data_4YNR # _model_server_result.job_id yktDaCQEuNbHrsCvEw_qqw _model_server_result.datetime_utc '2024-10-19 01:31:14' _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 4ynr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 4YNR # _exptl.entry_id 4YNR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 2 _entity.src_method nat _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 90 _cell.angle_gamma 90 _cell.entry_id 4YNR _cell.length_a 33.505 _cell.length_b 79.247 _cell.length_c 109.451 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YNR _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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,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 93 A HIS 149 1_555 C FE HEM . A HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc2 C FE HEM . A HEM 301 1_555 D C CMO . A CMO 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.881 sing metalc ? metalc3 B NE2 HIS 93 B HIS 149 1_555 E FE HEM . B HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc4 E FE HEM . B HEM 301 1_555 F C CMO . B CMO 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.825 sing # _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 117 n n CHA C4D HEM doub 118 n n CHA HHA HEM sing 119 n n CHB C4A HEM sing 120 n n CHB C1B HEM doub 121 n n CHB HHB HEM sing 122 n n CHC C4B HEM sing 123 n n CHC C1C HEM doub 124 n n CHC HHC HEM sing 125 n n CHD C4C HEM doub 126 n n CHD C1D HEM sing 127 n n CHD HHD HEM sing 128 n n C1A C2A HEM doub 129 n y C1A NA HEM sing 130 n y C2A C3A HEM sing 131 n y C2A CAA HEM sing 132 n n C3A C4A HEM doub 133 n y C3A CMA HEM sing 134 n n C4A NA HEM sing 135 n y CMA HMA HEM sing 136 n n CMA HMAA HEM sing 137 n n CMA HMAB HEM sing 138 n n CAA CBA HEM sing 139 n n CAA HAA HEM sing 140 n n CAA HAAA HEM sing 141 n n CBA CGA HEM sing 142 n n CBA HBA HEM sing 143 n n CBA HBAA HEM sing 144 n n CGA O1A HEM doub 145 n n CGA O2A HEM sing 146 n n C1B C2B HEM sing 147 n n C1B NB HEM sing 148 n n C2B C3B HEM doub 149 n n C2B CMB HEM sing 150 n n C3B C4B HEM sing 151 n n C3B CAB HEM sing 152 n n C4B NB HEM doub 153 n n CMB HMB HEM sing 154 n n CMB HMBA HEM sing 155 n n CMB HMBB HEM sing 156 n n CAB CBB HEM doub 157 n n CAB HAB HEM sing 158 n n CBB HBB HEM sing 159 n n CBB HBBA HEM sing 160 n n C1C C2C HEM sing 161 n y C1C NC HEM sing 162 n y C2C C3C HEM doub 163 n y C2C CMC HEM sing 164 n n C3C C4C HEM sing 165 n y C3C CAC HEM sing 166 n n C4C NC HEM sing 167 n y CMC HMC HEM sing 168 n n CMC HMCA HEM sing 169 n n CMC HMCB HEM sing 170 n n CAC CBC HEM doub 171 n n CAC HAC HEM sing 172 n n CBC HBC HEM sing 173 n n CBC HBCA HEM sing 174 n n C1D C2D HEM sing 175 n n C1D ND HEM doub 176 n n C2D C3D HEM doub 177 n n C2D CMD HEM sing 178 n n C3D C4D HEM sing 179 n n C3D CAD HEM sing 180 n n C4D ND HEM sing 181 n n CMD HMD HEM sing 182 n n CMD HMDA HEM sing 183 n n CMD HMDB HEM sing 184 n n CAD CBD HEM sing 185 n n CAD HAD HEM sing 186 n n CAD HADA HEM sing 187 n n CBD CGD HEM sing 188 n n CBD HBD HEM sing 189 n n CBD HBDA HEM sing 190 n n CGD O1D HEM doub 191 n n CGD O2D HEM sing 192 n n O2A H2A HEM sing 193 n n O2D H2D HEM sing 194 n n FE NA HEM sing 195 n n FE NB HEM sing 196 n n FE NC HEM sing 197 n n FE ND HEM sing 198 n n # _atom_sites.entry_id 4YNR _atom_sites.fract_transf_matrix[1][1] 0.029846 _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] 0.012619 _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] 0.009137 _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 1 301 301 HEM HEM . D 3 CMO A 1 302 302 CMO CMO . E 2 HEM B 1 301 301 HEM HEM . F 3 CMO B 1 302 302 CMO CMO . G 4 HOH A 1 401 401 HOH HOH . G 4 HOH A 2 402 402 HOH HOH . G 4 HOH A 3 403 403 HOH HOH . G 4 HOH A 4 404 404 HOH HOH . G 4 HOH A 5 405 405 HOH HOH . G 4 HOH A 6 406 406 HOH HOH . G 4 HOH A 7 407 407 HOH HOH . G 4 HOH A 8 408 408 HOH HOH . G 4 HOH A 9 409 409 HOH HOH . G 4 HOH A 10 410 410 HOH HOH . G 4 HOH A 11 411 411 HOH HOH . G 4 HOH A 12 412 412 HOH HOH . G 4 HOH A 13 413 413 HOH HOH . G 4 HOH A 14 414 414 HOH HOH . G 4 HOH A 15 415 415 HOH HOH . G 4 HOH A 16 416 416 HOH HOH . G 4 HOH A 17 417 417 HOH HOH . G 4 HOH A 18 418 418 HOH HOH . G 4 HOH A 19 419 419 HOH HOH . G 4 HOH A 20 420 420 HOH HOH . G 4 HOH A 21 421 421 HOH HOH . G 4 HOH A 22 422 422 HOH HOH . G 4 HOH A 23 423 423 HOH HOH . G 4 HOH A 24 424 424 HOH HOH . G 4 HOH A 25 425 425 HOH HOH . G 4 HOH A 26 426 426 HOH HOH . G 4 HOH A 27 427 427 HOH HOH . G 4 HOH A 28 428 428 HOH HOH . G 4 HOH A 29 429 429 HOH HOH . G 4 HOH A 30 430 430 HOH HOH . G 4 HOH A 31 431 431 HOH HOH . G 4 HOH A 32 432 432 HOH HOH . G 4 HOH A 33 433 433 HOH HOH . G 4 HOH A 34 434 434 HOH HOH . G 4 HOH A 35 435 435 HOH HOH . G 4 HOH A 36 436 436 HOH HOH . G 4 HOH A 37 437 437 HOH HOH . G 4 HOH A 38 438 438 HOH HOH . G 4 HOH A 39 439 439 HOH HOH . G 4 HOH A 40 440 440 HOH HOH . G 4 HOH A 41 441 441 HOH HOH . G 4 HOH A 42 442 442 HOH HOH . G 4 HOH A 43 443 443 HOH HOH . G 4 HOH A 44 444 444 HOH HOH . G 4 HOH A 45 445 445 HOH HOH . G 4 HOH A 46 446 446 HOH HOH . G 4 HOH A 47 447 447 HOH HOH . G 4 HOH A 48 448 448 HOH HOH . G 4 HOH A 49 449 449 HOH HOH . G 4 HOH A 50 450 450 HOH HOH . G 4 HOH A 51 451 451 HOH HOH . G 4 HOH A 52 452 453 HOH HOH . G 4 HOH A 53 453 454 HOH HOH . G 4 HOH A 54 454 455 HOH HOH . G 4 HOH A 55 456 457 HOH HOH . G 4 HOH A 56 457 458 HOH HOH . G 4 HOH A 57 458 459 HOH HOH . G 4 HOH A 58 459 460 HOH HOH . G 4 HOH A 59 460 461 HOH HOH . G 4 HOH A 60 461 462 HOH HOH . G 4 HOH A 61 462 463 HOH HOH . G 4 HOH A 62 463 464 HOH HOH . G 4 HOH A 63 464 465 HOH HOH . G 4 HOH A 64 465 466 HOH HOH . G 4 HOH A 65 466 467 HOH HOH . G 4 HOH A 66 467 468 HOH HOH . G 4 HOH A 67 468 469 HOH HOH . G 4 HOH A 68 469 470 HOH HOH . G 4 HOH A 69 470 471 HOH HOH . G 4 HOH A 70 471 472 HOH HOH . H 4 HOH B 1 401 401 HOH HOH . H 4 HOH B 2 402 402 HOH HOH . H 4 HOH B 3 403 403 HOH HOH . H 4 HOH B 4 404 404 HOH HOH . H 4 HOH B 5 405 405 HOH HOH . H 4 HOH B 6 406 406 HOH HOH . H 4 HOH B 7 407 407 HOH HOH . H 4 HOH B 8 408 408 HOH HOH . H 4 HOH B 9 409 409 HOH HOH . H 4 HOH B 10 410 410 HOH HOH . H 4 HOH B 11 411 411 HOH HOH . H 4 HOH B 12 412 412 HOH HOH . H 4 HOH B 13 413 413 HOH HOH . H 4 HOH B 14 414 414 HOH HOH . H 4 HOH B 15 415 415 HOH HOH . H 4 HOH B 16 416 416 HOH HOH . H 4 HOH B 17 417 417 HOH HOH . H 4 HOH B 18 418 418 HOH HOH . H 4 HOH B 19 419 419 HOH HOH . H 4 HOH B 20 420 420 HOH HOH . H 4 HOH B 21 421 421 HOH HOH . H 4 HOH B 22 422 422 HOH HOH . H 4 HOH B 23 423 423 HOH HOH . H 4 HOH B 24 424 424 HOH HOH . H 4 HOH B 25 425 425 HOH HOH . H 4 HOH B 26 426 426 HOH HOH . H 4 HOH B 27 427 427 HOH HOH . H 4 HOH B 28 428 428 HOH HOH . H 4 HOH B 29 429 429 HOH HOH . H 4 HOH B 30 430 430 HOH HOH . H 4 HOH B 31 431 431 HOH HOH . H 4 HOH B 32 432 432 HOH HOH . H 4 HOH B 33 433 433 HOH HOH . H 4 HOH B 34 434 434 HOH HOH . H 4 HOH B 35 435 435 HOH HOH . H 4 HOH B 36 436 436 HOH HOH . H 4 HOH B 37 437 437 HOH HOH . H 4 HOH B 38 438 438 HOH HOH . H 4 HOH B 39 439 439 HOH HOH . H 4 HOH B 40 440 440 HOH HOH . H 4 HOH B 41 441 441 HOH HOH . H 4 HOH B 42 442 442 HOH HOH . H 4 HOH B 43 443 443 HOH HOH . H 4 HOH B 44 444 444 HOH HOH . H 4 HOH B 45 445 445 HOH HOH . H 4 HOH B 46 446 446 HOH HOH . H 4 HOH B 47 447 447 HOH HOH . H 4 HOH B 48 448 448 HOH HOH . H 4 HOH B 49 449 449 HOH HOH . H 4 HOH B 50 450 450 HOH HOH . H 4 HOH B 51 451 451 HOH HOH . H 4 HOH B 52 453 453 HOH HOH . H 4 HOH B 53 454 454 HOH HOH . H 4 HOH B 54 455 455 HOH HOH . H 4 HOH B 55 456 456 HOH HOH . H 4 HOH B 56 457 457 HOH HOH . H 4 HOH B 57 458 458 HOH HOH . H 4 HOH B 58 459 459 HOH HOH . H 4 HOH B 59 460 460 HOH HOH . H 4 HOH B 60 461 461 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 6.405 57.128 -26.669 1 34.85 ? CHA HEM 301 B 1 HETATM 2 C CHB HEM . . . E 2 9.014 59.176 -23.057 1 31.97 ? CHB HEM 301 B 1 HETATM 3 C CHC HEM . . . E 2 11.508 61.876 -26.312 1 31.7 ? CHC HEM 301 B 1 HETATM 4 C CHD HEM . . . E 2 8.511 60.275 -29.853 1 33.22 ? CHD HEM 301 B 1 HETATM 5 C C1A HEM . . . E 2 6.863 57.41 -25.389 1 38.51 ? C1A HEM 301 B 1 HETATM 6 C C2A HEM . . . E 2 6.388 56.888 -24.119 1 42.13 ? C2A HEM 301 B 1 HETATM 7 C C3A HEM . . . E 2 7.122 57.457 -23.129 1 36.79 ? C3A HEM 301 B 1 HETATM 8 C C4A HEM . . . E 2 8.089 58.368 -23.717 1 34.93 ? C4A HEM 301 B 1 HETATM 9 C CMA HEM . . . E 2 6.985 57.223 -21.611 1 38.25 ? CMA HEM 301 B 1 HETATM 10 C CAA HEM . . . E 2 5.235 55.86 -23.967 1 30.88 ? CAA HEM 301 B 1 HETATM 11 C CBA HEM . . . E 2 5.79 54.46 -24.216 1 35.75 ? CBA HEM 301 B 1 HETATM 12 C CGA HEM . . . E 2 4.679 53.413 -24.248 1 32.42 ? CGA HEM 301 B 1 HETATM 13 O O1A HEM . . . E 2 3.47 53.756 -24.195 1 35.7 ? O1A HEM 301 B 1 HETATM 14 O O2A HEM . . . E 2 5.034 52.216 -24.336 1 41.76 ? O2A HEM 301 B 1 HETATM 15 C C1B HEM . . . E 2 9.898 60.124 -23.568 1 28.86 ? C1B HEM 301 B 1 HETATM 16 C C2B HEM . . . E 2 10.771 61.01 -22.838 1 27.67 ? C2B HEM 301 B 1 HETATM 17 C C3B HEM . . . E 2 11.479 61.739 -23.726 1 30.95 ? C3B HEM 301 B 1 HETATM 18 C C4B HEM . . . E 2 11.066 61.39 -25.08 1 33.62 ? C4B HEM 301 B 1 HETATM 19 C CMB HEM . . . E 2 10.888 61.083 -21.294 1 30.6 ? CMB HEM 301 B 1 HETATM 20 C CAB HEM . . . E 2 12.522 62.804 -23.333 1 35.39 ? CAB HEM 301 B 1 HETATM 21 C CBB HEM . . . E 2 13.626 62.937 -24.083 1 29.04 ? CBB HEM 301 B 1 HETATM 22 C C1C HEM . . . E 2 10.928 61.739 -27.572 1 30.21 ? C1C HEM 301 B 1 HETATM 23 C C2C HEM . . . E 2 11.256 62.42 -28.809 1 30.18 ? C2C HEM 301 B 1 HETATM 24 C C3C HEM . . . E 2 10.429 61.956 -29.793 1 28.41 ? C3C HEM 301 B 1 HETATM 25 C C4C HEM . . . E 2 9.52 60.989 -29.214 1 35.18 ? C4C HEM 301 B 1 HETATM 26 C CMC HEM . . . E 2 12.401 63.466 -28.909 1 26.62 ? CMC HEM 301 B 1 HETATM 27 C CAC HEM . . . E 2 10.334 62.36 -31.279 1 32.59 ? CAC HEM 301 B 1 HETATM 28 C CBC HEM . . . E 2 10.735 63.563 -31.703 1 40.55 ? CBC HEM 301 B 1 HETATM 29 C C1D HEM . . . E 2 7.613 59.336 -29.354 1 40.67 ? C1D HEM 301 B 1 HETATM 30 C C2D HEM . . . E 2 6.517 58.728 -30.069 1 34.92 ? C2D HEM 301 B 1 HETATM 31 C C3D HEM . . . E 2 5.844 57.757 -29.08 1 37.16 ? C3D HEM 301 B 1 HETATM 32 C C4D HEM . . . E 2 6.603 57.84 -27.851 1 40.65 ? C4D HEM 301 B 1 HETATM 33 C CMD HEM . . . E 2 6.093 59.018 -31.525 1 36.84 ? CMD HEM 301 B 1 HETATM 34 C CAD HEM . . . E 2 4.617 56.873 -29.364 1 34.02 ? CAD HEM 301 B 1 HETATM 35 C CBD HEM . . . E 2 3.448 57.422 -28.547 1 40.07 ? CBD HEM 301 B 1 HETATM 36 C CGD HEM . . . E 2 2.907 58.717 -29.104 1 36.29 ? CGD HEM 301 B 1 HETATM 37 O O1D HEM . . . E 2 2.471 59.563 -28.29 1 35.95 ? O1D HEM 301 B 1 HETATM 38 O O2D HEM . . . E 2 2.908 58.917 -30.347 1 40.72 ? O2D HEM 301 B 1 HETATM 39 N NA HEM . . . E 2 7.887 58.267 -25.073 1 27.54 ? NA HEM 301 B 1 HETATM 40 N NB HEM . . . E 2 10.136 60.4 -24.896 1 30.84 ? NB HEM 301 B 1 HETATM 41 N NC HEM . . . E 2 9.888 60.918 -27.903 1 25.9 ? NC HEM 301 B 1 HETATM 42 N ND HEM . . . E 2 7.607 58.766 -28.094 1 37.24 ? ND HEM 301 B 1 HETATM 43 FE FE HEM . . . E 2 8.868 59.653 -26.495 1 30.86 ? FE HEM 301 B 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #