data_1BGY # _model_server_result.job_id RTTRKjHxMG7HUSZTBTflUw _model_server_result.datetime_utc '2024-11-05 21:28:55' _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 1bgy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"X","auth_seq_id":381}' # _entry.id 1BGY # _exptl.entry_id 1BGY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 12 _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 90 _cell.angle_gamma 120 _cell.entry_id 1BGY _cell.length_a 130.11 _cell.length_b 130.11 _cell.length_c 720.94 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1BGY _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details 22-meric _pdbx_struct_assembly.oligomeric_count 22 _pdbx_struct_assembly.details author_and_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,U,V,W,X,Y,Z,AA,BA,CA _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 ? 12 W N N ? 12 X N N ? 12 Z N N ? 12 AA 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 H SG CYS 24 H CYS 24 1_555 H SG CYS 68 H CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf2 H SG CYS 40 H CYS 40 1_555 H SG CYS 54 H CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf3 P SG CYS 144 Q CYS 144 1_555 P SG CYS 160 Q CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf4 S SG CYS 24 T CYS 24 1_555 S SG CYS 68 T CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf5 S SG CYS 40 T CYS 40 1_555 S SG CYS 54 T CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? covale ? covale1 D SG CYS 37 D CYS 37 1_555 Y CAB HEC . D HEC 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.843 ? covale ? covale2 D SG CYS 40 D CYS 40 1_555 Y CAC HEC . D HEC 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.838 ? covale ? covale3 O SG CYS 37 P CYS 37 1_555 BA CAB HEC . P HEC 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.867 ? covale ? covale4 O SG CYS 40 P CYS 40 1_555 BA CAC HEC . P HEC 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.856 ? metalc ? metalc1 C NE2 HIS 83 C HIS 83 1_555 W FE HEM . C HEM 380 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc2 C NE2 HIS 97 C HIS 97 1_555 X FE HEM . C HEM 381 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc3 C NE2 HIS 182 C HIS 182 1_555 W FE HEM . C HEM 380 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc4 C NE2 HIS 196 C HIS 196 1_555 X FE HEM . C HEM 381 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc5 D NE2 HIS 41 D HIS 41 1_555 Y FE HEC . D HEC 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.919 ? metalc ? metalc6 D SD MET 160 D MET 160 1_555 Y FE HEC . D HEC 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc7 N NE2 HIS 83 O HIS 83 1_555 Z FE HEM . O HEM 380 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc8 N NE2 HIS 97 O HIS 97 1_555 AA FE HEM . O HEM 381 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc9 N NE2 HIS 182 O HIS 182 1_555 Z FE HEM . O HEM 380 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc10 N NE2 HIS 196 O HIS 196 1_555 AA FE HEM . O HEM 381 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc11 O NE2 HIS 41 P HIS 41 1_555 BA FE HEC . P HEC 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? metalc ? metalc12 O SD MET 160 P MET 160 1_555 BA FE HEC . P HEC 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc13 P SG CYS 139 Q CYS 139 1_555 CA FE1 FES . Q FES 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc14 P ND1 HIS 141 Q HIS 141 1_555 CA FE2 FES . Q FES 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc15 P SG CYS 158 Q CYS 158 1_555 CA FE1 FES . Q FES 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc16 P ND1 HIS 161 Q HIS 161 1_555 CA FE2 FES . Q FES 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? # _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 1BGY _atom_sites.fract_transf_matrix[1][1] 0.007686 _atom_sites.fract_transf_matrix[1][2] 0.004437 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008875 _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] 0.001387 _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 W 12 HEM C 1 380 1 HEM HEM . X 12 HEM C 1 381 2 HEM HEM . Y 13 HEC D 1 242 3 HEC HEC . Z 12 HEM O 1 380 1 HEM HEM . AA 12 HEM O 1 381 2 HEM HEM . BA 13 HEC P 1 242 3 HEC HEC . CA 14 FES Q 1 197 4 FES FES . # 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 . . . X 12 10.456 98.264 21.688 1 7.22 ? CHA HEM 381 C 1 HETATM 2 C CHB HEM . . . X 12 15.031 99.386 22.534 1 2.16 ? CHB HEM 381 C 1 HETATM 3 C CHC HEM . . . X 12 15.131 96.419 26.233 1 5.68 ? CHC HEM 381 C 1 HETATM 4 C CHD HEM . . . X 12 10.957 94.61 24.839 1 5.79 ? CHD HEM 381 C 1 HETATM 5 C C1A HEM . . . X 12 11.672 98.917 21.636 1 6.65 ? C1A HEM 381 C 1 HETATM 6 C C2A HEM . . . X 12 11.975 100.126 20.897 1 6.33 ? C2A HEM 381 C 1 HETATM 7 C C3A HEM . . . X 12 13.248 100.452 21.12 1 5.74 ? C3A HEM 381 C 1 HETATM 8 C C4A HEM . . . X 12 13.832 99.436 21.983 1 2.16 ? C4A HEM 381 C 1 HETATM 9 C CMA HEM . . . X 12 14.109 101.609 20.601 1 4.26 ? CMA HEM 381 C 1 HETATM 10 C CAA HEM . . . X 12 10.869 100.837 20.09 1 5.21 ? CAA HEM 381 C 1 HETATM 11 C CBA HEM . . . X 12 10.026 101.85 20.878 1 9.28 ? CBA HEM 381 C 1 HETATM 12 C CGA HEM . . . X 12 9.183 101.492 22.05 1 7.04 ? CGA HEM 381 C 1 HETATM 13 O O1A HEM . . . X 12 9.445 101.964 23.19 1 12.08 ? O1A HEM 381 C 1 HETATM 14 O O2A HEM . . . X 12 8.201 100.731 21.987 1 2.22 ? O2A HEM 381 C 1 HETATM 15 C C1B HEM . . . X 12 15.542 98.693 23.569 1 4.75 ? C1B HEM 381 C 1 HETATM 16 C C2B HEM . . . X 12 16.866 98.742 24.129 1 2.16 ? C2B HEM 381 C 1 HETATM 17 C C3B HEM . . . X 12 16.885 97.919 25.188 1 5.88 ? C3B HEM 381 C 1 HETATM 18 C C4B HEM . . . X 12 15.581 97.3 25.274 1 5.51 ? C4B HEM 381 C 1 HETATM 19 C CMB HEM . . . X 12 17.983 99.676 23.622 1 2.16 ? CMB HEM 381 C 1 HETATM 20 C CAB HEM . . . X 12 17.987 97.57 26.186 1 6.07 ? CAB HEM 381 C 1 HETATM 21 C CBB HEM . . . X 12 19.181 97.11 25.842 1 8.66 ? CBB HEM 381 C 1 HETATM 22 C C1C HEM . . . X 12 13.975 95.666 26.249 1 6.15 ? C1C HEM 381 C 1 HETATM 23 C C2C HEM . . . X 12 13.636 94.591 27.222 1 2.16 ? C2C HEM 381 C 1 HETATM 24 C C3C HEM . . . X 12 12.507 94.036 26.71 1 2.16 ? C3C HEM 381 C 1 HETATM 25 C C4C HEM . . . X 12 12.087 94.852 25.58 1 6.01 ? C4C HEM 381 C 1 HETATM 26 C CMC HEM . . . X 12 14.515 94.213 28.398 1 7.42 ? CMC HEM 381 C 1 HETATM 27 C CAC HEM . . . X 12 11.604 92.987 27.311 1 4.81 ? CAC HEM 381 C 1 HETATM 28 C CBC HEM . . . X 12 12.044 91.941 27.982 1 2.8 ? CBC HEM 381 C 1 HETATM 29 C C1D HEM . . . X 12 10.449 95.453 23.891 1 5.93 ? C1D HEM 381 C 1 HETATM 30 C C2D HEM . . . X 12 9.172 95.281 23.263 1 2.16 ? C2D HEM 381 C 1 HETATM 31 C C3D HEM . . . X 12 8.988 96.305 22.39 1 6.28 ? C3D HEM 381 C 1 HETATM 32 C C4D HEM . . . X 12 10.188 97.12 22.417 1 6.05 ? C4D HEM 381 C 1 HETATM 33 C CMD HEM . . . X 12 8.148 94.167 23.542 1 6.78 ? CMD HEM 381 C 1 HETATM 34 C CAD HEM . . . X 12 7.774 96.606 21.467 1 2.16 ? CAD HEM 381 C 1 HETATM 35 C CBD HEM . . . X 12 6.528 97.27 22.047 1 2.16 ? CBD HEM 381 C 1 HETATM 36 C CGD HEM . . . X 12 5.482 97.78 21.172 1 4.71 ? CGD HEM 381 C 1 HETATM 37 O O1D HEM . . . X 12 5.677 98.855 20.596 1 2.16 ? O1D HEM 381 C 1 HETATM 38 O O2D HEM . . . X 12 4.441 97.088 21.05 1 2.52 ? O2D HEM 381 C 1 HETATM 39 N NA HEM . . . X 12 12.822 98.533 22.306 1 4.53 ? NA HEM 381 C 1 HETATM 40 N NB HEM . . . X 12 14.763 97.784 24.272 1 6.68 ? NB HEM 381 C 1 HETATM 41 N NC HEM . . . X 12 12.941 95.884 25.306 1 2.16 ? NC HEM 381 C 1 HETATM 42 N ND HEM . . . X 12 11.032 96.586 23.361 1 2.16 ? ND HEM 381 C 1 HETATM 43 FE FE HEM . . . X 12 12.874 97.258 23.824 1 2.58 ? FE HEM 381 C 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 37 _model_server_stats.query_time_ms 339 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #