data_5YCG # _model_server_result.job_id DBSBDIQjwn9JWlFrzOT6wg _model_server_result.datetime_utc '2024-10-22 21:42:11' _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 5ycg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 5YCG # _exptl.entry_id 5YCG _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 112.65 _cell.angle_gamma 90 _cell.entry_id 5YCG _cell.length_a 55.39 _cell.length_b 29.74 _cell.length_c 58.36 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YCG _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 metalc ? metalc1 A NE2 HIS 97 A HIS 93 1_555 B FE HEM . A HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? metalc ? metalc2 B FE HEM . A HEM 201 1_555 C O HOH . A HOH 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? # _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 5YCG _atom_sites.fract_transf_matrix[1][1] 0.018054 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007534 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.033625 _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] 0.018567 _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 19 HOH HOH . C 3 HOH A 2 302 8 HOH HOH . C 3 HOH A 3 303 33 HOH HOH . C 3 HOH A 4 304 53 HOH HOH . C 3 HOH A 5 305 74 HOH HOH . C 3 HOH A 6 306 44 HOH HOH . C 3 HOH A 7 307 38 HOH HOH . C 3 HOH A 8 308 69 HOH HOH . C 3 HOH A 9 309 45 HOH HOH . C 3 HOH A 10 310 4 HOH HOH . C 3 HOH A 11 311 32 HOH HOH . C 3 HOH A 12 312 16 HOH HOH . C 3 HOH A 13 313 66 HOH HOH . C 3 HOH A 14 314 51 HOH HOH . C 3 HOH A 15 315 22 HOH HOH . C 3 HOH A 16 316 24 HOH HOH . C 3 HOH A 17 317 6 HOH HOH . C 3 HOH A 18 318 41 HOH HOH . C 3 HOH A 19 319 15 HOH HOH . C 3 HOH A 20 320 36 HOH HOH . C 3 HOH A 21 321 49 HOH HOH . C 3 HOH A 22 322 21 HOH HOH . C 3 HOH A 23 323 34 HOH HOH . C 3 HOH A 24 324 1 HOH HOH . C 3 HOH A 25 325 65 HOH HOH . C 3 HOH A 26 326 25 HOH HOH . C 3 HOH A 27 327 9 HOH HOH . C 3 HOH A 28 328 71 HOH HOH . C 3 HOH A 29 329 10 HOH HOH . C 3 HOH A 30 330 5 HOH HOH . C 3 HOH A 31 331 59 HOH HOH . C 3 HOH A 32 332 72 HOH HOH . C 3 HOH A 33 333 73 HOH HOH . C 3 HOH A 34 334 23 HOH HOH . C 3 HOH A 35 335 12 HOH HOH . C 3 HOH A 36 336 42 HOH HOH . C 3 HOH A 37 337 64 HOH HOH . C 3 HOH A 38 338 50 HOH HOH . C 3 HOH A 39 339 27 HOH HOH . C 3 HOH A 40 340 67 HOH HOH . C 3 HOH A 41 341 20 HOH HOH . C 3 HOH A 42 342 28 HOH HOH . C 3 HOH A 43 343 57 HOH HOH . C 3 HOH A 44 344 43 HOH HOH . C 3 HOH A 45 345 35 HOH HOH . C 3 HOH A 46 346 3 HOH HOH . C 3 HOH A 47 347 7 HOH HOH . C 3 HOH A 48 348 48 HOH HOH . C 3 HOH A 49 349 54 HOH HOH . C 3 HOH A 50 350 58 HOH HOH . C 3 HOH A 51 351 46 HOH HOH . C 3 HOH A 52 352 17 HOH HOH . C 3 HOH A 53 353 80 HOH HOH . C 3 HOH A 54 354 26 HOH HOH . C 3 HOH A 55 355 18 HOH HOH . C 3 HOH A 56 356 11 HOH HOH . C 3 HOH A 57 357 47 HOH HOH . C 3 HOH A 58 358 56 HOH HOH . C 3 HOH A 59 359 13 HOH HOH . C 3 HOH A 60 360 76 HOH HOH . C 3 HOH A 61 361 63 HOH HOH . C 3 HOH A 62 362 39 HOH HOH . C 3 HOH A 63 363 61 HOH HOH . C 3 HOH A 64 364 29 HOH HOH . C 3 HOH A 65 365 55 HOH HOH . C 3 HOH A 66 366 70 HOH HOH . C 3 HOH A 67 367 77 HOH HOH . C 3 HOH A 68 368 14 HOH HOH . C 3 HOH A 69 369 75 HOH HOH . C 3 HOH A 70 370 2 HOH HOH . C 3 HOH A 71 371 52 HOH HOH . C 3 HOH A 72 372 78 HOH HOH . C 3 HOH A 73 373 79 HOH HOH . C 3 HOH A 74 374 68 HOH HOH . C 3 HOH A 75 375 60 HOH HOH . C 3 HOH A 76 376 31 HOH HOH . C 3 HOH A 77 377 62 HOH HOH . C 3 HOH A 78 378 30 HOH HOH . C 3 HOH A 79 379 37 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 48.217 -8.765 59.139 1 17.31 ? CHA HEM 201 A 1 HETATM 2 C CHB HEM . . . B 2 49.984 -5.92 62.584 1 11.71 ? CHB HEM 201 A 1 HETATM 3 C CHC HEM . . . B 2 49.152 -2.007 59.919 1 9.23 ? CHC HEM 201 A 1 HETATM 4 C CHD HEM . . . B 2 47.292 -4.822 56.536 1 12.62 ? CHD HEM 201 A 1 HETATM 5 C C1A HEM . . . B 2 48.754 -8.322 60.306 1 15.24 ? C1A HEM 201 A 1 HETATM 6 C C2A HEM . . . B 2 49.117 -9.21 61.373 1 15.33 ? C2A HEM 201 A 1 HETATM 7 C C3A HEM . . . B 2 49.596 -8.43 62.344 1 14.16 ? C3A HEM 201 A 1 HETATM 8 C C4A HEM . . . B 2 49.564 -7.033 61.895 1 12.78 ? C4A HEM 201 A 1 HETATM 9 C CMA HEM . . . B 2 50.132 -8.943 63.691 1 16.02 ? CMA HEM 201 A 1 HETATM 10 C CAA HEM . . . B 2 48.892 -10.759 61.356 1 16.48 ? CAA HEM 201 A 1 HETATM 11 C CBA HEM . . . B 2 50.165 -11.57 61.274 1 21.11 ? CBA HEM 201 A 1 HETATM 12 C CGA HEM . . . B 2 51.07 -10.878 60.32 1 23.27 ? CGA HEM 201 A 1 HETATM 13 O O1A HEM . . . B 2 52.163 -10.39 60.742 1 29.94 ? O1A HEM 201 A 1 HETATM 14 O O2A HEM . . . B 2 50.669 -10.817 59.132 1 34 ? O2A HEM 201 A 1 HETATM 15 C C1B HEM . . . B 2 49.917 -4.626 62.153 1 11.07 ? C1B HEM 201 A 1 HETATM 16 C C2B HEM . . . B 2 50.381 -3.473 62.905 1 10.1 ? C2B HEM 201 A 1 HETATM 17 C C3B HEM . . . B 2 50.151 -2.393 62.157 1 11.29 ? C3B HEM 201 A 1 HETATM 18 C C4B HEM . . . B 2 49.531 -2.841 60.938 1 10.02 ? C4B HEM 201 A 1 HETATM 19 C CMB HEM . . . B 2 51.016 -3.589 64.309 1 10.32 ? CMB HEM 201 A 1 HETATM 20 C CAB HEM . . . B 2 50.399 -0.893 62.423 1 9.43 ? CAB HEM 201 A 1 HETATM 21 C CBB HEM . . . B 2 50.646 -0.388 63.633 1 8.37 ? CBB HEM 201 A 1 HETATM 22 C C1C HEM . . . B 2 48.516 -2.449 58.807 1 10.54 ? C1C HEM 201 A 1 HETATM 23 C C2C HEM . . . B 2 47.891 -1.602 57.816 1 9.79 ? C2C HEM 201 A 1 HETATM 24 C C3C HEM . . . B 2 47.374 -2.381 56.873 1 11.86 ? C3C HEM 201 A 1 HETATM 25 C C4C HEM . . . B 2 47.662 -3.734 57.272 1 11.72 ? C4C HEM 201 A 1 HETATM 26 C CMC HEM . . . B 2 47.904 -0.065 57.91 1 9.6 ? CMC HEM 201 A 1 HETATM 27 C CAC HEM . . . B 2 46.589 -2.058 55.569 1 10.99 ? CAC HEM 201 A 1 HETATM 28 C CBC HEM . . . B 2 46.014 -0.879 55.297 1 11.41 ? CBC HEM 201 A 1 HETATM 29 C C1D HEM . . . B 2 47.295 -6.11 56.956 1 15.22 ? C1D HEM 201 A 1 HETATM 30 C C2D HEM . . . B 2 46.554 -7.16 56.313 1 17.3 ? C2D HEM 201 A 1 HETATM 31 C C3D HEM . . . B 2 46.857 -8.4 57.127 1 21.31 ? C3D HEM 201 A 1 HETATM 32 C C4D HEM . . . B 2 47.726 -7.953 58.176 1 17.2 ? C4D HEM 201 A 1 HETATM 33 C CMD HEM . . . B 2 45.66 -7.082 55.052 1 17.32 ? CMD HEM 201 A 1 HETATM 34 C CAD HEM . . . B 2 46.284 -9.804 56.893 1 26.5 ? CAD HEM 201 A 1 HETATM 35 C CBD HEM . . . B 2 44.817 -9.587 57.265 1 32.07 ? CBD HEM 201 A 1 HETATM 36 C CGD HEM . . . B 2 44.077 -10.852 57.581 1 46.79 ? CGD HEM 201 A 1 HETATM 37 O O1D HEM . . . B 2 44.467 -11.947 57.092 1 73.78 ? O1D HEM 201 A 1 HETATM 38 O O2D HEM . . . B 2 43.07 -10.737 58.328 1 53.24 ? O2D HEM 201 A 1 HETATM 39 N NA HEM . . . B 2 49.042 -7.005 60.638 1 14.95 ? NA HEM 201 A 1 HETATM 40 N NB HEM . . . B 2 49.422 -4.207 60.945 1 10.49 ? NB HEM 201 A 1 HETATM 41 N NC HEM . . . B 2 48.367 -3.751 58.453 1 13.26 ? NC HEM 201 A 1 HETATM 42 N ND HEM . . . B 2 47.979 -6.597 58.056 1 15.33 ? ND HEM 201 A 1 HETATM 43 FE FE HEM . . . B 2 48.711 -5.423 59.512 1 10.79 ? FE HEM 201 A 1 # _model_server_stats.io_time_ms 45 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 43 #