data_1VGI # _model_server_result.job_id 4ofj9S7cosxVGLsDcgs9WQ _model_server_result.datetime_utc '2025-02-17 06:54:17' _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 1vgi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":300}' # _entry.id 1VGI # _exptl.entry_id 1VGI _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 1VGI _cell.length_a 65.1 _cell.length_b 65.1 _cell.length_c 120.5 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VGI _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 25 A HIS 25 1_555 B FE HEM . A HEM 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc2 B FE HEM . A HEM 300 1_555 E O HOH . A HOH 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? # _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 120 n n CHA C4D HEM doub 121 n n CHA HHA HEM sing 122 n n CHB C4A HEM sing 123 n n CHB C1B HEM doub 124 n n CHB HHB HEM sing 125 n n CHC C4B HEM sing 126 n n CHC C1C HEM doub 127 n n CHC HHC HEM sing 128 n n CHD C4C HEM doub 129 n n CHD C1D HEM sing 130 n n CHD HHD HEM sing 131 n n C1A C2A HEM doub 132 n y C1A NA HEM sing 133 n y C2A C3A HEM sing 134 n y C2A CAA HEM sing 135 n n C3A C4A HEM doub 136 n y C3A CMA HEM sing 137 n n C4A NA HEM sing 138 n y CMA HMA HEM sing 139 n n CMA HMAA HEM sing 140 n n CMA HMAB HEM sing 141 n n CAA CBA HEM sing 142 n n CAA HAA HEM sing 143 n n CAA HAAA HEM sing 144 n n CBA CGA HEM sing 145 n n CBA HBA HEM sing 146 n n CBA HBAA HEM sing 147 n n CGA O1A HEM doub 148 n n CGA O2A HEM sing 149 n n C1B C2B HEM sing 150 n n C1B NB HEM sing 151 n n C2B C3B HEM doub 152 n n C2B CMB HEM sing 153 n n C3B C4B HEM sing 154 n n C3B CAB HEM sing 155 n n C4B NB HEM doub 156 n n CMB HMB HEM sing 157 n n CMB HMBA HEM sing 158 n n CMB HMBB HEM sing 159 n n CAB CBB HEM doub 160 n n CAB HAB HEM sing 161 n n CBB HBB HEM sing 162 n n CBB HBBA HEM sing 163 n n C1C C2C HEM sing 164 n y C1C NC HEM sing 165 n y C2C C3C HEM doub 166 n y C2C CMC HEM sing 167 n n C3C C4C HEM sing 168 n y C3C CAC HEM sing 169 n n C4C NC HEM sing 170 n y CMC HMC HEM sing 171 n n CMC HMCA HEM sing 172 n n CMC HMCB HEM sing 173 n n CAC CBC HEM doub 174 n n CAC HAC HEM sing 175 n n CBC HBC HEM sing 176 n n CBC HBCA HEM sing 177 n n C1D C2D HEM sing 178 n n C1D ND HEM doub 179 n n C2D C3D HEM doub 180 n n C2D CMD HEM sing 181 n n C3D C4D HEM sing 182 n n C3D CAD HEM sing 183 n n C4D ND HEM sing 184 n n CMD HMD HEM sing 185 n n CMD HMDA HEM sing 186 n n CMD HMDB HEM sing 187 n n CAD CBD HEM sing 188 n n CAD HAD HEM sing 189 n n CAD HADA HEM sing 190 n n CBD CGD HEM sing 191 n n CBD HBD HEM sing 192 n n CBD HBDA HEM sing 193 n n CGD O1D HEM doub 194 n n CGD O2D HEM sing 195 n n O2A H2A HEM sing 196 n n O2D H2D HEM sing 197 n n FE NA HEM sing 198 n n FE NB HEM sing 199 n n FE NC HEM sing 200 n n FE ND HEM sing 201 n n # _atom_sites.entry_id 1VGI _atom_sites.fract_transf_matrix[1][1] 0.015361 _atom_sites.fract_transf_matrix[1][2] 0.008869 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017737 _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] 0.008299 _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 1 300 300 HEM HEM . C 3 XE A 1 301 2 XE XE . D 4 FMT A 1 302 1 FMT FMT . E 5 HOH A 1 303 1 HOH WAT . E 5 HOH A 2 304 2 HOH WAT . E 5 HOH A 3 305 3 HOH WAT . E 5 HOH A 4 306 4 HOH WAT . E 5 HOH A 5 307 5 HOH WAT . E 5 HOH A 6 308 6 HOH WAT . E 5 HOH A 7 309 7 HOH WAT . E 5 HOH A 8 310 8 HOH WAT . E 5 HOH A 9 311 9 HOH WAT . E 5 HOH A 10 312 10 HOH WAT . E 5 HOH A 11 313 12 HOH WAT . E 5 HOH A 12 314 13 HOH WAT . E 5 HOH A 13 315 14 HOH WAT . E 5 HOH A 14 316 15 HOH WAT . E 5 HOH A 15 317 16 HOH WAT . E 5 HOH A 16 318 17 HOH WAT . E 5 HOH A 17 319 18 HOH WAT . E 5 HOH A 18 320 19 HOH WAT . E 5 HOH A 19 321 20 HOH WAT . E 5 HOH A 20 322 21 HOH WAT . E 5 HOH A 21 323 22 HOH WAT . E 5 HOH A 22 324 23 HOH WAT . E 5 HOH A 23 325 24 HOH WAT . E 5 HOH A 24 326 25 HOH WAT . E 5 HOH A 25 327 26 HOH WAT . E 5 HOH A 26 328 27 HOH WAT . E 5 HOH A 27 329 28 HOH WAT . E 5 HOH A 28 330 29 HOH WAT . E 5 HOH A 29 331 30 HOH WAT . E 5 HOH A 30 332 31 HOH WAT . E 5 HOH A 31 333 32 HOH WAT . E 5 HOH A 32 334 33 HOH WAT . E 5 HOH A 33 335 34 HOH WAT . E 5 HOH A 34 336 35 HOH WAT . E 5 HOH A 35 337 36 HOH WAT . E 5 HOH A 36 338 37 HOH WAT . E 5 HOH A 37 339 38 HOH WAT . E 5 HOH A 38 340 39 HOH WAT . E 5 HOH A 39 341 40 HOH WAT . E 5 HOH A 40 342 41 HOH WAT . E 5 HOH A 41 343 42 HOH WAT . E 5 HOH A 42 344 43 HOH WAT . E 5 HOH A 43 345 44 HOH WAT . E 5 HOH A 44 346 45 HOH WAT . E 5 HOH A 45 347 46 HOH WAT . E 5 HOH A 46 348 47 HOH WAT . E 5 HOH A 47 349 48 HOH WAT . E 5 HOH A 48 350 49 HOH WAT . E 5 HOH A 49 351 50 HOH WAT . E 5 HOH A 50 352 51 HOH WAT . E 5 HOH A 51 353 52 HOH WAT . E 5 HOH A 52 354 53 HOH WAT . E 5 HOH A 53 355 54 HOH WAT . E 5 HOH A 54 356 55 HOH WAT . E 5 HOH A 55 357 56 HOH WAT . E 5 HOH A 56 358 57 HOH WAT . E 5 HOH A 57 359 58 HOH WAT . E 5 HOH A 58 360 59 HOH WAT . E 5 HOH A 59 361 60 HOH WAT . E 5 HOH A 60 362 61 HOH WAT . E 5 HOH A 61 363 62 HOH WAT . E 5 HOH A 62 364 63 HOH WAT . E 5 HOH A 63 365 64 HOH WAT . E 5 HOH A 64 366 65 HOH WAT . E 5 HOH A 65 367 66 HOH WAT . E 5 HOH A 66 368 67 HOH WAT . E 5 HOH A 67 369 68 HOH WAT . # 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 -88.811 -8.91 -87.38 1 30.15 ? CHA HEM 300 A 1 HETATM 2 C CHB HEM . . . B 2 -89.053 -11.902 -91.151 1 34.1 ? CHB HEM 300 A 1 HETATM 3 C CHC HEM . . . B 2 -91.896 -14.875 -88.606 1 28.61 ? CHC HEM 300 A 1 HETATM 4 C CHD HEM . . . B 2 -92.138 -11.604 -85.099 1 25.92 ? CHD HEM 300 A 1 HETATM 5 C C1A HEM . . . B 2 -88.608 -9.456 -88.647 1 31.96 ? C1A HEM 300 A 1 HETATM 6 C C2A HEM . . . B 2 -87.777 -8.879 -89.689 1 36.22 ? C2A HEM 300 A 1 HETATM 7 C C3A HEM . . . B 2 -87.973 -9.645 -90.801 1 35.78 ? C3A HEM 300 A 1 HETATM 8 C C4A HEM . . . B 2 -88.771 -10.795 -90.368 1 32.83 ? C4A HEM 300 A 1 HETATM 9 C CMA HEM . . . B 2 -87.498 -9.413 -92.207 1 36.8 ? CMA HEM 300 A 1 HETATM 10 C CAA HEM . . . B 2 -86.869 -7.649 -89.539 1 40.08 ? CAA HEM 300 A 1 HETATM 11 C CBA HEM . . . B 2 -87.603 -6.274 -89.699 1 45.96 ? CBA HEM 300 A 1 HETATM 12 C CGA HEM . . . B 2 -87.004 -5.111 -89.108 1 51.03 ? CGA HEM 300 A 1 HETATM 13 O O1A HEM . . . B 2 -85.847 -5.263 -88.528 1 51.49 ? O1A HEM 300 A 1 HETATM 14 O O2A HEM . . . B 2 -87.548 -3.981 -89.129 1 50.74 ? O2A HEM 300 A 1 HETATM 15 C C1B HEM . . . B 2 -89.908 -12.95 -90.802 1 33.48 ? C1B HEM 300 A 1 HETATM 16 C C2B HEM . . . B 2 -90.281 -14.03 -91.705 1 35.86 ? C2B HEM 300 A 1 HETATM 17 C C3B HEM . . . B 2 -90.942 -14.947 -90.945 1 35.21 ? C3B HEM 300 A 1 HETATM 18 C C4B HEM . . . B 2 -91.152 -14.319 -89.641 1 32.02 ? C4B HEM 300 A 1 HETATM 19 C CMB HEM . . . B 2 -89.95 -14.059 -93.183 1 36.79 ? CMB HEM 300 A 1 HETATM 20 C CAB HEM . . . B 2 -91.354 -16.355 -91.298 1 38.12 ? CAB HEM 300 A 1 HETATM 21 C CBB HEM . . . B 2 -92.679 -16.438 -92.077 1 43.24 ? CBB HEM 300 A 1 HETATM 22 C C1C HEM . . . B 2 -92.179 -14.273 -87.412 1 29.05 ? C1C HEM 300 A 1 HETATM 23 C C2C HEM . . . B 2 -93.014 -14.848 -86.37 1 29.28 ? C2C HEM 300 A 1 HETATM 24 C C3C HEM . . . B 2 -93.12 -13.894 -85.422 1 29.73 ? C3C HEM 300 A 1 HETATM 25 C C4C HEM . . . B 2 -92.307 -12.773 -85.83 1 26.3 ? C4C HEM 300 A 1 HETATM 26 C CMC HEM . . . B 2 -93.603 -16.251 -86.409 1 27.94 ? CMC HEM 300 A 1 HETATM 27 C CAC HEM . . . B 2 -93.925 -13.965 -84.118 1 30.02 ? CAC HEM 300 A 1 HETATM 28 C CBC HEM . . . B 2 -95.456 -13.785 -84.369 1 36.5 ? CBC HEM 300 A 1 HETATM 29 C C1D HEM . . . B 2 -91.222 -10.583 -85.385 1 26.63 ? C1D HEM 300 A 1 HETATM 30 C C2D HEM . . . B 2 -90.957 -9.444 -84.501 1 27.22 ? C2D HEM 300 A 1 HETATM 31 C C3D HEM . . . B 2 -90.06 -8.682 -85.159 1 29.26 ? C3D HEM 300 A 1 HETATM 32 C C4D HEM . . . B 2 -89.739 -9.371 -86.428 1 29.21 ? C4D HEM 300 A 1 HETATM 33 C CMD HEM . . . B 2 -91.607 -9.248 -83.157 1 25.82 ? CMD HEM 300 A 1 HETATM 34 C CAD HEM . . . B 2 -89.449 -7.358 -84.775 1 31.4 ? CAD HEM 300 A 1 HETATM 35 C CBD HEM . . . B 2 -88.079 -7.517 -83.988 1 33.77 ? CBD HEM 300 A 1 HETATM 36 C CGD HEM . . . B 2 -87.577 -6.272 -83.543 1 35.31 ? CGD HEM 300 A 1 HETATM 37 O O1D HEM . . . B 2 -87.478 -6.048 -82.297 1 36.14 ? O1D HEM 300 A 1 HETATM 38 O O2D HEM . . . B 2 -87.227 -5.375 -84.361 1 37.02 ? O2D HEM 300 A 1 HETATM 39 N NA HEM . . . B 2 -89.201 -10.631 -89.072 1 31.83 ? NA HEM 300 A 1 HETATM 40 N NB HEM . . . B 2 -90.503 -13.098 -89.567 1 32.05 ? NB HEM 300 A 1 HETATM 41 N NC HEM . . . B 2 -91.702 -13.003 -87.036 1 27.83 ? NC HEM 300 A 1 HETATM 42 N ND HEM . . . B 2 -90.461 -10.517 -86.542 1 28.42 ? ND HEM 300 A 1 HETATM 43 FE FE HEM . . . B 2 -90.446 -11.829 -88.042 1 28.13 ? FE HEM 300 A 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #