data_1YEB # _model_server_result.job_id ptgUHQAzs87IVdEV2mQMIw _model_server_result.datetime_utc '2024-10-14 07:28:14' _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 1yeb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":104}' # _entry.id 1YEB # _exptl.entry_id 1YEB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 618.503 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'HEME C' _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 1YEB _cell.length_a 36.39 _cell.length_b 36.39 _cell.length_c 137.28 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YEB _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 ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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_465 y-1,x+1,-z 0 1 0 1 0 0 0 0 -1 -36.39 36.39 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 covale ? covale1 A SG CYS 19 A CYS 14 1_555 C CAB HEC . A HEC 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.749 ? covale ? covale2 A SG CYS 22 A CYS 17 1_555 C CAC HEC . A HEC 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.828 ? covale ? covale3 A C PRO 76 A PRO 71 1_555 A N M3L 77 A M3L 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale4 A C M3L 77 A M3L 72 1_555 A N LYS 78 A LYS 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? metalc ? metalc1 A NE2 HIS 23 A HIS 18 1_555 C FE HEC . A HEC 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc2 A SD MET 85 A MET 80 1_555 C FE HEC . A HEC 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? # _chem_comp.formula 'C34 H34 Fe N4 O4' _chem_comp.formula_weight 618.503 _chem_comp.id HEC _chem_comp.mon_nstd_flag . _chem_comp.name 'HEME C' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 1YEB _atom_sites.fract_transf_matrix[1][1] 0.02748 _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] 0.02748 _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] 0.007284 _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 SO4 A 1 105 105 SO4 SO4 . C 3 HEC A 1 104 104 HEC HEM . D 4 HOH A 1 106 106 HOH HOH . D 4 HOH A 2 107 107 HOH HOH . D 4 HOH A 3 108 108 HOH HOH . D 4 HOH A 4 109 109 HOH HOH . D 4 HOH A 5 110 110 HOH HOH . D 4 HOH A 6 111 111 HOH HOH . D 4 HOH A 7 112 112 HOH HOH . D 4 HOH A 8 113 113 HOH HOH . D 4 HOH A 9 114 114 HOH HOH . D 4 HOH A 10 115 115 HOH HOH . D 4 HOH A 11 116 116 HOH HOH . D 4 HOH A 12 117 117 HOH HOH . D 4 HOH A 13 118 118 HOH HOH . D 4 HOH A 14 119 119 HOH HOH . D 4 HOH A 15 120 120 HOH HOH . D 4 HOH A 16 121 121 HOH HOH . D 4 HOH A 17 122 122 HOH HOH . D 4 HOH A 18 123 123 HOH HOH . D 4 HOH A 19 124 124 HOH HOH . D 4 HOH A 20 125 125 HOH HOH . D 4 HOH A 21 126 126 HOH HOH . D 4 HOH A 22 127 127 HOH HOH . D 4 HOH A 23 128 128 HOH HOH . D 4 HOH A 24 129 129 HOH HOH . D 4 HOH A 25 130 130 HOH HOH . D 4 HOH A 26 131 131 HOH HOH . D 4 HOH A 27 132 132 HOH HOH . D 4 HOH A 28 133 133 HOH HOH . D 4 HOH A 29 134 134 HOH HOH . D 4 HOH A 30 135 135 HOH HOH . D 4 HOH A 31 136 136 HOH HOH . D 4 HOH A 32 137 137 HOH HOH . D 4 HOH A 33 138 138 HOH HOH . D 4 HOH A 34 139 139 HOH HOH . D 4 HOH A 35 140 140 HOH HOH . D 4 HOH A 36 141 141 HOH HOH . D 4 HOH A 37 142 142 HOH HOH . D 4 HOH A 38 143 143 HOH HOH . D 4 HOH A 39 144 144 HOH HOH . D 4 HOH A 40 145 145 HOH HOH . D 4 HOH A 41 146 146 HOH HOH . D 4 HOH A 42 147 147 HOH HOH . D 4 HOH A 43 148 148 HOH HOH . D 4 HOH A 44 149 149 HOH HOH . D 4 HOH A 45 150 150 HOH HOH . D 4 HOH A 46 151 151 HOH HOH . D 4 HOH A 47 152 152 HOH HOH . D 4 HOH A 48 153 153 HOH HOH . D 4 HOH A 49 154 154 HOH HOH . D 4 HOH A 50 155 155 HOH HOH . D 4 HOH A 51 156 156 HOH HOH . D 4 HOH A 52 157 157 HOH HOH . D 4 HOH A 53 158 158 HOH HOH . D 4 HOH A 54 159 159 HOH HOH . D 4 HOH A 55 160 160 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 FE FE HEC . . . C 3 2.703 20.839 13.254 1 6.61 ? FE HEC 104 A 1 HETATM 2 C CHA HEC . . . C 3 4.978 18.712 14.403 1 7.64 ? CHA HEC 104 A 1 HETATM 3 C CHB HEC . . . C 3 3.897 20.576 10.091 1 6.48 ? CHB HEC 104 A 1 HETATM 4 C CHC HEC . . . C 3 0.088 22.759 12.059 1 6.55 ? CHC HEC 104 A 1 HETATM 5 C CHD HEC . . . C 3 1.935 21.858 16.464 1 5.59 ? CHD HEC 104 A 1 HETATM 6 N NA HEC . . . C 3 4.199 19.835 12.395 1 4.7 ? NA HEC 104 A 1 HETATM 7 C C1A HEC . . . C 3 5.006 18.925 13.023 1 6.48 ? C1A HEC 104 A 1 HETATM 8 C C2A HEC . . . C 3 5.801 18.257 12.032 1 6.29 ? C2A HEC 104 A 1 HETATM 9 C C3A HEC . . . C 3 5.508 18.778 10.848 1 5.21 ? C3A HEC 104 A 1 HETATM 10 C C4A HEC . . . C 3 4.483 19.79 11.077 1 5.1 ? C4A HEC 104 A 1 HETATM 11 C CMA HEC . . . C 3 6.024 18.484 9.392 1 5.26 ? CMA HEC 104 A 1 HETATM 12 C CAA HEC . . . C 3 6.846 17.177 12.428 1 9.68 ? CAA HEC 104 A 1 HETATM 13 C CBA HEC . . . C 3 8.303 17.643 12.051 1 10.82 ? CBA HEC 104 A 1 HETATM 14 C CGA HEC . . . C 3 9.432 16.892 12.714 1 12.5 ? CGA HEC 104 A 1 HETATM 15 O O1A HEC . . . C 3 10.512 17.556 12.972 1 9.71 ? O1A HEC 104 A 1 HETATM 16 O O2A HEC . . . C 3 9.159 15.653 12.89 1 10.97 ? O2A HEC 104 A 1 HETATM 17 N NB HEC . . . C 3 2.088 21.498 11.437 1 5.41 ? NB HEC 104 A 1 HETATM 18 C C1B HEC . . . C 3 2.81 21.4 10.27 1 6.61 ? C1B HEC 104 A 1 HETATM 19 C C2B HEC . . . C 3 2.105 22.117 9.199 1 7.23 ? C2B HEC 104 A 1 HETATM 20 C C3B HEC . . . C 3 1.067 22.723 9.736 1 7.48 ? C3B HEC 104 A 1 HETATM 21 C C4B HEC . . . C 3 1.042 22.325 11.162 1 6.23 ? C4B HEC 104 A 1 HETATM 22 C CMB HEC . . . C 3 2.653 22.125 7.738 1 7.77 ? CMB HEC 104 A 1 HETATM 23 C CAB HEC . . . C 3 -0.051 23.63 9.142 1 9.13 ? CAB HEC 104 A 1 HETATM 24 C CBB HEC . . . C 3 -1.198 23.026 8.324 1 8.49 ? CBB HEC 104 A 1 HETATM 25 N NC HEC . . . C 3 1.3 22.038 14.079 1 6.08 ? NC HEC 104 A 1 HETATM 26 C C1C HEC . . . C 3 0.339 22.774 13.406 1 7.32 ? C1C HEC 104 A 1 HETATM 27 C C2C HEC . . . C 3 -0.401 23.583 14.342 1 7.8 ? C2C HEC 104 A 1 HETATM 28 C C3C HEC . . . C 3 0.051 23.279 15.584 1 7.56 ? C3C HEC 104 A 1 HETATM 29 C C4C HEC . . . C 3 1.176 22.349 15.427 1 7.41 ? C4C HEC 104 A 1 HETATM 30 C CMC HEC . . . C 3 -1.592 24.488 13.931 1 8.56 ? CMC HEC 104 A 1 HETATM 31 C CAC HEC . . . C 3 -0.342 23.914 16.93 1 5.47 ? CAC HEC 104 A 1 HETATM 32 C CBC HEC . . . C 3 -1.84 23.896 17.259 1 5.46 ? CBC HEC 104 A 1 HETATM 33 N ND HEC . . . C 3 3.345 20.38 15.087 1 5.69 ? ND HEC 104 A 1 HETATM 34 C C1D HEC . . . C 3 2.859 20.842 16.317 1 5.31 ? C1D HEC 104 A 1 HETATM 35 C C2D HEC . . . C 3 3.413 20.032 17.38 1 6.48 ? C2D HEC 104 A 1 HETATM 36 C C3D HEC . . . C 3 4.264 19.133 16.827 1 6.14 ? C3D HEC 104 A 1 HETATM 37 C C4D HEC . . . C 3 4.241 19.364 15.381 1 6.79 ? C4D HEC 104 A 1 HETATM 38 C CMD HEC . . . C 3 3.093 20.19 18.871 1 7.62 ? CMD HEC 104 A 1 HETATM 39 C CAD HEC . . . C 3 5.174 18.082 17.498 1 3.86 ? CAD HEC 104 A 1 HETATM 40 C CBD HEC . . . C 3 4.657 16.637 17.47 1 2.82 ? CBD HEC 104 A 1 HETATM 41 C CGD HEC . . . C 3 5.328 15.654 18.368 1 3.68 ? CGD HEC 104 A 1 HETATM 42 O O1D HEC . . . C 3 6.481 15.883 18.796 1 2.75 ? O1D HEC 104 A 1 HETATM 43 O O2D HEC . . . C 3 4.665 14.569 18.576 1 3.46 ? O2D HEC 104 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 43 #