data_2YIU # _model_server_result.job_id Imod39QURKyNpb1hbW2sAg _model_server_result.datetime_utc '2024-11-13 20:40:13' _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 2yiu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":500}' # _entry.id 2YIU # _exptl.entry_id 2YIU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 103.18 _cell.angle_gamma 90 _cell.entry_id 2YIU _cell.length_a 85.3 _cell.length_b 164.91 _cell.length_c 100.61 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YIU _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 hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T _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 ? 4 G N N ? 4 H N N ? 4 L N N ? 4 M 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 disulf ? disulf1 C SG CYS 137 C CYS 137 1_555 C SG CYS 154 C CYS 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf2 F SG CYS 137 F CYS 137 1_555 F SG CYS 154 F CYS 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 B SG CYS 58 B CYS 82 1_555 J CAB HEC . B HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.63 ? covale ? covale2 B SG CYS 61 B CYS 85 1_555 J CAC HEC . B HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.673 ? covale ? covale3 E SG CYS 58 E CYS 82 1_555 O CAB HEC . E HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.627 ? covale ? covale4 E SG CYS 61 E CYS 85 1_555 O CAC HEC . E HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.664 ? metalc ? metalc1 A NE2 HIS 97 A HIS 97 1_555 G FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.899 ? metalc ? metalc2 A NE2 HIS 111 A HIS 111 1_555 H FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc3 A NE2 HIS 198 A HIS 198 1_555 G FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.829 ? metalc ? metalc4 A NE2 HIS 212 A HIS 212 1_555 H FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc5 B NE2 HIS 62 B HIS 86 1_555 J FE HEC . B HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc6 B SD MET 186 B MET 210 1_555 J FE HEC . B HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc7 C SG CYS 132 C CYS 132 1_555 K FE2 FES . C FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc8 C ND1 HIS 134 C HIS 134 1_555 K FE1 FES . C FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? metalc ? metalc9 C SG CYS 152 C CYS 152 1_555 K FE2 FES . C FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc10 C ND1 HIS 155 C HIS 155 1_555 K FE1 FES . C FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc11 D NE2 HIS 97 D HIS 97 1_555 L FE HEM . D HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? metalc ? metalc12 D NE2 HIS 111 D HIS 111 1_555 M FE HEM . D HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc13 D NE2 HIS 198 D HIS 198 1_555 L FE HEM . D HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.909 ? metalc ? metalc14 D NE2 HIS 212 D HIS 212 1_555 M FE HEM . D HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc15 E NE2 HIS 62 E HIS 86 1_555 O FE HEC . E HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc16 E SD MET 186 E MET 210 1_555 O FE HEC . E HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc17 F SG CYS 132 F CYS 132 1_555 P FE2 FES . F FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc18 F ND1 HIS 134 F HIS 134 1_555 P FE1 FES . F FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc19 F SG CYS 152 F CYS 152 1_555 P FE2 FES . F FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc20 F ND1 HIS 155 F HIS 155 1_555 P FE1 FES . F FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? # _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 217 n n CHA C4D HEM doub 218 n n CHA HHA HEM sing 219 n n CHB C4A HEM sing 220 n n CHB C1B HEM doub 221 n n CHB HHB HEM sing 222 n n CHC C4B HEM sing 223 n n CHC C1C HEM doub 224 n n CHC HHC HEM sing 225 n n CHD C4C HEM doub 226 n n CHD C1D HEM sing 227 n n CHD HHD HEM sing 228 n n C1A C2A HEM doub 229 n y C1A NA HEM sing 230 n y C2A C3A HEM sing 231 n y C2A CAA HEM sing 232 n n C3A C4A HEM doub 233 n y C3A CMA HEM sing 234 n n C4A NA HEM sing 235 n y CMA HMA HEM sing 236 n n CMA HMAA HEM sing 237 n n CMA HMAB HEM sing 238 n n CAA CBA HEM sing 239 n n CAA HAA HEM sing 240 n n CAA HAAA HEM sing 241 n n CBA CGA HEM sing 242 n n CBA HBA HEM sing 243 n n CBA HBAA HEM sing 244 n n CGA O1A HEM doub 245 n n CGA O2A HEM sing 246 n n C1B C2B HEM sing 247 n n C1B NB HEM sing 248 n n C2B C3B HEM doub 249 n n C2B CMB HEM sing 250 n n C3B C4B HEM sing 251 n n C3B CAB HEM sing 252 n n C4B NB HEM doub 253 n n CMB HMB HEM sing 254 n n CMB HMBA HEM sing 255 n n CMB HMBB HEM sing 256 n n CAB CBB HEM doub 257 n n CAB HAB HEM sing 258 n n CBB HBB HEM sing 259 n n CBB HBBA HEM sing 260 n n C1C C2C HEM sing 261 n y C1C NC HEM sing 262 n y C2C C3C HEM doub 263 n y C2C CMC HEM sing 264 n n C3C C4C HEM sing 265 n y C3C CAC HEM sing 266 n n C4C NC HEM sing 267 n y CMC HMC HEM sing 268 n n CMC HMCA HEM sing 269 n n CMC HMCB HEM sing 270 n n CAC CBC HEM doub 271 n n CAC HAC HEM sing 272 n n CBC HBC HEM sing 273 n n CBC HBCA HEM sing 274 n n C1D C2D HEM sing 275 n n C1D ND HEM doub 276 n n C2D C3D HEM doub 277 n n C2D CMD HEM sing 278 n n C3D C4D HEM sing 279 n n C3D CAD HEM sing 280 n n C4D ND HEM sing 281 n n CMD HMD HEM sing 282 n n CMD HMDA HEM sing 283 n n CMD HMDB HEM sing 284 n n CAD CBD HEM sing 285 n n CAD HAD HEM sing 286 n n CAD HADA HEM sing 287 n n CBD CGD HEM sing 288 n n CBD HBD HEM sing 289 n n CBD HBDA HEM sing 290 n n CGD O1D HEM doub 291 n n CGD O2D HEM sing 292 n n O2A H2A HEM sing 293 n n O2D H2D HEM sing 294 n n FE NA HEM sing 295 n n FE NB HEM sing 296 n n FE NC HEM sing 297 n n FE ND HEM sing 298 n n # _atom_sites.entry_id 2YIU _atom_sites.fract_transf_matrix[1][1] 0.011723 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002745 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006064 _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] 0.010208 _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 G 4 HEM A 1 500 500 HEM HEM . H 4 HEM A 1 501 501 HEM HEM . I 5 SMA A 1 502 502 SMA SMA . J 6 HEC B 1 500 500 HEC HEC . K 7 FES C 1 500 500 FES FES . L 4 HEM D 1 500 500 HEM HEM . M 4 HEM D 1 501 501 HEM HEM . N 5 SMA D 1 502 502 SMA SMA . O 6 HEC E 1 500 500 HEC HEC . P 7 FES F 1 500 500 FES FES . Q 8 HOH A 1 2001 2001 HOH HOH . Q 8 HOH A 2 2002 2002 HOH HOH . Q 8 HOH A 3 2003 2003 HOH HOH . R 8 HOH B 1 2001 2001 HOH HOH . S 8 HOH D 1 2001 2001 HOH HOH . T 8 HOH F 1 2001 2001 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 . . . L 4 -11.902 -37.921 -9.274 1 15.39 ? CHA HEM 500 D 1 HETATM 2 C CHB HEM . . . L 4 -12.146 -42.201 -6.969 1 16.2 ? CHB HEM 500 D 1 HETATM 3 C CHC HEM . . . L 4 -10.607 -44.361 -11.029 1 16.59 ? CHC HEM 500 D 1 HETATM 4 C CHD HEM . . . L 4 -9.692 -40.097 -13.101 1 15.38 ? CHD HEM 500 D 1 HETATM 5 C C1A HEM . . . L 4 -12.172 -38.903 -8.335 1 17.14 ? C1A HEM 500 D 1 HETATM 6 C C2A HEM . . . L 4 -12.877 -38.688 -7.1 1 17.39 ? C2A HEM 500 D 1 HETATM 7 C C3A HEM . . . L 4 -12.961 -39.849 -6.433 1 16.17 ? C3A HEM 500 D 1 HETATM 8 C C4A HEM . . . L 4 -12.291 -40.852 -7.25 1 14.89 ? C4A HEM 500 D 1 HETATM 9 C CMA HEM . . . L 4 -13.647 -40.065 -5.052 1 14.31 ? CMA HEM 500 D 1 HETATM 10 C CAA HEM . . . L 4 -13.45 -37.325 -6.693 1 18.83 ? CAA HEM 500 D 1 HETATM 11 C CBA HEM . . . L 4 -14.899 -37.334 -7.187 1 20.23 ? CBA HEM 500 D 1 HETATM 12 C CGA HEM . . . L 4 -15.386 -35.907 -7.199 1 23.43 ? CGA HEM 500 D 1 HETATM 13 O O1A HEM . . . L 4 -15.308 -35.207 -8.251 1 23.95 ? O1A HEM 500 D 1 HETATM 14 O O2A HEM . . . L 4 -15.836 -35.443 -6.12 1 25.34 ? O2A HEM 500 D 1 HETATM 15 C C1B HEM . . . L 4 -11.785 -43.182 -7.874 1 14.07 ? C1B HEM 500 D 1 HETATM 16 C C2B HEM . . . L 4 -11.767 -44.61 -7.649 1 14.51 ? C2B HEM 500 D 1 HETATM 17 C C3B HEM . . . L 4 -11.349 -45.141 -8.79 1 14.25 ? C3B HEM 500 D 1 HETATM 18 C C4B HEM . . . L 4 -11.084 -44.125 -9.759 1 14.98 ? C4B HEM 500 D 1 HETATM 19 C CMB HEM . . . L 4 -12.147 -45.399 -6.347 1 13.06 ? CMB HEM 500 D 1 HETATM 20 C CAB HEM . . . L 4 -11.163 -46.62 -9.081 1 15.03 ? CAB HEM 500 D 1 HETATM 21 C CBB HEM . . . L 4 -10.729 -47.355 -8.067 1 18.55 ? CBB HEM 500 D 1 HETATM 22 C C1C HEM . . . L 4 -10.095 -43.427 -11.897 1 17.83 ? C1C HEM 500 D 1 HETATM 23 C C2C HEM . . . L 4 -9.275 -43.667 -13.08 1 19.24 ? C2C HEM 500 D 1 HETATM 24 C C3C HEM . . . L 4 -9.047 -42.475 -13.643 1 18.44 ? C3C HEM 500 D 1 HETATM 25 C C4C HEM . . . L 4 -9.696 -41.444 -12.863 1 16.6 ? C4C HEM 500 D 1 HETATM 26 C CMC HEM . . . L 4 -8.721 -45.014 -13.651 1 17.02 ? CMC HEM 500 D 1 HETATM 27 C CAC HEM . . . L 4 -8.187 -42.304 -14.911 1 21.3 ? CAC HEM 500 D 1 HETATM 28 C CBC HEM . . . L 4 -8.55 -41.431 -15.85 1 25.49 ? CBC HEM 500 D 1 HETATM 29 C C1D HEM . . . L 4 -10.222 -39.137 -12.281 1 14.86 ? C1D HEM 500 D 1 HETATM 30 C C2D HEM . . . L 4 -10.198 -37.709 -12.551 1 16.46 ? C2D HEM 500 D 1 HETATM 31 C C3D HEM . . . L 4 -10.864 -37.046 -11.343 1 15.48 ? C3D HEM 500 D 1 HETATM 32 C C4D HEM . . . L 4 -11.247 -38.116 -10.472 1 14.87 ? C4D HEM 500 D 1 HETATM 33 C CMD HEM . . . L 4 -9.595 -36.983 -13.768 1 16.28 ? CMD HEM 500 D 1 HETATM 34 C CAD HEM . . . L 4 -11.128 -35.562 -11.124 1 15.62 ? CAD HEM 500 D 1 HETATM 35 C CBD HEM . . . L 4 -12.476 -35.268 -11.788 1 15.3 ? CBD HEM 500 D 1 HETATM 36 C CGD HEM . . . L 4 -13.599 -35.401 -10.787 1 17.22 ? CGD HEM 500 D 1 HETATM 37 O O1D HEM . . . L 4 -13.478 -34.926 -9.624 1 18.81 ? O1D HEM 500 D 1 HETATM 38 O O2D HEM . . . L 4 -14.639 -36.005 -11.136 1 19.63 ? O2D HEM 500 D 1 HETATM 39 N NA HEM . . . L 4 -11.814 -40.246 -8.392 1 15.11 ? NA HEM 500 D 1 HETATM 40 N NB HEM . . . L 4 -11.371 -42.928 -9.171 1 15.02 ? NB HEM 500 D 1 HETATM 41 N NC HEM . . . L 4 -10.338 -42.062 -11.809 1 17.59 ? NC HEM 500 D 1 HETATM 42 N ND HEM . . . L 4 -10.859 -39.336 -11.058 1 14.88 ? ND HEM 500 D 1 HETATM 43 FE FE HEM . . . L 4 -11.121 -41.124 -10.131 1 12.09 ? FE HEM 500 D 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #