data_6VDU # _model_server_result.job_id oeXgFygWl9_y-IGxivZw0Q _model_server_result.datetime_utc '2025-01-07 13:21:50' _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 6vdu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":201}' # _entry.id 6VDU # _exptl.entry_id 6VDU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 564.413 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'FE(III) DEUTEROPORPHYRIN IX' _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 6VDU _cell.length_a 59.174 _cell.length_b 67.901 _cell.length_c 67.905 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6VDU _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,I,N 1 1 B,J,K,L,M,O 2 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 J N N # _chem_comp.formula 'C30 H28 Fe N4 O4' _chem_comp.formula_weight 564.413 _chem_comp.id FDE _chem_comp.mon_nstd_flag . _chem_comp.name 'FE(III) DEUTEROPORPHYRIN IX' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 FDE sing 92 n n CHA C4D FDE doub 93 n n CHA HHA FDE sing 94 n n C1A C2A FDE sing 95 n n C1A NA FDE doub 96 n n C2A CAA FDE sing 97 n n C2A C3A FDE doub 98 n n CAA CBA FDE sing 99 n n CAA HAA1 FDE sing 100 n n CAA HAA2 FDE sing 101 n n CBA CGA FDE sing 102 n n CBA HBA1 FDE sing 103 n n CBA HBA2 FDE sing 104 n n CGA O1A FDE sing 105 n n CGA O2A FDE doub 106 n n O1A H1A FDE sing 107 n n C3A CMA FDE sing 108 n n C3A C4A FDE sing 109 n n CMA HMA1 FDE sing 110 n n CMA HMA2 FDE sing 111 n n CMA HMA3 FDE sing 112 n n C4A NA FDE sing 113 n n C4A CHB FDE doub 114 n n NA FE FDE sing 115 n n CHB C1B FDE sing 116 n n CHB HHB FDE sing 117 n n C1B C2B FDE doub 118 n y C1B NB FDE sing 119 n y C2B C3B FDE sing 120 n y C2B H2B FDE sing 121 n n C3B CME FDE sing 122 n n C3B C4B FDE doub 123 n y CME HME1 FDE sing 124 n n CME HME2 FDE sing 125 n n CME HME3 FDE sing 126 n n C4B NB FDE sing 127 n y C4B CHC FDE sing 128 n n NB FE FDE sing 129 n n CHC C1C FDE doub 130 n n CHC HHC FDE sing 131 n n C1C C2C FDE sing 132 n n C1C NC FDE sing 133 n n C2C C3C FDE doub 134 n n C2C H2C FDE sing 135 n n C3C CMF FDE sing 136 n n C3C C4C FDE sing 137 n n CMF HMF1 FDE sing 138 n n CMF HMF2 FDE sing 139 n n CMF HMF3 FDE sing 140 n n C4C NC FDE doub 141 n n C4C CHD FDE sing 142 n n NC FE FDE sing 143 n n CHD C1D FDE doub 144 n n CHD HHD FDE sing 145 n n C1D C2D FDE sing 146 n n C1D ND FDE sing 147 n n C2D CMD FDE sing 148 n n C2D C3D FDE doub 149 n n CMD HMD1 FDE sing 150 n n CMD HMD2 FDE sing 151 n n CMD HMD3 FDE sing 152 n n C3D CAD FDE sing 153 n n C3D C4D FDE sing 154 n n CAD CBD FDE sing 155 n n CAD HAD1 FDE sing 156 n n CAD HAD2 FDE sing 157 n n CBD CGD FDE sing 158 n n CBD HBD1 FDE sing 159 n n CBD HBD2 FDE sing 160 n n CGD O1D FDE sing 161 n n CGD O2D FDE doub 162 n n O1D H1D FDE sing 163 n n C4D ND FDE sing 164 n n ND FE FDE sing 165 n n # _atom_sites.entry_id 6VDU _atom_sites.fract_transf_matrix[1][1] 0.016899 _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] 0.014727 _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] 0.014726 _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 FDE A 1 201 201 FDE FDE . D 3 T6C A 1 202 301 T6C T6C . E 4 EDO A 1 203 401 EDO EDO . F 4 EDO A 1 204 501 EDO EDO . G 5 PEG A 1 205 601 PEG PEG . H 6 SO4 A 1 206 1 SO4 SO4 . I 6 SO4 A 1 207 2 SO4 SO4 . J 2 FDE B 1 201 201 FDE FDE . K 3 T6C B 1 202 301 T6C T6C . L 4 EDO B 1 203 401 EDO EDO . M 4 EDO B 1 204 501 EDO EDO . N 7 HOH A 1 301 65 HOH HOH . N 7 HOH A 2 302 4 HOH HOH . N 7 HOH A 3 303 88 HOH HOH . N 7 HOH A 4 304 76 HOH HOH . N 7 HOH A 5 305 67 HOH HOH . N 7 HOH A 6 306 66 HOH HOH . N 7 HOH A 7 307 40 HOH HOH . N 7 HOH A 8 308 62 HOH HOH . N 7 HOH A 9 309 60 HOH HOH . N 7 HOH A 10 310 41 HOH HOH . N 7 HOH A 11 311 54 HOH HOH . N 7 HOH A 12 312 27 HOH HOH . N 7 HOH A 13 313 1 HOH HOH . N 7 HOH A 14 314 10 HOH HOH . N 7 HOH A 15 315 33 HOH HOH . N 7 HOH A 16 316 22 HOH HOH . N 7 HOH A 17 317 86 HOH HOH . N 7 HOH A 18 318 36 HOH HOH . N 7 HOH A 19 319 64 HOH HOH . N 7 HOH A 20 320 57 HOH HOH . N 7 HOH A 21 321 50 HOH HOH . N 7 HOH A 22 322 43 HOH HOH . N 7 HOH A 23 323 19 HOH HOH . N 7 HOH A 24 324 89 HOH HOH . N 7 HOH A 25 325 26 HOH HOH . N 7 HOH A 26 326 52 HOH HOH . N 7 HOH A 27 327 30 HOH HOH . N 7 HOH A 28 328 55 HOH HOH . N 7 HOH A 29 329 23 HOH HOH . N 7 HOH A 30 330 42 HOH HOH . N 7 HOH A 31 331 15 HOH HOH . N 7 HOH A 32 332 28 HOH HOH . N 7 HOH A 33 333 25 HOH HOH . N 7 HOH A 34 334 16 HOH HOH . N 7 HOH A 35 335 38 HOH HOH . N 7 HOH A 36 336 68 HOH HOH . N 7 HOH A 37 337 75 HOH HOH . N 7 HOH A 38 338 74 HOH HOH . N 7 HOH A 39 339 71 HOH HOH . N 7 HOH A 40 340 2 HOH HOH . N 7 HOH A 41 341 13 HOH HOH . N 7 HOH A 42 342 72 HOH HOH . N 7 HOH A 43 343 44 HOH HOH . N 7 HOH A 44 344 20 HOH HOH . N 7 HOH A 45 345 69 HOH HOH . N 7 HOH A 46 346 87 HOH HOH . N 7 HOH A 47 347 32 HOH HOH . O 7 HOH B 1 301 6 HOH HOH . O 7 HOH B 2 302 78 HOH HOH . O 7 HOH B 3 303 91 HOH HOH . O 7 HOH B 4 304 85 HOH HOH . O 7 HOH B 5 305 34 HOH HOH . O 7 HOH B 6 306 8 HOH HOH . O 7 HOH B 7 307 81 HOH HOH . O 7 HOH B 8 308 12 HOH HOH . O 7 HOH B 9 309 3 HOH HOH . O 7 HOH B 10 310 14 HOH HOH . O 7 HOH B 11 311 7 HOH HOH . O 7 HOH B 12 312 29 HOH HOH . O 7 HOH B 13 313 70 HOH HOH . O 7 HOH B 14 314 63 HOH HOH . O 7 HOH B 15 315 35 HOH HOH . O 7 HOH B 16 316 47 HOH HOH . O 7 HOH B 17 317 92 HOH HOH . O 7 HOH B 18 318 61 HOH HOH . O 7 HOH B 19 319 48 HOH HOH . O 7 HOH B 20 320 39 HOH HOH . O 7 HOH B 21 321 83 HOH HOH . O 7 HOH B 22 322 5 HOH HOH . O 7 HOH B 23 323 46 HOH HOH . O 7 HOH B 24 324 82 HOH HOH . O 7 HOH B 25 325 84 HOH HOH . O 7 HOH B 26 326 77 HOH HOH . O 7 HOH B 27 327 24 HOH HOH . O 7 HOH B 28 328 37 HOH HOH . O 7 HOH B 29 329 21 HOH HOH . O 7 HOH B 30 330 59 HOH HOH . O 7 HOH B 31 331 49 HOH HOH . O 7 HOH B 32 332 58 HOH HOH . O 7 HOH B 33 333 80 HOH HOH . O 7 HOH B 34 334 56 HOH HOH . O 7 HOH B 35 335 90 HOH HOH . O 7 HOH B 36 336 51 HOH HOH . O 7 HOH B 37 337 79 HOH HOH . O 7 HOH B 38 338 17 HOH HOH . O 7 HOH B 39 339 18 HOH HOH . O 7 HOH B 40 340 73 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 FDE . . . J 2 -37.073 -6.86 22.256 0.6 77.32 ? CHA FDE 201 B 1 HETATM 2 C C1A FDE . . . J 2 -36.109 -7.395 21.287 0.6 78.29 ? C1A FDE 201 B 1 HETATM 3 C C2A FDE . . . J 2 -34.827 -8.047 21.673 0.6 79.19 ? C2A FDE 201 B 1 HETATM 4 C CAA FDE . . . J 2 -34.295 -8.301 23.056 0.6 76.5 ? CAA FDE 201 B 1 HETATM 5 C CBA FDE . . . J 2 -34.791 -9.675 23.487 0.6 75.33 ? CBA FDE 201 B 1 HETATM 6 C CGA FDE . . . J 2 -35.74 -9.543 24.648 0.6 75.03 ? CGA FDE 201 B 1 HETATM 7 O O1A FDE . . . J 2 -36.725 -8.781 24.547 0.6 75.2 ? O1A FDE 201 B 1 HETATM 8 O O2A FDE . . . J 2 -35.5 -10.212 25.671 0.6 75.32 ? O2A FDE 201 B 1 HETATM 9 C C3A FDE . . . J 2 -34.148 -8.416 20.408 0.6 79.85 ? C3A FDE 201 B 1 HETATM 10 C CMA FDE . . . J 2 -32.803 -9.081 20.287 0.6 78.57 ? CMA FDE 201 B 1 HETATM 11 C C4A FDE . . . J 2 -35.052 -7.955 19.317 0.6 77.92 ? C4A FDE 201 B 1 HETATM 12 N NA FDE . . . J 2 -36.331 -7.428 19.837 0.6 76.41 ? NA FDE 201 B 1 HETATM 13 C CHB FDE . . . J 2 -34.735 -8.112 17.885 0.6 73.82 ? CHB FDE 201 B 1 HETATM 14 C C1B FDE . . . J 2 -35.453 -7.41 16.819 0.6 73.35 ? C1B FDE 201 B 1 HETATM 15 C C2B FDE . . . J 2 -35 -7.568 15.514 0.6 73.94 ? C2B FDE 201 B 1 HETATM 16 C C3B FDE . . . J 2 -35.88 -6.788 14.8 0.6 74.03 ? C3B FDE 201 B 1 HETATM 17 C CME FDE . . . J 2 -35.703 -6.716 13.305 0.6 71.03 ? CME FDE 201 B 1 HETATM 18 C C4B FDE . . . J 2 -36.811 -6.195 15.793 0.6 73.51 ? C4B FDE 201 B 1 HETATM 19 N NB FDE . . . J 2 -36.507 -6.608 17.041 0.6 73.43 ? NB FDE 201 B 1 HETATM 20 C CHC FDE . . . J 2 -37.928 -5.277 15.461 0.6 72.17 ? CHC FDE 201 B 1 HETATM 21 C C1C FDE . . . J 2 -38.802 -4.63 16.459 0.6 70.59 ? C1C FDE 201 B 1 HETATM 22 C C2C FDE . . . J 2 -39.755 -3.718 16 0.6 67.15 ? C2C FDE 201 B 1 HETATM 23 C C3C FDE . . . J 2 -40.359 -3.313 17.159 0.6 67.66 ? C3C FDE 201 B 1 HETATM 24 C CMF FDE . . . J 2 -41.459 -2.304 17.092 0.6 63.6 ? CMF FDE 201 B 1 HETATM 25 C C4C FDE . . . J 2 -39.691 -4.04 18.255 0.6 74.2 ? C4C FDE 201 B 1 HETATM 26 N NC FDE . . . J 2 -38.719 -4.848 17.792 0.6 75.24 ? NC FDE 201 B 1 HETATM 27 C CHD FDE . . . J 2 -40.047 -3.89 19.678 0.6 74.79 ? CHD FDE 201 B 1 HETATM 28 C C1D FDE . . . J 2 -39.398 -4.602 20.81 0.6 78.16 ? C1D FDE 201 B 1 HETATM 29 C C2D FDE . . . J 2 -39.845 -4.376 22.214 0.6 79.16 ? C2D FDE 201 B 1 HETATM 30 C CMD FDE . . . J 2 -40.942 -3.467 22.717 0.6 79.72 ? CMD FDE 201 B 1 HETATM 31 C C3D FDE . . . J 2 -38.95 -5.26 22.988 0.6 77.59 ? C3D FDE 201 B 1 HETATM 32 C CAD FDE . . . J 2 -38.875 -5.507 24.483 0.6 77.69 ? CAD FDE 201 B 1 HETATM 33 C CBD FDE . . . J 2 -39.419 -4.337 25.3 0.6 77.44 ? CBD FDE 201 B 1 HETATM 34 C CGD FDE . . . J 2 -38.94 -4.436 26.73 0.6 78.37 ? CGD FDE 201 B 1 HETATM 35 O O1D FDE . . . J 2 -38.645 -3.382 27.337 0.6 74.98 ? O1D FDE 201 B 1 HETATM 36 O O2D FDE . . . J 2 -38.864 -5.568 27.258 0.6 78.8 ? O2D FDE 201 B 1 HETATM 37 C C4D FDE . . . J 2 -38.127 -5.892 21.924 0.6 77.88 ? C4D FDE 201 B 1 HETATM 38 N ND FDE . . . J 2 -38.38 -5.497 20.657 0.6 78.49 ? ND FDE 201 B 1 HETATM 39 FE FE FDE . . . J 2 -37.427 -6.131 18.869 0.6 80.93 ? FE FDE 201 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 39 #