data_3S3D # _model_server_result.job_id ARJqoNVjea7mDHo1nss9-A _model_server_result.datetime_utc '2024-11-04 23:06:40' _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 3s3d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":800}' # _entry.id 3S3D # _exptl.entry_id 3S3D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 5 _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 90 _cell.entry_id 3S3D _cell.length_a 110.03 _cell.length_b 110.03 _cell.length_c 170.23 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3S3D _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 5 _struct_asym.id E _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 78 A HIS 72 1_555 E FE HEM . A HEM 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.921 ? metalc ? metalc2 A ND1 HIS 239 A HIS 233 1_555 D CU CU . A CU 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.91 ? metalc ? metalc3 A NE2 HIS 288 A HIS 282 1_555 D CU CU . A CU 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? metalc ? metalc4 A NE2 HIS 289 A HIS 283 1_555 D CU CU . A CU 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? metalc ? metalc5 A NE2 HIS 390 A HIS 384 1_555 F FE HAS . A HAS 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc6 A NE2 HIS 392 A HIS 386 1_555 E FE HEM . A HEM 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc7 B ND1 HIS 112 B HIS 114 1_555 J CU2 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.843 ? metalc ? metalc8 B SG CYS 147 B CYS 149 1_555 J CU1 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc9 B SG CYS 147 B CYS 149 1_555 J CU2 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc10 B O GLN 149 B GLN 151 1_555 J CU1 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.618 ? metalc ? metalc11 B SG CYS 151 B CYS 153 1_555 J CU1 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? metalc ? metalc12 B SG CYS 151 B CYS 153 1_555 J CU2 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc13 B ND1 HIS 155 B HIS 157 1_555 J CU1 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc14 B SD MET 158 B MET 160 1_555 J CU2 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? # _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 266 n n CHA C4D HEM doub 267 n n CHA HHA HEM sing 268 n n CHB C4A HEM sing 269 n n CHB C1B HEM doub 270 n n CHB HHB HEM sing 271 n n CHC C4B HEM sing 272 n n CHC C1C HEM doub 273 n n CHC HHC HEM sing 274 n n CHD C4C HEM doub 275 n n CHD C1D HEM sing 276 n n CHD HHD HEM sing 277 n n C1A C2A HEM doub 278 n y C1A NA HEM sing 279 n y C2A C3A HEM sing 280 n y C2A CAA HEM sing 281 n n C3A C4A HEM doub 282 n y C3A CMA HEM sing 283 n n C4A NA HEM sing 284 n y CMA HMA HEM sing 285 n n CMA HMAA HEM sing 286 n n CMA HMAB HEM sing 287 n n CAA CBA HEM sing 288 n n CAA HAA HEM sing 289 n n CAA HAAA HEM sing 290 n n CBA CGA HEM sing 291 n n CBA HBA HEM sing 292 n n CBA HBAA HEM sing 293 n n CGA O1A HEM doub 294 n n CGA O2A HEM sing 295 n n C1B C2B HEM sing 296 n n C1B NB HEM sing 297 n n C2B C3B HEM doub 298 n n C2B CMB HEM sing 299 n n C3B C4B HEM sing 300 n n C3B CAB HEM sing 301 n n C4B NB HEM doub 302 n n CMB HMB HEM sing 303 n n CMB HMBA HEM sing 304 n n CMB HMBB HEM sing 305 n n CAB CBB HEM doub 306 n n CAB HAB HEM sing 307 n n CBB HBB HEM sing 308 n n CBB HBBA HEM sing 309 n n C1C C2C HEM sing 310 n y C1C NC HEM sing 311 n y C2C C3C HEM doub 312 n y C2C CMC HEM sing 313 n n C3C C4C HEM sing 314 n y C3C CAC HEM sing 315 n n C4C NC HEM sing 316 n y CMC HMC HEM sing 317 n n CMC HMCA HEM sing 318 n n CMC HMCB HEM sing 319 n n CAC CBC HEM doub 320 n n CAC HAC HEM sing 321 n n CBC HBC HEM sing 322 n n CBC HBCA HEM sing 323 n n C1D C2D HEM sing 324 n n C1D ND HEM doub 325 n n C2D C3D HEM doub 326 n n C2D CMD HEM sing 327 n n C3D C4D HEM sing 328 n n C3D CAD HEM sing 329 n n C4D ND HEM sing 330 n n CMD HMD HEM sing 331 n n CMD HMDA HEM sing 332 n n CMD HMDB HEM sing 333 n n CAD CBD HEM sing 334 n n CAD HAD HEM sing 335 n n CAD HADA HEM sing 336 n n CBD CGD HEM sing 337 n n CBD HBD HEM sing 338 n n CBD HBDA HEM sing 339 n n CGD O1D HEM doub 340 n n CGD O2D HEM sing 341 n n O2A H2A HEM sing 342 n n O2D H2D HEM sing 343 n n FE NA HEM sing 344 n n FE NB HEM sing 345 n n FE NC HEM sing 346 n n FE ND HEM sing 347 n n # _atom_sites.entry_id 3S3D _atom_sites.fract_transf_matrix[1][1] 0.009088 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009088 _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] 0.005874 _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 D 4 CU A 1 803 803 CU CU . E 5 HEM A 1 800 800 HEM HEM . F 6 HAS A 1 801 801 HAS HAS . G 7 XE A 1 563 563 XE XE . H 7 XE A 1 564 564 XE XE . I 7 XE A 1 565 565 XE XE . J 8 CUA B 1 802 802 CUA CUA . # 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 5 -34.072 19.461 -6.09 1 61.11 ? CHA HEM 800 A 1 HETATM 2 C CHB HEM . . . E 5 -38.239 18.387 -3.972 1 61.11 ? CHB HEM 800 A 1 HETATM 3 C CHC HEM . . . E 5 -40.339 22.052 -6.332 1 61.11 ? CHC HEM 800 A 1 HETATM 4 C CHD HEM . . . E 5 -36.003 23.674 -7.552 1 61.11 ? CHD HEM 800 A 1 HETATM 5 C C1A HEM . . . E 5 -34.992 18.844 -5.281 1 61.11 ? C1A HEM 800 A 1 HETATM 6 C C2A HEM . . . E 5 -34.749 17.745 -4.357 1 61.11 ? C2A HEM 800 A 1 HETATM 7 C C3A HEM . . . E 5 -35.913 17.464 -3.783 1 61.11 ? C3A HEM 800 A 1 HETATM 8 C C4A HEM . . . E 5 -36.913 18.361 -4.317 1 61.11 ? C4A HEM 800 A 1 HETATM 9 C CMA HEM . . . E 5 -36.154 16.366 -2.725 1 61.11 ? CMA HEM 800 A 1 HETATM 10 C CAA HEM . . . E 5 -33.401 17.022 -4.079 1 61.11 ? CAA HEM 800 A 1 HETATM 11 C CBA HEM . . . E 5 -33.087 16.083 -5.253 1 61.11 ? CBA HEM 800 A 1 HETATM 12 C CGA HEM . . . E 5 -31.612 15.769 -5.415 1 61.11 ? CGA HEM 800 A 1 HETATM 13 O O1A HEM . . . E 5 -31.336 14.812 -6.181 1 61.11 ? O1A HEM 800 A 1 HETATM 14 O O2A HEM . . . E 5 -30.724 16.441 -4.816 1 61.11 ? O2A HEM 800 A 1 HETATM 15 C C1B HEM . . . E 5 -39.182 19.226 -4.507 1 61.11 ? C1B HEM 800 A 1 HETATM 16 C C2B HEM . . . E 5 -40.612 19.057 -4.393 1 61.11 ? C2B HEM 800 A 1 HETATM 17 C C3B HEM . . . E 5 -41.189 20.063 -5.043 1 61.11 ? C3B HEM 800 A 1 HETATM 18 C C4B HEM . . . E 5 -40.147 20.908 -5.596 1 61.11 ? C4B HEM 800 A 1 HETATM 19 C CMB HEM . . . E 5 -41.341 17.913 -3.664 1 61.11 ? CMB HEM 800 A 1 HETATM 20 C CAB HEM . . . E 5 -42.712 20.274 -5.196 1 61.11 ? CAB HEM 800 A 1 HETATM 21 C CBB HEM . . . E 5 -43.326 19.653 -6.231 1 61.11 ? CBB HEM 800 A 1 HETATM 22 C C1C HEM . . . E 5 -39.344 22.88 -6.77 1 61.11 ? C1C HEM 800 A 1 HETATM 23 C C2C HEM . . . E 5 -39.506 24.242 -7.232 1 61.11 ? C2C HEM 800 A 1 HETATM 24 C C3C HEM . . . E 5 -38.299 24.682 -7.566 1 61.11 ? C3C HEM 800 A 1 HETATM 25 C C4C HEM . . . E 5 -37.352 23.614 -7.322 1 61.11 ? C4C HEM 800 A 1 HETATM 26 C CMC HEM . . . E 5 -40.834 25.029 -7.32 1 61.11 ? CMC HEM 800 A 1 HETATM 27 C CAC HEM . . . E 5 -37.92 26.072 -8.119 1 61.11 ? CAC HEM 800 A 1 HETATM 28 C CBC HEM . . . E 5 -38.836 27.045 -8.302 1 61.11 ? CBC HEM 800 A 1 HETATM 29 C C1D HEM . . . E 5 -35.079 22.684 -7.313 1 61.11 ? C1D HEM 800 A 1 HETATM 30 C C2D HEM . . . E 5 -33.661 22.777 -7.613 1 61.11 ? C2D HEM 800 A 1 HETATM 31 C C3D HEM . . . E 5 -33.08 21.454 -7.143 1 61.11 ? C3D HEM 800 A 1 HETATM 32 C C4D HEM . . . E 5 -34.189 20.714 -6.619 1 61.11 ? C4D HEM 800 A 1 HETATM 33 C CMD HEM . . . E 5 -32.894 23.959 -8.258 1 61.11 ? CMD HEM 800 A 1 HETATM 34 C CAD HEM . . . E 5 -31.626 20.978 -7.194 1 61.11 ? CAD HEM 800 A 1 HETATM 35 C CBD HEM . . . E 5 -31.408 20.304 -8.525 1 61.11 ? CBD HEM 800 A 1 HETATM 36 C CGD HEM . . . E 5 -29.946 20.023 -8.6 1 61.11 ? CGD HEM 800 A 1 HETATM 37 O O1D HEM . . . E 5 -29.422 20.055 -9.744 1 61.11 ? O1D HEM 800 A 1 HETATM 38 O O2D HEM . . . E 5 -29.334 19.772 -7.525 1 61.11 ? O2D HEM 800 A 1 HETATM 39 N NA HEM . . . E 5 -36.318 19.198 -5.234 1 61.11 ? NA HEM 800 A 1 HETATM 40 N NB HEM . . . E 5 -38.927 20.363 -5.254 1 61.11 ? NB HEM 800 A 1 HETATM 41 N NC HEM . . . E 5 -38.016 22.525 -6.831 1 61.11 ? NC HEM 800 A 1 HETATM 42 N ND HEM . . . E 5 -35.353 21.453 -6.738 1 61.11 ? ND HEM 800 A 1 HETATM 43 FE FE HEM . . . E 5 -37.146 20.939 -5.982 1 61.11 ? FE HEM 800 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 20 _model_server_stats.element_count 43 #