data_1YST # _model_server_result.job_id V4Qvwoj3O1WAbuZURzk7RA _model_server_result.datetime_utc '2025-03-06 07:57:29' _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 1yst # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":274}' # _entry.id 1YST # _exptl.entry_id 1YST _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 911.504 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'BACTERIOCHLOROPHYLL A' _entity.pdbx_number_of_molecules 4 _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 1YST _cell.length_a 143.7 _cell.length_b 139.8 _cell.length_c 78.65 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YST _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 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,K,L,M _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 ? 4 D N N ? 4 E N N ? 4 I N N ? 4 J 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 153 L HIS 153 1_555 E MG BCL . L BCL 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc2 A NE2 HIS 173 L HIS 173 1_555 D MG BCL . L BCL 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc3 A NE2 HIS 190 L HIS 190 1_555 H MN MN . M MN 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc4 A NE2 HIS 230 L HIS 230 1_555 H MN MN . M MN 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc5 B NE2 HIS 182 M HIS 182 1_555 I MG BCL . M BCL 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc6 B NE2 HIS 202 M HIS 202 1_555 J MG BCL . M BCL 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc7 B NE2 HIS 219 M HIS 219 1_555 H MN MN . M MN 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? metalc ? metalc8 B OE1 GLU 234 M GLU 234 1_555 H MN MN . M MN 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc9 B OE2 GLU 234 M GLU 234 1_555 H MN MN . M MN 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc10 B NE2 HIS 266 M HIS 266 1_555 H MN MN . M MN 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? # _chem_comp.formula 'C55 H74 Mg N4 O6' _chem_comp.formula_weight 911.504 _chem_comp.id BCL _chem_comp.mon_nstd_flag . _chem_comp.name 'BACTERIOCHLOROPHYLL A' _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 MG NA BCL sing 70 n n MG NB BCL sing 71 n n MG NC BCL sing 72 n n MG ND BCL sing 73 n n CHA C1A BCL sing 74 n n CHA C4D BCL doub 75 n n CHA CBD BCL sing 76 n n CHB C4A BCL doub 77 n n CHB C1B BCL sing 78 n n CHB HHB BCL sing 79 n n CHC C4B BCL sing 80 n n CHC C1C BCL doub 81 n n CHC HHC BCL sing 82 n n CHD C4C BCL sing 83 n n CHD C1D BCL doub 84 n n CHD HHD BCL sing 85 n n NA C1A BCL doub 86 n n NA C4A BCL sing 87 n n C1A C2A BCL sing 88 n n C2A C3A BCL sing 89 n n C2A CAA BCL sing 90 n n C2A H2A BCL sing 91 n n C3A C4A BCL sing 92 n n C3A CMA BCL sing 93 n n C3A H3A BCL sing 94 n n CMA HMA1 BCL sing 95 n n CMA HMA2 BCL sing 96 n n CMA HMA3 BCL sing 97 n n CAA CBA BCL sing 98 n n CAA HAA1 BCL sing 99 n n CAA HAA2 BCL sing 100 n n CBA CGA BCL sing 101 n n CBA HBA1 BCL sing 102 n n CBA HBA2 BCL sing 103 n n CGA O1A BCL doub 104 n n CGA O2A BCL sing 105 n n O2A C1 BCL sing 106 n n NB C1B BCL sing 107 n y NB C4B BCL sing 108 n y C1B C2B BCL doub 109 n y C2B C3B BCL sing 110 n y C2B CMB BCL sing 111 n n C3B C4B BCL doub 112 n y C3B CAB BCL sing 113 n n CMB HMB1 BCL sing 114 n n CMB HMB2 BCL sing 115 n n CMB HMB3 BCL sing 116 n n CAB OBB BCL doub 117 n n CAB CBB BCL sing 118 n n CBB HBB1 BCL sing 119 n n CBB HBB2 BCL sing 120 n n CBB HBB3 BCL sing 121 n n NC C1C BCL sing 122 n n NC C4C BCL doub 123 n n C1C C2C BCL sing 124 n n C2C C3C BCL sing 125 n n C2C CMC BCL sing 126 n n C2C H2C BCL sing 127 n n C3C C4C BCL sing 128 n n C3C CAC BCL sing 129 n n C3C H3C BCL sing 130 n n CMC HMC1 BCL sing 131 n n CMC HMC2 BCL sing 132 n n CMC HMC3 BCL sing 133 n n CAC CBC BCL sing 134 n n CAC HAC1 BCL sing 135 n n CAC HAC2 BCL sing 136 n n CBC HBC1 BCL sing 137 n n CBC HBC2 BCL sing 138 n n CBC HBC3 BCL sing 139 n n ND C1D BCL sing 140 n n ND C4D BCL sing 141 n n C1D C2D BCL sing 142 n n C2D C3D BCL doub 143 n n C2D CMD BCL sing 144 n n C3D C4D BCL sing 145 n n C3D CAD BCL sing 146 n n CMD HMD1 BCL sing 147 n n CMD HMD2 BCL sing 148 n n CMD HMD3 BCL sing 149 n n CAD OBD BCL doub 150 n n CAD CBD BCL sing 151 n n CBD CGD BCL sing 152 n n CBD HBD BCL sing 153 n n CGD O1D BCL doub 154 n n CGD O2D BCL sing 155 n n O2D CED BCL sing 156 n n CED HED1 BCL sing 157 n n CED HED2 BCL sing 158 n n CED HED3 BCL sing 159 n n C1 C2 BCL sing 160 n n C1 H11 BCL sing 161 n n C1 H12 BCL sing 162 n n C2 C3 BCL doub 163 e n C2 H2 BCL sing 164 n n C3 C4 BCL sing 165 n n C3 C5 BCL sing 166 n n C4 H41 BCL sing 167 n n C4 H42 BCL sing 168 n n C4 H43 BCL sing 169 n n C5 C6 BCL sing 170 n n C5 H51 BCL sing 171 n n C5 H52 BCL sing 172 n n C6 C7 BCL sing 173 n n C6 H61 BCL sing 174 n n C6 H62 BCL sing 175 n n C7 C8 BCL sing 176 n n C7 H71 BCL sing 177 n n C7 H72 BCL sing 178 n n C8 C9 BCL sing 179 n n C8 C10 BCL sing 180 n n C8 H8 BCL sing 181 n n C9 H91 BCL sing 182 n n C9 H92 BCL sing 183 n n C9 H93 BCL sing 184 n n C10 C11 BCL sing 185 n n C10 H101 BCL sing 186 n n C10 H102 BCL sing 187 n n C11 C12 BCL sing 188 n n C11 H111 BCL sing 189 n n C11 H112 BCL sing 190 n n C12 C13 BCL sing 191 n n C12 H121 BCL sing 192 n n C12 H122 BCL sing 193 n n C13 C14 BCL sing 194 n n C13 C15 BCL sing 195 n n C13 H13 BCL sing 196 n n C14 H141 BCL sing 197 n n C14 H142 BCL sing 198 n n C14 H143 BCL sing 199 n n C15 C16 BCL sing 200 n n C15 H151 BCL sing 201 n n C15 H152 BCL sing 202 n n C16 C17 BCL sing 203 n n C16 H161 BCL sing 204 n n C16 H162 BCL sing 205 n n C17 C18 BCL sing 206 n n C17 H171 BCL sing 207 n n C17 H172 BCL sing 208 n n C18 C19 BCL sing 209 n n C18 C20 BCL sing 210 n n C18 H18 BCL sing 211 n n C19 H191 BCL sing 212 n n C19 H192 BCL sing 213 n n C19 H193 BCL sing 214 n n C20 H201 BCL sing 215 n n C20 H202 BCL sing 216 n n C20 H203 BCL sing 217 n n # _atom_sites.entry_id 1YST _atom_sites.fract_transf_matrix[1][1] 0.006959 _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] 0.007153 _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] 0.012715 _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 BCL L 1 274 2 BCL BCL . E 4 BCL L 1 275 4 BCL BCL . F 5 BPH L 1 276 6 BPH BPH . G 6 U10 L 1 277 10 U10 U10 . H 7 MN M 1 306 8 MN MN . I 4 BCL M 1 307 1 BCL BCL . J 4 BCL M 1 308 3 BCL BCL . K 5 BPH M 1 309 5 BPH BPH . L 8 SPO M 1 310 7 SPO SPO . M 6 U10 M 1 311 9 U10 U10 . # 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 MG MG BCL . . . D 4 -24.338 -33.079 9.684 1 22.9 ? MG BCL 274 L 1 HETATM 2 C CHA BCL . . . D 4 -23.877 -36.347 8.826 1 27.28 ? CHA BCL 274 L 1 HETATM 3 C CHB BCL . . . D 4 -21.679 -32.327 7.855 1 26.17 ? CHB BCL 274 L 1 HETATM 4 C CHC BCL . . . D 4 -24.83 -29.853 10.563 1 28.3 ? CHC BCL 274 L 1 HETATM 5 C CHD BCL . . . D 4 -27.166 -33.966 11.489 1 18.56 ? CHD BCL 274 L 1 HETATM 6 N NA BCL . . . D 4 -22.909 -34.071 8.506 1 22.97 ? NA BCL 274 L 1 HETATM 7 C C1A BCL . . . D 4 -22.975 -35.495 8.311 1 26.49 ? C1A BCL 274 L 1 HETATM 8 C C2A BCL . . . D 4 -21.67 -35.856 7.356 1 25.23 ? C2A BCL 274 L 1 HETATM 9 C C3A BCL . . . D 4 -21.058 -34.51 7.162 1 24.23 ? C3A BCL 274 L 1 HETATM 10 C C4A BCL . . . D 4 -21.942 -33.642 7.906 1 22.88 ? C4A BCL 274 L 1 HETATM 11 C CMA BCL . . . D 4 -19.65 -34.407 7.712 1 23.76 ? CMA BCL 274 L 1 HETATM 12 C CAA BCL . . . D 4 -21.984 -36.719 5.888 1 28.14 ? CAA BCL 274 L 1 HETATM 13 C CBA BCL . . . D 4 -20.666 -37.173 5.106 1 25.6 ? CBA BCL 274 L 1 HETATM 14 C CGA BCL . . . D 4 -20.812 -38.349 4.079 1 25.93 ? CGA BCL 274 L 1 HETATM 15 O O1A BCL . . . D 4 -20.072 -38.47 3.099 1 19.89 ? O1A BCL 274 L 1 HETATM 16 O O2A BCL . . . D 4 -21.649 -39.249 4.297 1 24.94 ? O2A BCL 274 L 1 HETATM 17 N NB BCL . . . D 4 -23.42 -31.41 9.277 1 27.25 ? NB BCL 274 L 1 HETATM 18 C C1B BCL . . . D 4 -22.361 -31.225 8.522 1 28.76 ? C1B BCL 274 L 1 HETATM 19 C C2B BCL . . . D 4 -21.984 -29.964 8.356 1 29.64 ? C2B BCL 274 L 1 HETATM 20 C C3B BCL . . . D 4 -22.837 -29.236 9.077 1 29.85 ? C3B BCL 274 L 1 HETATM 21 C C4B BCL . . . D 4 -23.847 -30.199 9.819 1 29.33 ? C4B BCL 274 L 1 HETATM 22 C CMB BCL . . . D 4 -20.904 -29.388 7.469 1 26.93 ? CMB BCL 274 L 1 HETATM 23 C CAB BCL . . . D 4 -22.79 -27.729 9.16 1 29.53 ? CAB BCL 274 L 1 HETATM 24 O OBB BCL . . . D 4 -24.112 -27.154 9.697 1 30.81 ? OBB BCL 274 L 1 HETATM 25 C CBB BCL . . . D 4 -21.934 -27.022 8.69 1 29.82 ? CBB BCL 274 L 1 HETATM 26 N NC BCL . . . D 4 -25.689 -32.051 10.81 1 20.53 ? NC BCL 274 L 1 HETATM 27 C C1C BCL . . . D 4 -25.826 -30.773 11.144 1 24.53 ? C1C BCL 274 L 1 HETATM 28 C C2C BCL . . . D 4 -26.846 -30.367 12.169 1 21.43 ? C2C BCL 274 L 1 HETATM 29 C C3C BCL . . . D 4 -27.713 -31.492 12.292 1 17.83 ? C3C BCL 274 L 1 HETATM 30 C C4C BCL . . . D 4 -26.851 -32.763 11.481 1 19.13 ? C4C BCL 274 L 1 HETATM 31 C CMC BCL . . . D 4 -27.433 -28.968 12.009 1 26.03 ? CMC BCL 274 L 1 HETATM 32 C CAC BCL . . . D 4 -29.244 -31.232 11.56 1 13.82 ? CAC BCL 274 L 1 HETATM 33 C CBC BCL . . . D 4 -29.215 -30.924 10.067 1 6.34 ? CBC BCL 274 L 1 HETATM 34 N ND BCL . . . D 4 -25.256 -34.758 10.091 1 15.31 ? ND BCL 274 L 1 HETATM 35 C C1D BCL . . . D 4 -26.497 -34.872 10.904 1 18.97 ? C1D BCL 274 L 1 HETATM 36 C C2D BCL . . . D 4 -26.767 -36.362 10.779 1 22.29 ? C2D BCL 274 L 1 HETATM 37 C C3D BCL . . . D 4 -25.749 -36.909 9.988 1 22.24 ? C3D BCL 274 L 1 HETATM 38 C C4D BCL . . . D 4 -24.991 -35.928 9.598 1 21.36 ? C4D BCL 274 L 1 HETATM 39 C CMD BCL . . . D 4 -28.044 -37.113 11.407 1 15.52 ? CMD BCL 274 L 1 HETATM 40 C CAD BCL . . . D 4 -25.238 -38.146 9.261 1 23.57 ? CAD BCL 274 L 1 HETATM 41 O OBD BCL . . . D 4 -25.672 -39.288 9.279 1 26.37 ? OBD BCL 274 L 1 HETATM 42 C CBD BCL . . . D 4 -24.032 -37.796 8.583 1 24.1 ? CBD BCL 274 L 1 HETATM 43 C CGD BCL . . . D 4 -23.103 -38.532 9.204 1 24.22 ? CGD BCL 274 L 1 HETATM 44 O O1D BCL . . . D 4 -22.983 -38.711 10.398 1 24.52 ? O1D BCL 274 L 1 HETATM 45 O O2D BCL . . . D 4 -22.339 -38.986 8.342 1 26.55 ? O2D BCL 274 L 1 HETATM 46 C CED BCL . . . D 4 -22.961 -39.716 7.244 1 23.52 ? CED BCL 274 L 1 HETATM 47 C C1 BCL . . . D 4 -21.279 -40.479 3.787 1 25.32 ? C1 BCL 274 L 1 HETATM 48 C C2 BCL . . . D 4 -22.212 -40.927 2.625 1 22.27 ? C2 BCL 274 L 1 HETATM 49 C C3 BCL . . . D 4 -22.194 -40.591 1.343 1 20.8 ? C3 BCL 274 L 1 HETATM 50 C C4 BCL . . . D 4 -21.189 -39.648 0.762 1 24.14 ? C4 BCL 274 L 1 HETATM 51 C C5 BCL . . . D 4 -23.179 -41.139 0.315 1 19.44 ? C5 BCL 274 L 1 HETATM 52 C C6 BCL . . . D 4 -22.532 -42.099 -0.69 1 15.62 ? C6 BCL 274 L 1 HETATM 53 C C7 BCL . . . D 4 -23.574 -43.046 -1.267 1 7.23 ? C7 BCL 274 L 1 HETATM 54 C C8 BCL . . . D 4 -23.009 -44.174 -2.137 1 8.8 ? C8 BCL 274 L 1 HETATM 55 C C9 BCL . . . D 4 -21.892 -44.926 -1.475 1 5.47 ? C9 BCL 274 L 1 HETATM 56 C C10 BCL . . . D 4 -22.785 -43.821 -3.606 1 10.16 ? C10 BCL 274 L 1 HETATM 57 C C11 BCL . . . D 4 -24.097 -43.352 -4.337 1 13.27 ? C11 BCL 274 L 1 HETATM 58 C C12 BCL . . . D 4 -23.939 -43.332 -5.832 1 5.78 ? C12 BCL 274 L 1 HETATM 59 C C13 BCL . . . D 4 -25.2 -43.005 -6.636 1 10.61 ? C13 BCL 274 L 1 HETATM 60 C C14 BCL . . . D 4 -26.363 -43.914 -6.325 1 13.12 ? C14 BCL 274 L 1 HETATM 61 C C15 BCL . . . D 4 -24.932 -43.054 -8.143 1 11.58 ? C15 BCL 274 L 1 HETATM 62 C C16 BCL . . . D 4 -26.034 -42.51 -9.024 1 18.12 ? C16 BCL 274 L 1 HETATM 63 C C17 BCL . . . D 4 -25.438 -41.701 -10.179 1 19.33 ? C17 BCL 274 L 1 HETATM 64 C C18 BCL . . . D 4 -26.212 -41.72 -11.511 1 17.96 ? C18 BCL 274 L 1 HETATM 65 C C19 BCL . . . D 4 -25.379 -40.963 -12.56 1 16.37 ? C19 BCL 274 L 1 HETATM 66 C C20 BCL . . . D 4 -26.359 -43.136 -11.992 1 17.27 ? C20 BCL 274 L 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 66 #