -12.622 7.396 0.81 40.33 ? CBA HEM 201 A 1 HETATM 12 C CGA HEM . . . B 2 9.242 -14.082 7.07 0.81 43.26 ? CGA HEM 201 A 1 HETATM 13 O O1A HEM . . . B 2 8.187 -14.67 7.425 0.81 43.69 ? O1A HEM 201 A 1 HETATM 14 O O2A HEM . . . B 2 10.183 -14.645 6.452 0.81 43.9 ? O2A HEM 201 A 1 HETATM 15 C C1B HEM . . . B 2 10.738 -6.795 10.644 0.81 22.28 ? C1B HEM 201 A 1 HETATM 16 C C2B HEM . . . B 2 11.725 -5.908 11.207 0.81 21.32 ? C2B HEM 201 A 1 HETATM 17 C C3B HEM . . . B 2 11.23 -4.675 11.215 0.81 23.5 ? C3B HEM 201 A 1 HETATM 18 C C4B HEM . . . B 2 9.886 -4.723 10.645 0.81 21.23 ? C4B HEM 201 A 1 HETATM 19 C CMB HEM . . . B 2 13.119 -6.316 11.721 0.81 21.52 ? CMB HEM 201 A 1 HETATM 20 C CAB HEM . . . B 2 12.018 -3.461 11.757 0.81 24.21 ? CAB HEM 201 A 1 HETATM 21 C CBB HEM . . . B 2 11.534 -2.223 11.691 0.81 23.04 ? CBB HEM 201 A 1 HETATM 22 C C1C HEM . . . B 2 7.765 -3.74 9.853 0.81 19.22 ? C1C HEM 201 A 1 HETATM 23 C C2C HEM . . . B 2 6.834 -2.639 9.703 0.81 18.89 ? C2C HEM 201 A 1 HETATM 24 C C3C HEM . . . B 2 5.745 -3.09 9.058 0.81 19.99 ? C3C HEM 201 A 1 HETATM 25 C C4C HEM . . . B 2 5.966 -4.493 8.766 0.81 22.41 ? C4C HEM 201 A 1 HETATM 26 C CMC HEM . . . B 2 7.093 -1.214 10.234 0.81 22.21 ? CMC HEM 201 A 1 HETATM 27 C CAC HEM . . . B 2 4.466 -2.326 8.638 0.81 20.72 ? CAC HEM 201 A 1 HETATM 28 C CBC HEM . . . B 2 4.38 -0.987 8.564 0.81 22.8 ? CBC HEM 201 A 1 HETATM 29 C C1D HEM . . . B 2 5.345 -6.625 7.725 0.81 23.16 ? C1D HEM 201 A 1 HETATM 30 C C2D HEM . . . B 2 4.581 -7.357 6.744 0.81 24.61 ? C2D HEM 201 A 1 HETATM 31 C C3D HEM . . . B 2 5.223 -8.743 6.669 0.81 26.74 ? C3D HEM 201 A 1 HETATM 32 C C4D HEM . . . B 2 6.314 -8.706 7.615 0.81 25.09 ? C4D HEM 201 A 1 HETATM 33 C CMD HEM . . . B 2 3.369 -6.842 5.947 0.81 25.89 ? CMD HEM 201 A 1 HETATM 34 C CAD HEM . . . B 2 4.805 -9.931 5.772 0.81 30.21 ? CAD HEM 201 A 1 HETATM 35 C CBD HEM . . . B 2 4.015 -10.937 6.601 0.81 34.41 ? CBD HEM 201 A 1 HETATM 36 C CGD HEM . . . B 2 3.598 -12.095 5.73 0.81 37.74 ? CGD HEM 201 A 1 HETATM 37 O O1D HEM . . . B 2 4.116 -12.199 4.587 0.81 37.92 ? O1D HEM 201 A 1 HETATM 38 O O2D HEM . . . B 2 2.75 -12.913 6.181 0.81 40.46 ? O2D HEM 201 A 1 HETATM 39 N NA HEM . . . B 2 8.908 -8.585 9.115 0.81 26.61 ? NA HEM 201 A 1 HETATM 40 N NB HEM . . . B 2 9.629 -6.039 10.308 0.81 21.45 ? NB HEM 201 A 1 HETATM 41 N NC HEM . . . B 2 7.204 -4.852 9.266 0.81 21 ? NC HEM 201 A 1 HETATM 42 N ND HEM . . . B 2 6.363 -7.448 8.216 0.81 22.41 ? ND HEM 201 A 1 HETATM 43 FE FE HEM . . . B 2 8.032 -6.706 9.234 0.81 23.59 ? FE HEM 201 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 43 #