data_3VHB # _model_server_result.job_id ilrohKBJeCrvdnvGc3JOkQ _model_server_result.datetime_utc '2025-07-04 17:30:46' _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 3vhb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":150}' # _entry.id 3VHB # _exptl.entry_id 3VHB _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 105.71 _cell.angle_gamma 90 _cell.entry_id 3VHB _cell.length_a 61.64 _cell.length_b 41.73 _cell.length_c 61.56 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VHB _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 ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N 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 85 A HIS 85 1_555 C FE HEM . A HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc2 C FE HEM . A HEM 150 1_555 D N1 IMD . A IMD 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? metalc ? metalc3 B NE2 HIS 85 B HIS 85 1_555 E FE HEM . B HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc4 E FE HEM . B HEM 150 1_555 F N3 IMD . B IMD 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? # _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 3VHB _atom_sites.fract_transf_matrix[1][1] 0.016223 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004563 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.023963 _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] 0.016875 _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 C 2 HEM A 1 150 150 HEM HEM . D 3 IMD A 1 160 160 IMD IMI . E 2 HEM B 1 150 150 HEM HEM . F 3 IMD B 1 170 170 IMD IMI . G 4 HOH A 1 201 201 HOH HOH . G 4 HOH A 2 205 205 HOH HOH . G 4 HOH A 3 206 206 HOH HOH . G 4 HOH A 4 207 207 HOH HOH . G 4 HOH A 5 208 208 HOH HOH . G 4 HOH A 6 211 211 HOH HOH . G 4 HOH A 7 212 212 HOH HOH . G 4 HOH A 8 214 214 HOH HOH . G 4 HOH A 9 215 215 HOH HOH . G 4 HOH A 10 216 216 HOH HOH . G 4 HOH A 11 217 217 HOH HOH . G 4 HOH A 12 219 219 HOH HOH . G 4 HOH A 13 220 220 HOH HOH . G 4 HOH A 14 223 223 HOH HOH . G 4 HOH A 15 224 224 HOH HOH . G 4 HOH A 16 230 230 HOH HOH . G 4 HOH A 17 231 231 HOH HOH . G 4 HOH A 18 232 232 HOH HOH . G 4 HOH A 19 233 233 HOH HOH . G 4 HOH A 20 234 234 HOH HOH . G 4 HOH A 21 235 235 HOH HOH . G 4 HOH A 22 236 236 HOH HOH . G 4 HOH A 23 237 237 HOH HOH . G 4 HOH A 24 239 239 HOH HOH . G 4 HOH A 25 240 240 HOH HOH . G 4 HOH A 26 241 241 HOH HOH . G 4 HOH A 27 242 242 HOH HOH . G 4 HOH A 28 244 244 HOH HOH . G 4 HOH A 29 249 249 HOH HOH . G 4 HOH A 30 251 251 HOH HOH . G 4 HOH A 31 256 256 HOH HOH . G 4 HOH A 32 258 258 HOH HOH . G 4 HOH A 33 259 259 HOH HOH . G 4 HOH A 34 260 260 HOH HOH . G 4 HOH A 35 261 261 HOH HOH . G 4 HOH A 36 262 262 HOH HOH . G 4 HOH A 37 263 263 HOH HOH . G 4 HOH A 38 266 266 HOH HOH . G 4 HOH A 39 271 271 HOH HOH . G 4 HOH A 40 272 272 HOH HOH . G 4 HOH A 41 274 274 HOH HOH . G 4 HOH A 42 276 276 HOH HOH . G 4 HOH A 43 277 277 HOH HOH . G 4 HOH A 44 279 279 HOH HOH . G 4 HOH A 45 280 280 HOH HOH . G 4 HOH A 46 284 284 HOH HOH . G 4 HOH A 47 289 289 HOH HOH . H 4 HOH B 1 200 200 HOH HOH . H 4 HOH B 2 202 202 HOH HOH . H 4 HOH B 3 203 203 HOH HOH . H 4 HOH B 4 204 204 HOH HOH . H 4 HOH B 5 209 209 HOH HOH . H 4 HOH B 6 210 210 HOH HOH . H 4 HOH B 7 213 213 HOH HOH . H 4 HOH B 8 218 218 HOH HOH . H 4 HOH B 9 221 221 HOH HOH . H 4 HOH B 10 222 222 HOH HOH . H 4 HOH B 11 225 225 HOH HOH . H 4 HOH B 12 226 226 HOH HOH . H 4 HOH B 13 227 227 HOH HOH . H 4 HOH B 14 228 228 HOH HOH . H 4 HOH B 15 229 229 HOH HOH . H 4 HOH B 16 238 238 HOH HOH . H 4 HOH B 17 243 243 HOH HOH . H 4 HOH B 18 245 245 HOH HOH . H 4 HOH B 19 246 246 HOH HOH . H 4 HOH B 20 247 247 HOH HOH . H 4 HOH B 21 248 248 HOH HOH . H 4 HOH B 22 250 250 HOH HOH . H 4 HOH B 23 252 252 HOH HOH . H 4 HOH B 24 253 253 HOH HOH . H 4 HOH B 25 254 254 HOH HOH . H 4 HOH B 26 255 255 HOH HOH . H 4 HOH B 27 257 257 HOH HOH . H 4 HOH B 28 264 264 HOH HOH . H 4 HOH B 29 265 265 HOH HOH . H 4 HOH B 30 267 267 HOH HOH . H 4 HOH B 31 270 270 HOH HOH . H 4 HOH B 32 273 273 HOH HOH . H 4 HOH B 33 275 275 HOH HOH . H 4 HOH B 34 278 278 HOH HOH . H 4 HOH B 35 281 281 HOH HOH . H 4 HOH B 36 282 282 HOH HOH . H 4 HOH B 37 283 283 HOH HOH . H 4 HOH B 38 285 285 HOH HOH . H 4 HOH B 39 287 287 HOH HOH . H 4 HOH B 40 288 288 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 . . . E 2 24.036 11.351 29.679 1 38.26 ? CHA HEM 150 B 1 HETATM 2 C CHB HEM . . . E 2 21.798 9.779 33.645 1 16.7 ? CHB HEM 150 B 1 HETATM 3 C CHC HEM . . . E 2 20.514 14.29 34.899 1 25.11 ? CHC HEM 150 B 1 HETATM 4 C CHD HEM . . . E 2 21.782 15.546 30.397 1 11.59 ? CHD HEM 150 B 1 HETATM 5 C C1A HEM . . . E 2 23.577 10.54 30.695 1 22.36 ? C1A HEM 150 B 1 HETATM 6 C C2A HEM . . . E 2 23.803 9.105 30.816 1 25.1 ? C2A HEM 150 B 1 HETATM 7 C C3A HEM . . . E 2 23.092 8.63 31.826 1 15.34 ? C3A HEM 150 B 1 HETATM 8 C C4A HEM . . . E 2 22.442 9.779 32.428 1 12.04 ? C4A HEM 150 B 1 HETATM 9 C CMA HEM . . . E 2 23.131 7.206 32.444 1 25.21 ? CMA HEM 150 B 1 HETATM 10 C CAA HEM . . . E 2 24.692 8.362 29.806 1 17.81 ? CAA HEM 150 B 1 HETATM 11 C CBA HEM . . . E 2 26.16 8.083 30.173 1 26.88 ? CBA HEM 150 B 1 HETATM 12 C CGA HEM . . . E 2 26.891 7.095 29.311 1 29.61 ? CGA HEM 150 B 1 HETATM 13 O O1A HEM . . . E 2 26.627 5.872 29.498 1 39.34 ? O1A HEM 150 B 1 HETATM 14 O O2A HEM . . . E 2 27.741 7.583 28.519 1 47.31 ? O2A HEM 150 B 1 HETATM 15 C C1B HEM . . . E 2 21.442 10.875 34.381 1 19.27 ? C1B HEM 150 B 1 HETATM 16 C C2B HEM . . . E 2 20.846 10.773 35.679 1 30.47 ? C2B HEM 150 B 1 HETATM 17 C C3B HEM . . . E 2 20.494 12.029 35.998 1 25.12 ? C3B HEM 150 B 1 HETATM 18 C C4B HEM . . . E 2 20.803 12.934 34.905 1 31 ? C4B HEM 150 B 1 HETATM 19 C CMB HEM . . . E 2 20.717 9.436 36.449 1 15.68 ? CMB HEM 150 B 1 HETATM 20 C CAB HEM . . . E 2 19.83 12.493 37.307 1 20.94 ? CAB HEM 150 B 1 HETATM 21 C CBB HEM . . . E 2 20.274 11.855 38.396 1 26.65 ? CBB HEM 150 B 1 HETATM 22 C C1C HEM . . . E 2 20.653 14.968 33.7 1 16.52 ? C1C HEM 150 B 1 HETATM 23 C C2C HEM . . . E 2 20.196 16.334 33.501 1 20.37 ? C2C HEM 150 B 1 HETATM 24 C C3C HEM . . . E 2 20.562 16.711 32.273 1 12.54 ? C3C HEM 150 B 1 HETATM 25 C C4C HEM . . . E 2 21.252 15.589 31.664 1 8.68 ? C4C HEM 150 B 1 HETATM 26 C CMC HEM . . . E 2 19.491 17.11 34.633 1 21.05 ? CMC HEM 150 B 1 HETATM 27 C CAC HEM . . . E 2 20.29 18.072 31.587 1 24.42 ? CAC HEM 150 B 1 HETATM 28 C CBC HEM . . . E 2 20.04 18.146 30.285 1 22.85 ? CBC HEM 150 B 1 HETATM 29 C C1D HEM . . . E 2 22.473 14.535 29.776 1 19.96 ? C1D HEM 150 B 1 HETATM 30 C C2D HEM . . . E 2 23.182 14.615 28.514 1 20.91 ? C2D HEM 150 B 1 HETATM 31 C C3D HEM . . . E 2 23.825 13.451 28.359 1 19.68 ? C3D HEM 150 B 1 HETATM 32 C C4D HEM . . . E 2 23.563 12.623 29.503 1 35.74 ? C4D HEM 150 B 1 HETATM 33 C CMD HEM . . . E 2 23.231 15.885 27.623 1 33.2 ? CMD HEM 150 B 1 HETATM 34 C CAD HEM . . . E 2 24.897 13.023 27.333 1 19.64 ? CAD HEM 150 B 1 HETATM 35 C CBD HEM . . . E 2 24.565 12.318 26.016 1 58.52 ? CBD HEM 150 B 1 HETATM 36 C CGD HEM . . . E 2 25.847 11.737 25.476 1 100 ? CGD HEM 150 B 1 HETATM 37 O O1D HEM . . . E 2 25.856 10.482 25.349 1 100 ? O1D HEM 150 B 1 HETATM 38 O O2D HEM . . . E 2 26.841 12.511 25.355 1 100 ? O2D HEM 150 B 1 HETATM 39 N NA HEM . . . E 2 22.739 10.924 31.71 1 29.99 ? NA HEM 150 B 1 HETATM 40 N NB HEM . . . E 2 21.361 12.186 33.871 1 20.16 ? NB HEM 150 B 1 HETATM 41 N NC HEM . . . E 2 21.33 14.536 32.563 1 19.63 ? NC HEM 150 B 1 HETATM 42 N ND HEM . . . E 2 22.737 13.305 30.372 1 31.11 ? ND HEM 150 B 1 HETATM 43 FE FE HEM . . . E 2 22.142 12.746 32.128 1 24.65 ? FE HEM 150 B 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #