data_4XMC # _model_server_result.job_id WSBPpGLDOtCir-Onym86qA _model_server_result.datetime_utc '2024-11-23 02:42:17' _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 4xmc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4XMC # _exptl.entry_id 4XMC _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 116.57 _cell.angle_gamma 90 _cell.entry_id 4XMC _cell.length_a 38.419 _cell.length_b 66.999 _cell.length_c 38.997 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XMC _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 # 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf2 A SG CYS 41 A CYS 42 1_555 A SG CYS 172 A CYS 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc1 A NE2 HIS 59 A HIS 60 1_555 B FE HEM . A HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc2 B FE HEM . A HEM 201 1_555 C O HOH . A HOH 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? # _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 4XMC _atom_sites.fract_transf_matrix[1][1] 0.026029 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.01302 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014926 _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] 0.028672 _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 HOH A 1 301 262 HOH HOH . C 3 HOH A 2 302 281 HOH HOH . C 3 HOH A 3 303 253 HOH HOH . C 3 HOH A 4 304 228 HOH HOH . C 3 HOH A 5 305 271 HOH HOH . C 3 HOH A 6 306 218 HOH HOH . C 3 HOH A 7 307 238 HOH HOH . C 3 HOH A 8 308 239 HOH HOH . C 3 HOH A 9 309 266 HOH HOH . C 3 HOH A 10 310 217 HOH HOH . C 3 HOH A 11 311 227 HOH HOH . C 3 HOH A 12 312 223 HOH HOH . C 3 HOH A 13 313 203 HOH HOH . C 3 HOH A 14 314 279 HOH HOH . C 3 HOH A 15 315 258 HOH HOH . C 3 HOH A 16 316 211 HOH HOH . C 3 HOH A 17 317 214 HOH HOH . C 3 HOH A 18 318 263 HOH HOH . C 3 HOH A 19 319 219 HOH HOH . C 3 HOH A 20 320 257 HOH HOH . C 3 HOH A 21 321 261 HOH HOH . C 3 HOH A 22 322 273 HOH HOH . C 3 HOH A 23 323 275 HOH HOH . C 3 HOH A 24 324 249 HOH HOH . C 3 HOH A 25 325 270 HOH HOH . C 3 HOH A 26 326 272 HOH HOH . C 3 HOH A 27 327 233 HOH HOH . C 3 HOH A 28 328 222 HOH HOH . C 3 HOH A 29 329 201 HOH HOH . C 3 HOH A 30 330 202 HOH HOH . C 3 HOH A 31 331 204 HOH HOH . C 3 HOH A 32 332 205 HOH HOH . C 3 HOH A 33 333 206 HOH HOH . C 3 HOH A 34 334 207 HOH HOH . C 3 HOH A 35 335 208 HOH HOH . C 3 HOH A 36 336 209 HOH HOH . C 3 HOH A 37 337 210 HOH HOH . C 3 HOH A 38 338 212 HOH HOH . C 3 HOH A 39 339 213 HOH HOH . C 3 HOH A 40 340 215 HOH HOH . C 3 HOH A 41 341 216 HOH HOH . C 3 HOH A 42 342 220 HOH HOH . C 3 HOH A 43 343 221 HOH HOH . C 3 HOH A 44 344 224 HOH HOH . C 3 HOH A 45 345 225 HOH HOH . C 3 HOH A 46 346 226 HOH HOH . C 3 HOH A 47 347 229 HOH HOH . C 3 HOH A 48 348 230 HOH HOH . C 3 HOH A 49 349 231 HOH HOH . C 3 HOH A 50 350 232 HOH HOH . C 3 HOH A 51 351 234 HOH HOH . C 3 HOH A 52 352 236 HOH HOH . C 3 HOH A 53 353 237 HOH HOH . C 3 HOH A 54 354 240 HOH HOH . C 3 HOH A 55 355 241 HOH HOH . C 3 HOH A 56 356 242 HOH HOH . C 3 HOH A 57 357 243 HOH HOH . C 3 HOH A 58 358 244 HOH HOH . C 3 HOH A 59 359 245 HOH HOH . C 3 HOH A 60 360 246 HOH HOH . C 3 HOH A 61 361 247 HOH HOH . C 3 HOH A 62 362 248 HOH HOH . C 3 HOH A 63 363 250 HOH HOH . C 3 HOH A 64 364 251 HOH HOH . C 3 HOH A 65 365 252 HOH HOH . C 3 HOH A 66 366 254 HOH HOH . C 3 HOH A 67 367 255 HOH HOH . C 3 HOH A 68 368 256 HOH HOH . C 3 HOH A 69 369 259 HOH HOH . C 3 HOH A 70 370 260 HOH HOH . C 3 HOH A 71 371 264 HOH HOH . C 3 HOH A 72 372 265 HOH HOH . C 3 HOH A 73 373 267 HOH HOH . C 3 HOH A 74 374 268 HOH HOH . C 3 HOH A 75 375 269 HOH HOH . C 3 HOH A 76 376 274 HOH HOH . C 3 HOH A 77 377 276 HOH HOH . C 3 HOH A 78 378 277 HOH HOH . C 3 HOH A 79 379 278 HOH HOH . C 3 HOH A 80 380 280 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 7.043 -9.916 7.856 1 26.11 ? CHA HEM 201 A 1 HETATM 2 C CHB HEM . . . B 2 10.845 -8.317 10.358 1 27.57 ? CHB HEM 201 A 1 HETATM 3 C CHC HEM . . . B 2 8.911 -3.871 10.562 1 24.04 ? CHC HEM 201 A 1 HETATM 4 C CHD HEM . . . B 2 5.123 -5.402 7.936 1 22.7 ? CHD HEM 201 A 1 HETATM 5 C C1A HEM . . . B 2 8.217 -9.886 8.557 1 28.3 ? C1A HEM 201 A 1 HETATM 6 C C2A HEM . . . B 2 9.053 -11.029 8.862 1 31.96 ? C2A HEM 201 A 1 HETATM 7 C C3A HEM . . . B 2 10.101 -10.587 9.558 1 30.5 ? C3A HEM 201 A 1 HETATM 8 C C4A HEM . . . B 2 9.966 -9.152 9.712 1 28.46 ? C4A HEM 201 A 1 HETATM 9 C CMA HEM . . . B 2 11.262 -11.442 10.11 1 32.32 ? CMA HEM 201 A 1 HETATM 10 C CAA HEM . . . B 2 8.76 -12.49 8.454 1 35.76 ? CAA HEM 201 A 1 HETATM 11 C CBA HEM . . . B 2 9.568 -12.827 7.205 1 41.19 ? CBA HEM 201 A 1 HETATM 12 C CGA HEM . . . B 2 9.442 -14.287 6.856 1 45.53 ? CGA HEM 201 A 1 HETATM 13 O O1A HEM . . . B 2 8.4 -14.905 7.202 1 47.15 ? O1A HEM 201 A 1 HETATM 14 O O2A HEM . . . B 2 10.387 -14.828 6.218 1 47.43 ? O2A HEM 201 A 1 HETATM 15 C C1B HEM . . . B 2 10.678 -6.969 10.579 1 25.44 ? C1B HEM 201 A 1 HETATM 16 C C2B HEM . . . B 2 11.655 -6.099 11.186 1 26.1 ? C2B HEM 201 A 1 HETATM 17 C C3B HEM . . . B 2 11.154 -4.867 11.244 1 26.76 ? C3B HEM 201 A 1 HETATM 18 C C4B HEM . . . B 2 9.808 -4.907 10.682 1 24.6 ? C4B HEM 201 A 1 HETATM 19 C CMB HEM . . . B 2 13.06 -6.514 11.673 1 28.06 ? CMB HEM 201 A 1 HETATM 20 C CAB HEM . . . B 2 11.94 -3.678 11.847 1 29.46 ? CAB HEM 201 A 1 HETATM 21 C CBB HEM . . . B 2 11.577 -2.402 11.704 1 25.78 ? CBB HEM 201 A 1 HETATM 22 C C1C HEM . . . B 2 7.7 -3.915 9.901 1 22.8 ? C1C HEM 201 A 1 HETATM 23 C C2C HEM . . . B 2 6.775 -2.809 9.773 1 22.95 ? C2C HEM 201 A 1 HETATM 24 C C3C HEM . . . B 2 5.72 -3.224 9.05 1 23.23 ? C3C HEM 201 A 1 HETATM 25 C C4C HEM . . . B 2 5.959 -4.61 8.689 1 21.1 ? C4C HEM 201 A 1 HETATM 26 C CMC HEM . . . B 2 7.024 -1.426 10.413 1 25.36 ? CMC HEM 201 A 1 HETATM 27 C CAC HEM . . . B 2 4.463 -2.431 8.613 1 26 ? CAC HEM 201 A 1 HETATM 28 C CBC HEM . . . B 2 4.449 -1.096 8.483 1 28.04 ? CBC HEM 201 A 1 HETATM 29 C C1D HEM . . . B 2 5.316 -6.738 7.652 1 23.25 ? C1D HEM 201 A 1 HETATM 30 C C2D HEM . . . B 2 4.429 -7.537 6.834 1 25.99 ? C2D HEM 201 A 1 HETATM 31 C C3D HEM . . . B 2 5.028 -8.934 6.818 1 28.65 ? C3D HEM 201 A 1 HETATM 32 C C4D HEM . . . B 2 6.214 -8.846 7.629 1 25.27 ? C4D HEM 201 A 1 HETATM 33 C CMD HEM . . . B 2 3.144 -7.079 6.12 1 27.88 ? CMD HEM 201 A 1 HETATM 34 C CAD HEM . . . B 2 4.476 -10.181 6.088 1 33.28 ? CAD HEM 201 A 1 HETATM 35 C CBD HEM . . . B 2 4.837 -10.107 4.611 1 37.07 ? CBD HEM 201 A 1 HETATM 36 C CGD HEM . . . B 2 4.327 -11.338 3.91 1 40.95 ? CGD HEM 201 A 1 HETATM 37 O O1D HEM . . . B 2 4.374 -11.368 2.65 1 43.32 ? O1D HEM 201 A 1 HETATM 38 O O2D HEM . . . B 2 3.875 -12.284 4.609 1 40.99 ? O2D HEM 201 A 1 HETATM 39 N NA HEM . . . B 2 8.801 -8.755 9.086 1 26.12 ? NA HEM 201 A 1 HETATM 40 N NB HEM . . . B 2 9.559 -6.212 10.287 1 24.93 ? NB HEM 201 A 1 HETATM 41 N NC HEM . . . B 2 7.17 -4.999 9.226 1 21.43 ? NC HEM 201 A 1 HETATM 42 N ND HEM . . . B 2 6.368 -7.54 8.109 1 21.86 ? ND HEM 201 A 1 HETATM 43 FE FE HEM . . . B 2 8.021 -6.875 9.107 1 22.06 ? FE HEM 201 A 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 221 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 43 #