data_4Y4S # _model_server_result.job_id XFa2q3sCMKWMVrYCjTj1tw _model_server_result.datetime_utc '2025-03-04 07:30:24' _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 4y4s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 4Y4S # _exptl.entry_id 4Y4S _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 90 _cell.entry_id 4Y4S _cell.length_a 52.76 _cell.length_b 52.76 _cell.length_c 140.57 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Y4S _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 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 96 A HIS 84 1_555 B FE HEM . A HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc2 A NE2 HIS 152 A HIS 140 1_555 B FE HEM . A HEM 301 7_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? # _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 116 n n CHA C4D HEM doub 117 n n CHA HHA HEM sing 118 n n CHB C4A HEM sing 119 n n CHB C1B HEM doub 120 n n CHB HHB HEM sing 121 n n CHC C4B HEM sing 122 n n CHC C1C HEM doub 123 n n CHC HHC HEM sing 124 n n CHD C4C HEM doub 125 n n CHD C1D HEM sing 126 n n CHD HHD HEM sing 127 n n C1A C2A HEM doub 128 n y C1A NA HEM sing 129 n y C2A C3A HEM sing 130 n y C2A CAA HEM sing 131 n n C3A C4A HEM doub 132 n y C3A CMA HEM sing 133 n n C4A NA HEM sing 134 n y CMA HMA HEM sing 135 n n CMA HMAA HEM sing 136 n n CMA HMAB HEM sing 137 n n CAA CBA HEM sing 138 n n CAA HAA HEM sing 139 n n CAA HAAA HEM sing 140 n n CBA CGA HEM sing 141 n n CBA HBA HEM sing 142 n n CBA HBAA HEM sing 143 n n CGA O1A HEM doub 144 n n CGA O2A HEM sing 145 n n C1B C2B HEM sing 146 n n C1B NB HEM sing 147 n n C2B C3B HEM doub 148 n n C2B CMB HEM sing 149 n n C3B C4B HEM sing 150 n n C3B CAB HEM sing 151 n n C4B NB HEM doub 152 n n CMB HMB HEM sing 153 n n CMB HMBA HEM sing 154 n n CMB HMBB HEM sing 155 n n CAB CBB HEM doub 156 n n CAB HAB HEM sing 157 n n CBB HBB HEM sing 158 n n CBB HBBA HEM sing 159 n n C1C C2C HEM sing 160 n y C1C NC HEM sing 161 n y C2C C3C HEM doub 162 n y C2C CMC HEM sing 163 n n C3C C4C HEM sing 164 n y C3C CAC HEM sing 165 n n C4C NC HEM sing 166 n y CMC HMC HEM sing 167 n n CMC HMCA HEM sing 168 n n CMC HMCB HEM sing 169 n n CAC CBC HEM doub 170 n n CAC HAC HEM sing 171 n n CBC HBC HEM sing 172 n n CBC HBCA HEM sing 173 n n C1D C2D HEM sing 174 n n C1D ND HEM doub 175 n n C2D C3D HEM doub 176 n n C2D CMD HEM sing 177 n n C3D C4D HEM sing 178 n n C3D CAD HEM sing 179 n n C4D ND HEM sing 180 n n CMD HMD HEM sing 181 n n CMD HMDA HEM sing 182 n n CMD HMDB HEM sing 183 n n CAD CBD HEM sing 184 n n CAD HAD HEM sing 185 n n CAD HADA HEM sing 186 n n CBD CGD HEM sing 187 n n CBD HBD HEM sing 188 n n CBD HBDA HEM sing 189 n n CGD O1D HEM doub 190 n n CGD O2D HEM sing 191 n n O2A H2A HEM sing 192 n n O2D H2D HEM sing 193 n n FE NA HEM sing 194 n n FE NB HEM sing 195 n n FE NC HEM sing 196 n n FE ND HEM sing 197 n n # _atom_sites.entry_id 4Y4S _atom_sites.fract_transf_matrix[1][1] 0.018954 _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] 0.018954 _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] 0.007114 _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 1 301 200 HEM HEM . C 3 SO4 A 1 302 201 SO4 SO4 . D 4 HOH A 1 401 44 HOH HOH . D 4 HOH A 2 402 50 HOH HOH . D 4 HOH A 3 403 28 HOH HOH . D 4 HOH A 4 404 48 HOH HOH . D 4 HOH A 5 405 22 HOH HOH . D 4 HOH A 6 406 37 HOH HOH . D 4 HOH A 7 407 1 HOH HOH . D 4 HOH A 8 408 33 HOH HOH . D 4 HOH A 9 409 52 HOH HOH . D 4 HOH A 10 410 30 HOH HOH . D 4 HOH A 11 411 35 HOH HOH . D 4 HOH A 12 412 13 HOH HOH . D 4 HOH A 13 413 58 HOH HOH . D 4 HOH A 14 414 40 HOH HOH . D 4 HOH A 15 415 57 HOH HOH . D 4 HOH A 16 416 39 HOH HOH . D 4 HOH A 17 417 64 HOH HOH . D 4 HOH A 18 418 51 HOH HOH . D 4 HOH A 19 419 7 HOH HOH . D 4 HOH A 20 420 31 HOH HOH . D 4 HOH A 21 421 11 HOH HOH . D 4 HOH A 22 422 3 HOH HOH . D 4 HOH A 23 423 36 HOH HOH . D 4 HOH A 24 424 16 HOH HOH . D 4 HOH A 25 425 9 HOH HOH . D 4 HOH A 26 426 46 HOH HOH . D 4 HOH A 27 427 14 HOH HOH . D 4 HOH A 28 428 5 HOH HOH . D 4 HOH A 29 429 38 HOH HOH . D 4 HOH A 30 430 24 HOH HOH . D 4 HOH A 31 431 19 HOH HOH . D 4 HOH A 32 432 15 HOH HOH . D 4 HOH A 33 433 65 HOH HOH . D 4 HOH A 34 434 29 HOH HOH . D 4 HOH A 35 435 56 HOH HOH . D 4 HOH A 36 436 41 HOH HOH . D 4 HOH A 37 437 20 HOH HOH . D 4 HOH A 38 438 12 HOH HOH . D 4 HOH A 39 439 21 HOH HOH . D 4 HOH A 40 440 47 HOH HOH . D 4 HOH A 41 441 59 HOH HOH . D 4 HOH A 42 442 17 HOH HOH . D 4 HOH A 43 443 66 HOH HOH . D 4 HOH A 44 444 45 HOH HOH . D 4 HOH A 45 445 23 HOH HOH . D 4 HOH A 46 446 43 HOH HOH . D 4 HOH A 47 447 49 HOH HOH . D 4 HOH A 48 448 4 HOH HOH . D 4 HOH A 49 449 26 HOH HOH . D 4 HOH A 50 450 34 HOH HOH . D 4 HOH A 51 451 27 HOH HOH . D 4 HOH A 52 452 6 HOH HOH . D 4 HOH A 53 453 2 HOH HOH . D 4 HOH A 54 454 25 HOH HOH . D 4 HOH A 55 455 10 HOH HOH . D 4 HOH A 56 456 55 HOH HOH . D 4 HOH A 57 457 8 HOH HOH . D 4 HOH A 58 458 18 HOH HOH . D 4 HOH A 59 459 32 HOH HOH . D 4 HOH A 60 460 42 HOH HOH . D 4 HOH A 61 461 53 HOH HOH . D 4 HOH A 62 462 54 HOH HOH . D 4 HOH A 63 463 60 HOH HOH . D 4 HOH A 64 464 61 HOH HOH . D 4 HOH A 65 465 62 HOH HOH . D 4 HOH A 66 466 63 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 . . . B 2 -31.821 -26.925 0.957 1 24.44 ? CHA HEM 301 A 1 HETATM 2 C CHB HEM . . . B 2 -29.18 -24.124 3.974 1 23.58 ? CHB HEM 301 A 1 HETATM 3 C CHC HEM . . . B 2 -31.714 -20.237 2.546 1 22.47 ? CHC HEM 301 A 1 HETATM 4 C CHD HEM . . . B 2 -34.481 -23.06 -0.287 1 33.34 ? CHD HEM 301 A 1 HETATM 5 C C1A HEM . . . B 2 -30.941 -26.442 1.901 1 32.58 ? C1A HEM 301 A 1 HETATM 6 C C2A HEM . . . B 2 -30.057 -27.297 2.631 1 40.52 ? C2A HEM 301 A 1 HETATM 7 C C3A HEM . . . B 2 -29.309 -26.579 3.47 1 31.46 ? C3A HEM 301 A 1 HETATM 8 C C4A HEM . . . B 2 -29.709 -25.196 3.287 1 33.74 ? C4A HEM 301 A 1 HETATM 9 C CMA HEM . . . B 2 -28.225 -27.076 4.464 1 32.15 ? CMA HEM 301 A 1 HETATM 10 C CAA HEM . . . B 2 -30.087 -28.809 2.397 1 52.56 ? CAA HEM 301 A 1 HETATM 11 C CBA HEM . . . B 2 -28.711 -29.38 2.125 1 54.14 ? CBA HEM 301 A 1 HETATM 12 C CGA HEM . . . B 2 -27.68 -28.626 1.327 1 51.33 ? CGA HEM 301 A 1 HETATM 13 O O1A HEM . . . B 2 -26.964 -29.349 0.603 1 57.74 ? O1A HEM 301 A 1 HETATM 14 O O2A HEM . . . B 2 -27.521 -27.372 1.345 1 60.79 ? O2A HEM 301 A 1 HETATM 15 C C1B HEM . . . B 2 -29.623 -22.835 3.861 1 25.01 ? C1B HEM 301 A 1 HETATM 16 C C2B HEM . . . B 2 -29.118 -21.688 4.58 1 22.55 ? C2B HEM 301 A 1 HETATM 17 C C3B HEM . . . B 2 -29.778 -20.601 4.18 1 20.43 ? C3B HEM 301 A 1 HETATM 18 C C4B HEM . . . B 2 -30.777 -21.019 3.188 1 23.52 ? C4B HEM 301 A 1 HETATM 19 C CMB HEM . . . B 2 -27.984 -21.672 5.616 1 27.36 ? CMB HEM 301 A 1 HETATM 20 C CAB HEM . . . B 2 -29.431 -19.225 4.796 1 28.1 ? CAB HEM 301 A 1 HETATM 21 C CBB HEM . . . B 2 -29.7 -18.072 4.203 1 33.66 ? CBB HEM 301 A 1 HETATM 22 C C1C HEM . . . B 2 -32.726 -20.661 1.7 1 27.26 ? C1C HEM 301 A 1 HETATM 23 C C2C HEM . . . B 2 -33.802 -19.849 1.151 1 32.7 ? C2C HEM 301 A 1 HETATM 24 C C3C HEM . . . B 2 -34.56 -20.653 0.371 1 29.08 ? C3C HEM 301 A 1 HETATM 25 C C4C HEM . . . B 2 -33.993 -21.976 0.414 1 29.18 ? C4C HEM 301 A 1 HETATM 26 C CMC HEM . . . B 2 -33.999 -18.334 1.459 1 33.73 ? CMC HEM 301 A 1 HETATM 27 C CAC HEM . . . B 2 -35.83 -20.36 -0.46 1 36.48 ? CAC HEM 301 A 1 HETATM 28 C CBC HEM . . . B 2 -36.454 -19.179 -0.538 1 46.68 ? CBC HEM 301 A 1 HETATM 29 C C1D HEM . . . B 2 -33.983 -24.348 -0.294 1 31.79 ? C1D HEM 301 A 1 HETATM 30 C C2D HEM . . . B 2 -34.43 -25.411 -1.173 1 34.5 ? C2D HEM 301 A 1 HETATM 31 C C3D HEM . . . B 2 -33.594 -26.636 -0.808 1 31.17 ? C3D HEM 301 A 1 HETATM 32 C C4D HEM . . . B 2 -32.744 -26.184 0.274 1 31.94 ? C4D HEM 301 A 1 HETATM 33 C CMD HEM . . . B 2 -35.512 -25.321 -2.271 1 41.95 ? CMD HEM 301 A 1 HETATM 34 C CAD HEM . . . B 2 -33.691 -28.041 -1.45 1 33.76 ? CAD HEM 301 A 1 HETATM 35 C CBD HEM . . . B 2 -32.51 -28.3 -2.395 1 32.83 ? CBD HEM 301 A 1 HETATM 36 C CGD HEM . . . B 2 -32.162 -27.143 -3.318 1 32.94 ? CGD HEM 301 A 1 HETATM 37 O O1D HEM . . . B 2 -32.99 -26.86 -4.23 1 40.22 ? O1D HEM 301 A 1 HETATM 38 O O2D HEM . . . B 2 -31.054 -26.526 -3.188 1 28.96 ? O2D HEM 301 A 1 HETATM 39 N NA HEM . . . B 2 -30.707 -25.149 2.323 1 23.2 ? NA HEM 301 A 1 HETATM 40 N NB HEM . . . B 2 -30.637 -22.392 3.035 1 19.16 ? NB HEM 301 A 1 HETATM 41 N NC HEM . . . B 2 -32.88 -21.955 1.234 1 24.33 ? NC HEM 301 A 1 HETATM 42 N ND HEM . . . B 2 -32.987 -24.848 0.529 1 25.5 ? ND HEM 301 A 1 HETATM 43 FE FE HEM . . . B 2 -31.768 -23.602 1.785 1 24.44 ? FE HEM 301 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #