data_8VTK # _model_server_result.job_id aZRQ2cTbjP5CcSLSB_fuQw _model_server_result.datetime_utc '2025-07-31 15:17:42' _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 8vtk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":304}' # _entry.id 8VTK # _exptl.entry_id 8VTK _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 120 _cell.entry_id 8VTK _cell.length_a 140.95 _cell.length_b 140.95 _cell.length_c 186.72 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VTK _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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,N,O,P,Q,R,S _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 E N N ? 5 G 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 covale ? covale1 C C LEU 208 M LEU 209 1_555 C N 2L5 209 M 2L5 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale2 C C 2L5 209 M 2L5 210 1_555 C N GLY 210 M GLY 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? # _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 241 n n CGD O2D BPH sing 242 n n CGD CBD BPH sing 243 n n O2D CED BPH sing 244 n n CBD CHA BPH sing 245 n n CBD CAD BPH sing 246 n n CHA C4D BPH doub 247 n y CHA C1A BPH sing 248 n y C4D C3D BPH sing 249 n y C4D ND BPH sing 250 n y C3D CAD BPH sing 251 n n C3D C2D BPH doub 252 n y CAD OBD BPH doub 253 n n C2D CMD BPH sing 254 n n C2D C1D BPH sing 255 n y C1D ND BPH sing 256 n y C1D CHD BPH doub 257 n y CHD C4C BPH sing 258 n y C4C C3C BPH sing 259 n n C4C NC BPH doub 260 n y C3C CAC BPH sing 261 n n C3C C2C BPH sing 262 n n CAC CBC BPH sing 263 n n C2C CMC BPH sing 264 n n C2C C1C BPH sing 265 n n C1C NC BPH sing 266 n y C1C CHC BPH doub 267 n y CHC C4B BPH sing 268 n y C4B C3B BPH doub 269 n y C4B NB BPH sing 270 n y C3B CAB BPH sing 271 n n C3B C2B BPH sing 272 n y CAB CBB BPH sing 273 n n CAB OBB BPH doub 274 n n C2B CMB BPH sing 275 n n C2B C1B BPH doub 276 n y C1B NB BPH sing 277 n y C1B CHB BPH sing 278 n y CHB C4A BPH doub 279 n y C4A C3A BPH sing 280 n n C4A NA BPH sing 281 n y C3A CMA BPH sing 282 n n C3A C2A BPH sing 283 n n C2A C1A BPH sing 284 n n C2A CAA BPH sing 285 n n C1A NA BPH doub 286 n y CAA CBA BPH sing 287 n n CBA CGA BPH sing 288 n n CGA O1A BPH doub 289 n n CGA O2A BPH sing 290 n n O2A C1 BPH sing 291 n n C1 C2 BPH sing 292 n n C2 C3 BPH doub 293 e n C3 C4 BPH sing 294 n n C3 C5 BPH sing 295 n n C5 C6 BPH sing 296 n n C6 C7 BPH sing 297 n n C7 C8 BPH sing 298 n n C8 C9 BPH sing 299 n n C8 C10 BPH sing 300 n n C10 C11 BPH sing 301 n n C11 C12 BPH sing 302 n n C12 C13 BPH sing 303 n n C13 C14 BPH sing 304 n n C13 C15 BPH sing 305 n n C15 C16 BPH sing 306 n n C16 C17 BPH sing 307 n n C17 C18 BPH sing 308 n n C18 C19 BPH sing 309 n n C18 C20 BPH sing 310 n n CED HED1 BPH sing 311 n n CED HED2 BPH sing 312 n n CED HED3 BPH sing 313 n n CBD HBD BPH sing 314 n n CMD HMD1 BPH sing 315 n n CMD HMD2 BPH sing 316 n n CMD HMD3 BPH sing 317 n n ND HD BPH sing 318 n n CHD HHD BPH sing 319 n n C3C H3C BPH sing 320 n n CAC HAC1 BPH sing 321 n n CAC HAC2 BPH sing 322 n n CBC HBC1 BPH sing 323 n n CBC HBC2 BPH sing 324 n n CBC HBC3 BPH sing 325 n n C2C H2C BPH sing 326 n n CMC HMC1 BPH sing 327 n n CMC HMC2 BPH sing 328 n n CMC HMC3 BPH sing 329 n n CHC HHC BPH sing 330 n n CBB HBB1 BPH sing 331 n n CBB HBB2 BPH sing 332 n n CBB HBB3 BPH sing 333 n n CMB HMB1 BPH sing 334 n n CMB HMB2 BPH sing 335 n n CMB HMB3 BPH sing 336 n n NB HB BPH sing 337 n n CHB HHB BPH sing 338 n n C3A H3A BPH sing 339 n n CMA HMA1 BPH sing 340 n n CMA HMA2 BPH sing 341 n n CMA HMA3 BPH sing 342 n n C2A H2A BPH sing 343 n n CAA HAA1 BPH sing 344 n n CAA HAA2 BPH sing 345 n n CBA HBA1 BPH sing 346 n n CBA HBA2 BPH sing 347 n n C1 H1C1 BPH sing 348 n n C1 H1C2 BPH sing 349 n n C2 H2 BPH sing 350 n n C4 H4C1 BPH sing 351 n n C4 H4C2 BPH sing 352 n n C4 H4C3 BPH sing 353 n n C5 H5C1 BPH sing 354 n n C5 H5C2 BPH sing 355 n n C6 H6C1 BPH sing 356 n n C6 H6C2 BPH sing 357 n n C7 H7C1 BPH sing 358 n n C7 H7C2 BPH sing 359 n n C8 H8 BPH sing 360 n n C9 H9C1 BPH sing 361 n n C9 H9C2 BPH sing 362 n n C9 H9C3 BPH sing 363 n n C10 H101 BPH sing 364 n n C10 H102 BPH sing 365 n n C11 H111 BPH sing 366 n n C11 H112 BPH sing 367 n n C12 H121 BPH sing 368 n n C12 H122 BPH sing 369 n n C13 H13 BPH sing 370 n n C14 H141 BPH sing 371 n n C14 H142 BPH sing 372 n n C14 H143 BPH sing 373 n n C15 H151 BPH sing 374 n n C15 H152 BPH sing 375 n n C16 H161 BPH sing 376 n n C16 H162 BPH sing 377 n n C17 H171 BPH sing 378 n n C17 H172 BPH sing 379 n n C18 H18 BPH sing 380 n n C19 H191 BPH sing 381 n n C19 H192 BPH sing 382 n n C19 H193 BPH sing 383 n n C20 H201 BPH sing 384 n n C20 H202 BPH sing 385 n n C20 H203 BPH sing 386 n n # _atom_sites.entry_id 8VTK _atom_sites.fract_transf_matrix[1][1] 0.007095 _atom_sites.fract_transf_matrix[1][2] 0.004096 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008192 _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] 0.005356 _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 FE L 1 301 406 FE FE . E 5 BPH L 1 302 407 BPH BPH . F 6 BCL L 1 303 301 BCL BCL . G 5 BPH L 1 304 302 BPH BPH . H 7 U10 L 1 305 303 U10 U10 . I 6 BCL L 1 306 304 BCL BCL . J 8 CL L 1 307 306 CL CL . K 6 BCL M 1 401 401 BCL BCL . L 9 LDA M 1 402 403 LDA LDA . M 9 LDA M 1 403 405 LDA LDA . N 10 SPO M 1 404 409 SPO SPO . O 11 CDL M 1 405 410 CDL CDL . P 6 BCL M 1 406 305 BCL BCL . Q 12 HOH H 1 301 3 HOH HOH . Q 12 HOH H 2 302 7 HOH HOH . Q 12 HOH H 3 303 2 HOH HOH . Q 12 HOH H 4 304 12 HOH HOH . Q 12 HOH H 5 305 9 HOH HOH . R 12 HOH L 1 401 15 HOH HOH . R 12 HOH L 2 402 6 HOH HOH . R 12 HOH L 3 403 11 HOH HOH . R 12 HOH L 4 404 1 HOH HOH . S 12 HOH M 1 501 13 HOH HOH . S 12 HOH M 2 502 8 HOH HOH . S 12 HOH M 3 503 14 HOH HOH . S 12 HOH M 4 504 17 HOH HOH . S 12 HOH M 5 505 16 HOH HOH . S 12 HOH M 6 506 19 HOH HOH . S 12 HOH M 7 507 20 HOH HOH . S 12 HOH M 8 508 10 HOH HOH . S 12 HOH M 9 509 5 HOH HOH . S 12 HOH M 10 510 18 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 O O1D BPH . . . G 5 -58.344 40.641 10.091 1 55.31 ? O1D BPH 304 L 1 HETATM 2 C CGD BPH . . . G 5 -57.667 40.354 9.132 1 52.7 ? CGD BPH 304 L 1 HETATM 3 O O2D BPH . . . G 5 -56.49 39.775 9.246 1 51.04 ? O2D BPH 304 L 1 HETATM 4 C CED BPH . . . G 5 -56.099 39.399 10.568 1 44.91 ? CED BPH 304 L 1 HETATM 5 C CBD BPH . . . G 5 -58.053 40.6 7.75 1 52.05 ? CBD BPH 304 L 1 HETATM 6 C CHA BPH . . . G 5 -57.768 39.402 6.845 1 49.03 ? CHA BPH 304 L 1 HETATM 7 C C4D BPH . . . G 5 -56.867 39.942 5.902 1 49.32 ? C4D BPH 304 L 1 HETATM 8 C C3D BPH . . . G 5 -56.596 41.315 5.997 1 47.92 ? C3D BPH 304 L 1 HETATM 9 C CAD BPH . . . G 5 -57.278 41.787 7.108 1 47.76 ? CAD BPH 304 L 1 HETATM 10 O OBD BPH . . . G 5 -57.329 42.914 7.582 1 50.16 ? OBD BPH 304 L 1 HETATM 11 C C2D BPH . . . G 5 -55.73 41.648 4.983 1 50.55 ? C2D BPH 304 L 1 HETATM 12 C CMD BPH . . . G 5 -55.141 42.974 4.639 1 50.37 ? CMD BPH 304 L 1 HETATM 13 C C1D BPH . . . G 5 -55.491 40.441 4.289 1 49.28 ? C1D BPH 304 L 1 HETATM 14 N ND BPH . . . G 5 -56.212 39.371 4.847 1 48.46 ? ND BPH 304 L 1 HETATM 15 C CHD BPH . . . G 5 -54.635 40.215 3.184 1 49.81 ? CHD BPH 304 L 1 HETATM 16 C C4C BPH . . . G 5 -54.444 39.032 2.498 1 52.28 ? C4C BPH 304 L 1 HETATM 17 C C3C BPH . . . G 5 -53.396 38.804 1.401 1 47.52 ? C3C BPH 304 L 1 HETATM 18 C CAC BPH . . . G 5 -53.217 39.965 0.4 1 44.3 ? CAC BPH 304 L 1 HETATM 19 C CBC BPH . . . G 5 -54.557 40.489 -0.154 1 49.72 ? CBC BPH 304 L 1 HETATM 20 C C2C BPH . . . G 5 -53.921 37.503 0.777 1 46.61 ? C2C BPH 304 L 1 HETATM 21 C CMC BPH . . . G 5 -52.819 36.6 0.243 1 44.32 ? CMC BPH 304 L 1 HETATM 22 C C1C BPH . . . G 5 -54.685 36.913 1.92 1 49.26 ? C1C BPH 304 L 1 HETATM 23 N NC BPH . . . G 5 -55.066 37.849 2.844 1 48.12 ? NC BPH 304 L 1 HETATM 24 C CHC BPH . . . G 5 -55.103 35.581 1.988 1 47.4 ? CHC BPH 304 L 1 HETATM 25 C C4B BPH . . . G 5 -55.809 34.839 2.947 1 48.69 ? C4B BPH 304 L 1 HETATM 26 C C3B BPH . . . G 5 -56.089 33.41 2.942 1 56.02 ? C3B BPH 304 L 1 HETATM 27 C CAB BPH . . . G 5 -55.579 32.437 1.935 1 56.31 ? CAB BPH 304 L 1 HETATM 28 C CBB BPH . . . G 5 -54.299 32.683 1.209 1 46.42 ? CBB BPH 304 L 1 HETATM 29 O OBB BPH . . . G 5 -56.148 31.365 1.614 1 53.44 ? OBB BPH 304 L 1 HETATM 30 C C2B BPH . . . G 5 -56.911 33.195 4.073 1 48.7 ? C2B BPH 304 L 1 HETATM 31 C CMB BPH . . . G 5 -57.609 31.931 4.504 1 49.54 ? CMB BPH 304 L 1 HETATM 32 C C1B BPH . . . G 5 -57.004 34.416 4.775 1 50.53 ? C1B BPH 304 L 1 HETATM 33 N NB BPH . . . G 5 -56.349 35.418 4.054 1 48.77 ? NB BPH 304 L 1 HETATM 34 C CHB BPH . . . G 5 -57.678 34.661 6.041 1 50.87 ? CHB BPH 304 L 1 HETATM 35 C C4A BPH . . . G 5 -57.98 35.858 6.697 1 49.58 ? C4A BPH 304 L 1 HETATM 36 C C3A BPH . . . G 5 -58.573 35.987 8.068 1 45.87 ? C3A BPH 304 L 1 HETATM 37 C CMA BPH . . . G 5 -57.52 35.719 9.113 1 36.53 ? CMA BPH 304 L 1 HETATM 38 C C2A BPH . . . G 5 -59.053 37.451 8.071 1 46.36 ? C2A BPH 304 L 1 HETATM 39 C C1A BPH . . . G 5 -58.091 38.073 7.066 1 50.28 ? C1A BPH 304 L 1 HETATM 40 N NA BPH . . . G 5 -57.539 37.101 6.248 1 50.01 ? NA BPH 304 L 1 HETATM 41 C CAA BPH . . . G 5 -60.548 37.594 7.689 1 41.89 ? CAA BPH 304 L 1 HETATM 42 C CBA BPH . . . G 5 -61.458 37.077 8.804 1 41.62 ? CBA BPH 304 L 1 HETATM 43 C CGA BPH . . . G 5 -62.902 37.248 8.521 1 49.86 ? CGA BPH 304 L 1 HETATM 44 O O1A BPH . . . G 5 -63.368 37.753 7.475 1 50.23 ? O1A BPH 304 L 1 HETATM 45 O O2A BPH . . . G 5 -63.656 36.804 9.56 1 51.28 ? O2A BPH 304 L 1 HETATM 46 C C1 BPH . . . G 5 -65.122 36.898 9.38 1 48.09 ? C1 BPH 304 L 1 HETATM 47 C C2 BPH . . . G 5 -65.567 35.491 9.027 1 51.07 ? C2 BPH 304 L 1 HETATM 48 C C3 BPH . . . G 5 -65.515 34.502 9.924 1 57.91 ? C3 BPH 304 L 1 HETATM 49 C C4 BPH . . . G 5 -65.02 34.622 11.375 1 46.95 ? C4 BPH 304 L 1 HETATM 50 C C5 BPH . . . G 5 -65.958 33.081 9.564 1 55.27 ? C5 BPH 304 L 1 HETATM 51 C C6 BPH . . . G 5 -67.068 32.988 8.565 1 56.34 ? C6 BPH 304 L 1 HETATM 52 C C7 BPH . . . G 5 -67.393 31.531 8.274 1 61.68 ? C7 BPH 304 L 1 HETATM 53 C C8 BPH . . . G 5 -68.245 31.235 7.019 1 62.27 ? C8 BPH 304 L 1 HETATM 54 C C9 BPH . . . G 5 -69.625 31.944 6.992 1 59.08 ? C9 BPH 304 L 1 HETATM 55 C C10 BPH . . . G 5 -68.439 29.717 6.978 1 64.31 ? C10 BPH 304 L 1 HETATM 56 C C11 BPH . . . G 5 -67.18 29.205 6.351 1 57.48 ? C11 BPH 304 L 1 HETATM 57 C C12 BPH . . . G 5 -67.204 29.569 4.874 1 59.52 ? C12 BPH 304 L 1 HETATM 58 C C13 BPH . . . G 5 -65.829 29.392 4.218 1 59.37 ? C13 BPH 304 L 1 HETATM 59 C C14 BPH . . . G 5 -65.804 29.574 2.689 1 50.59 ? C14 BPH 304 L 1 HETATM 60 C C15 BPH . . . G 5 -65.327 28.001 4.605 1 54.28 ? C15 BPH 304 L 1 HETATM 61 C C16 BPH . . . G 5 -64.034 27.735 3.841 1 56.03 ? C16 BPH 304 L 1 HETATM 62 C C17 BPH . . . G 5 -62.984 26.72 4.382 1 57.31 ? C17 BPH 304 L 1 HETATM 63 C C18 BPH . . . G 5 -62.474 25.71 3.331 1 55.2 ? C18 BPH 304 L 1 HETATM 64 C C19 BPH . . . G 5 -61.224 24.976 3.874 1 50.94 ? C19 BPH 304 L 1 HETATM 65 C C20 BPH . . . G 5 -62.058 26.318 1.99 1 51.34 ? C20 BPH 304 L 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 356 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 65 #