data_1YST # _model_server_result.job_id 5lgpkQYcColOU-BAWiGPRw _model_server_result.datetime_utc '2025-03-06 08:03:24' _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 1yst # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":309}' # _entry.id 1YST # _exptl.entry_id 1YST _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 889.215 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'BACTERIOPHEOPHYTIN A' _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 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 ? 5 F N N ? 5 K 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 H76 N4 O6' _chem_comp.formula_weight 889.215 _chem_comp.id BPH _chem_comp.mon_nstd_flag . _chem_comp.name 'BACTERIOPHEOPHYTIN 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 O1D CGD BPH doub 218 n n CGD O2D BPH sing 219 n n CGD CBD BPH sing 220 n n O2D CED BPH sing 221 n n CBD CHA BPH sing 222 n n CBD CAD BPH sing 223 n n CHA C4D BPH doub 224 n y CHA C1A BPH sing 225 n y C4D C3D BPH sing 226 n y C4D ND BPH sing 227 n y C3D CAD BPH sing 228 n n C3D C2D BPH doub 229 n y CAD OBD BPH doub 230 n n C2D CMD BPH sing 231 n n C2D C1D BPH sing 232 n y C1D ND BPH sing 233 n y C1D CHD BPH doub 234 n y CHD C4C BPH sing 235 n y C4C C3C BPH sing 236 n n C4C NC BPH doub 237 n y C3C CAC BPH sing 238 n n C3C C2C BPH sing 239 n n CAC CBC BPH sing 240 n n C2C CMC BPH sing 241 n n C2C C1C BPH sing 242 n n C1C NC BPH sing 243 n y C1C CHC BPH doub 244 n y CHC C4B BPH sing 245 n y C4B C3B BPH doub 246 n y C4B NB BPH sing 247 n y C3B CAB BPH sing 248 n n C3B C2B BPH sing 249 n y CAB CBB BPH sing 250 n n CAB OBB BPH doub 251 n n C2B CMB BPH sing 252 n n C2B C1B BPH doub 253 n y C1B NB BPH sing 254 n y C1B CHB BPH sing 255 n y CHB C4A BPH doub 256 n y C4A C3A BPH sing 257 n n C4A NA BPH sing 258 n y C3A CMA BPH sing 259 n n C3A C2A BPH sing 260 n n C2A C1A BPH sing 261 n n C2A CAA BPH sing 262 n n C1A NA BPH doub 263 n y CAA CBA BPH sing 264 n n CBA CGA BPH sing 265 n n CGA O1A BPH doub 266 n n CGA O2A BPH sing 267 n n O2A C1 BPH sing 268 n n C1 C2 BPH sing 269 n n C2 C3 BPH doub 270 e n C3 C4 BPH sing 271 n n C3 C5 BPH sing 272 n n C5 C6 BPH sing 273 n n C6 C7 BPH sing 274 n n C7 C8 BPH sing 275 n n C8 C9 BPH sing 276 n n C8 C10 BPH sing 277 n n C10 C11 BPH sing 278 n n C11 C12 BPH sing 279 n n C12 C13 BPH sing 280 n n C13 C14 BPH sing 281 n n C13 C15 BPH sing 282 n n C15 C16 BPH sing 283 n n C16 C17 BPH sing 284 n n C17 C18 BPH sing 285 n n C18 C19 BPH sing 286 n n C18 C20 BPH sing 287 n n CED HED1 BPH sing 288 n n CED HED2 BPH sing 289 n n CED HED3 BPH sing 290 n n CBD HBD BPH sing 291 n n CMD HMD1 BPH sing 292 n n CMD HMD2 BPH sing 293 n n CMD HMD3 BPH sing 294 n n ND HD BPH sing 295 n n CHD HHD BPH sing 296 n n C3C H3C BPH sing 297 n n CAC HAC1 BPH sing 298 n n CAC HAC2 BPH sing 299 n n CBC HBC1 BPH sing 300 n n CBC HBC2 BPH sing 301 n n CBC HBC3 BPH sing 302 n n C2C H2C BPH sing 303 n n CMC HMC1 BPH sing 304 n n CMC HMC2 BPH sing 305 n n CMC HMC3 BPH sing 306 n n CHC HHC BPH sing 307 n n CBB HBB1 BPH sing 308 n n CBB HBB2 BPH sing 309 n n CBB HBB3 BPH sing 310 n n CMB HMB1 BPH sing 311 n n CMB HMB2 BPH sing 312 n n CMB HMB3 BPH sing 313 n n NB HB BPH sing 314 n n CHB HHB BPH sing 315 n n C3A H3A BPH sing 316 n n CMA HMA1 BPH sing 317 n n CMA HMA2 BPH sing 318 n n CMA HMA3 BPH sing 319 n n C2A H2A BPH sing 320 n n CAA HAA1 BPH sing 321 n n CAA HAA2 BPH sing 322 n n CBA HBA1 BPH sing 323 n n CBA HBA2 BPH sing 324 n n C1 H1C1 BPH sing 325 n n C1 H1C2 BPH sing 326 n n C2 H2 BPH sing 327 n n C4 H4C1 BPH sing 328 n n C4 H4C2 BPH sing 329 n n C4 H4C3 BPH sing 330 n n C5 H5C1 BPH sing 331 n n C5 H5C2 BPH sing 332 n n C6 H6C1 BPH sing 333 n n C6 H6C2 BPH sing 334 n n C7 H7C1 BPH sing 335 n n C7 H7C2 BPH sing 336 n n C8 H8 BPH sing 337 n n C9 H9C1 BPH sing 338 n n C9 H9C2 BPH sing 339 n n C9 H9C3 BPH sing 340 n n C10 H101 BPH sing 341 n n C10 H102 BPH sing 342 n n C11 H111 BPH sing 343 n n C11 H112 BPH sing 344 n n C12 H121 BPH sing 345 n n C12 H122 BPH sing 346 n n C13 H13 BPH sing 347 n n C14 H141 BPH sing 348 n n C14 H142 BPH sing 349 n n C14 H143 BPH sing 350 n n C15 H151 BPH sing 351 n n C15 H152 BPH sing 352 n n C16 H161 BPH sing 353 n n C16 H162 BPH sing 354 n n C17 H171 BPH sing 355 n n C17 H172 BPH sing 356 n n C18 H18 BPH sing 357 n n C19 H191 BPH sing 358 n n C19 H192 BPH sing 359 n n C19 H193 BPH sing 360 n n C20 H201 BPH sing 361 n n C20 H202 BPH sing 362 n n C20 H203 BPH sing 363 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 O O1D BPH . . . K 5 -2.711 -18.378 2.076 1 29.39 ? O1D BPH 309 M 1 HETATM 2 C CGD BPH . . . K 5 -3.763 -18.957 2.354 1 29.86 ? CGD BPH 309 M 1 HETATM 3 O O2D BPH . . . K 5 -3.824 -20.154 2.832 1 31.63 ? O2D BPH 309 M 1 HETATM 4 C CED BPH . . . K 5 -3.861 -21.209 1.891 1 37.37 ? CED BPH 309 M 1 HETATM 5 C CBD BPH . . . K 5 -5.052 -18.406 2.081 1 28.94 ? CBD BPH 309 M 1 HETATM 6 C CHA BPH . . . K 5 -6.255 -18.962 2.944 1 27.73 ? CHA BPH 309 M 1 HETATM 7 C C4D BPH . . . K 5 -7.166 -19.458 2.003 1 27.3 ? C4D BPH 309 M 1 HETATM 8 C C3D BPH . . . K 5 -6.74 -19.34 0.601 1 28.6 ? C3D BPH 309 M 1 HETATM 9 C CAD BPH . . . K 5 -5.448 -18.78 0.53 1 28.02 ? CAD BPH 309 M 1 HETATM 10 O OBD BPH . . . K 5 -4.768 -18.544 -0.439 1 26.44 ? OBD BPH 309 M 1 HETATM 11 C C2D BPH . . . K 5 -7.703 -19.815 -0.185 1 28.84 ? C2D BPH 309 M 1 HETATM 12 C CMD BPH . . . K 5 -7.653 -19.87 -1.701 1 23.94 ? CMD BPH 309 M 1 HETATM 13 C C1D BPH . . . K 5 -8.81 -20.241 0.698 1 26.7 ? C1D BPH 309 M 1 HETATM 14 N ND BPH . . . K 5 -8.426 -20.034 2.029 1 22.16 ? ND BPH 309 M 1 HETATM 15 C CHD BPH . . . K 5 -10.109 -20.782 0.322 1 25.04 ? CHD BPH 309 M 1 HETATM 16 C C4C BPH . . . K 5 -11.111 -21.274 1.118 1 21.2 ? C4C BPH 309 M 1 HETATM 17 C C3C BPH . . . K 5 -12.452 -21.838 0.548 1 17.01 ? C3C BPH 309 M 1 HETATM 18 C CAC BPH . . . K 5 -12.286 -22.742 -0.729 1 21.05 ? CAC BPH 309 M 1 HETATM 19 C CBC BPH . . . K 5 -11.642 -22.014 -1.977 1 18.29 ? CBC BPH 309 M 1 HETATM 20 C C2C BPH . . . K 5 -13.064 -22.486 1.755 1 16.94 ? C2C BPH 309 M 1 HETATM 21 C CMC BPH . . . K 5 -13.165 -23.959 1.664 1 16.93 ? CMC BPH 309 M 1 HETATM 22 C C1C BPH . . . K 5 -12.08 -22.052 2.874 1 18.24 ? C1C BPH 309 M 1 HETATM 23 N NC BPH . . . K 5 -11.01 -21.387 2.416 1 19.56 ? NC BPH 309 M 1 HETATM 24 C CHC BPH . . . K 5 -12.311 -22.323 4.189 1 15.75 ? CHC BPH 309 M 1 HETATM 25 C C4B BPH . . . K 5 -11.562 -21.945 5.284 1 17.47 ? C4B BPH 309 M 1 HETATM 26 C C3B BPH . . . K 5 -11.771 -22.24 6.69 1 18.79 ? C3B BPH 309 M 1 HETATM 27 C CAB BPH . . . K 5 -12.883 -23.063 7.236 1 25.46 ? CAB BPH 309 M 1 HETATM 28 C CBB BPH . . . K 5 -14.158 -22.806 6.452 1 33.63 ? CBB BPH 309 M 1 HETATM 29 O OBB BPH . . . K 5 -12.87 -23.611 8.315 1 23.99 ? OBB BPH 309 M 1 HETATM 30 C C2B BPH . . . K 5 -10.825 -21.65 7.395 1 17.62 ? C2B BPH 309 M 1 HETATM 31 C CMB BPH . . . K 5 -10.713 -21.725 8.817 1 16.64 ? CMB BPH 309 M 1 HETATM 32 C C1B BPH . . . K 5 -9.918 -20.972 6.496 1 21.99 ? C1B BPH 309 M 1 HETATM 33 N NB BPH . . . K 5 -10.422 -21.188 5.233 1 22.02 ? NB BPH 309 M 1 HETATM 34 C CHB BPH . . . K 5 -8.629 -20.194 6.892 1 23.85 ? CHB BPH 309 M 1 HETATM 35 C C4A BPH . . . K 5 -7.566 -19.543 6.029 1 22.09 ? C4A BPH 309 M 1 HETATM 36 C C3A BPH . . . K 5 -6.29 -18.876 6.604 1 20.43 ? C3A BPH 309 M 1 HETATM 37 C CMA BPH . . . K 5 -5.54 -19.808 7.401 1 27.15 ? CMA BPH 309 M 1 HETATM 38 C C2A BPH . . . K 5 -5.522 -18.424 5.519 1 18.2 ? C2A BPH 309 M 1 HETATM 39 C C1A BPH . . . K 5 -6.46 -18.968 4.327 1 24.36 ? C1A BPH 309 M 1 HETATM 40 N NA BPH . . . K 5 -7.579 -19.554 4.78 1 24.51 ? NA BPH 309 M 1 HETATM 41 C CAA BPH . . . K 5 -5.359 -16.738 5.602 1 20.96 ? CAA BPH 309 M 1 HETATM 42 C CBA BPH . . . K 5 -5.321 -16.192 7.106 1 27.28 ? CBA BPH 309 M 1 HETATM 43 C CGA BPH . . . K 5 -4.621 -14.813 7.377 1 28.49 ? CGA BPH 309 M 1 HETATM 44 O O1A BPH . . . K 5 -4.979 -13.769 6.844 1 27.54 ? O1A BPH 309 M 1 HETATM 45 O O2A BPH . . . K 5 -3.705 -14.789 8.262 1 31.95 ? O2A BPH 309 M 1 HETATM 46 C C1 BPH . . . K 5 -3.397 -13.555 8.827 1 29.48 ? C1 BPH 309 M 1 HETATM 47 C C2 BPH . . . K 5 -2.916 -13.715 10.39 1 18.48 ? C2 BPH 309 M 1 HETATM 48 C C3 BPH . . . K 5 -3.573 -14.316 11.414 1 23.71 ? C3 BPH 309 M 1 HETATM 49 C C4 BPH . . . K 5 -4.915 -14.952 11.278 1 29.07 ? C4 BPH 309 M 1 HETATM 50 C C5 BPH . . . K 5 -3.046 -14.426 12.882 1 33.2 ? C5 BPH 309 M 1 HETATM 51 C C6 BPH . . . K 5 -2.718 -15.876 13.327 1 40.45 ? C6 BPH 309 M 1 HETATM 52 C C7 BPH . . . K 5 -2.942 -16.137 14.846 1 42.87 ? C7 BPH 309 M 1 HETATM 53 C C8 BPH . . . K 5 -1.818 -16.9 15.582 1 45.68 ? C8 BPH 309 M 1 HETATM 54 C C9 BPH . . . K 5 -1.345 -18.154 14.838 1 45.09 ? C9 BPH 309 M 1 HETATM 55 C C10 BPH . . . K 5 -2.264 -17.309 16.994 1 50.97 ? C10 BPH 309 M 1 HETATM 56 C C11 BPH . . . K 5 -1.188 -17.338 18.079 1 50.02 ? C11 BPH 309 M 1 HETATM 57 C C12 BPH . . . K 5 -1.61 -16.445 19.243 1 52.13 ? C12 BPH 309 M 1 HETATM 58 C C13 BPH . . . K 5 -0.613 -16.386 20.422 1 55.35 ? C13 BPH 309 M 1 HETATM 59 C C14 BPH . . . K 5 -1.213 -15.555 21.578 1 53.58 ? C14 BPH 309 M 1 HETATM 60 C C15 BPH . . . K 5 0.811 -15.898 20.03 1 54.87 ? C15 BPH 309 M 1 HETATM 61 C C16 BPH . . . K 5 2.047 -16.543 20.78 1 47.67 ? C16 BPH 309 M 1 HETATM 62 C C17 BPH . . . K 5 1.77 -16.847 22.274 1 42.35 ? C17 BPH 309 M 1 HETATM 63 C C18 BPH . . . K 5 1.403 -18.307 22.619 1 37.13 ? C18 BPH 309 M 1 HETATM 64 C C19 BPH . . . K 5 0.215 -18.885 21.884 1 34.45 ? C19 BPH 309 M 1 HETATM 65 C C20 BPH . . . K 5 1.214 -18.541 24.1 1 38.24 ? C20 BPH 309 M 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 65 #