data_4YL3 # _model_server_result.job_id kz2xfPgurnLyfiAZBQS_yQ _model_server_result.datetime_utc '2024-12-26 10:56:45' _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 4yl3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":203}' # _entry.id 4YL3 # _exptl.entry_id 4YL3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 292.369 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'octyl beta-D-glucopyranoside' _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 4YL3 _cell.length_a 76.434 _cell.length_b 76.434 _cell.length_c 123.264 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YL3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 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 # _chem_comp.formula 'C14 H28 O6' _chem_comp.formula_weight 292.369 _chem_comp.id BOG _chem_comp.mon_nstd_flag n _chem_comp.name 'octyl beta-D-glucopyranoside' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 'Beta-Octylglucoside;octyl beta-D-glucoside;octyl D-glucoside;octyl glucoside' # 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 C1 O1 BOG sing 116 n n C1 C2 BOG sing 117 n n C1 O5 BOG sing 118 n n C1 H1 BOG sing 119 n n O1 C1' BOG sing 120 n n C2 O2 BOG sing 121 n n C2 C3 BOG sing 122 n n C2 H2 BOG sing 123 n n O2 HO2 BOG sing 124 n n C3 O3 BOG sing 125 n n C3 C4 BOG sing 126 n n C3 H3 BOG sing 127 n n O3 HO3 BOG sing 128 n n C4 O4 BOG sing 129 n n C4 C5 BOG sing 130 n n C4 H4 BOG sing 131 n n O4 HO4 BOG sing 132 n n C5 O5 BOG sing 133 n n C5 C6 BOG sing 134 n n C5 H5 BOG sing 135 n n C6 O6 BOG sing 136 n n C6 H61 BOG sing 137 n n C6 H62 BOG sing 138 n n O6 HO6 BOG sing 139 n n C1' C2' BOG sing 140 n n C1' "H1'1" BOG sing 141 n n C1' "H1'2" BOG sing 142 n n C2' C3' BOG sing 143 n n C2' "H2'1" BOG sing 144 n n C2' "H2'2" BOG sing 145 n n C3' C4' BOG sing 146 n n C3' "H3'1" BOG sing 147 n n C3' "H3'2" BOG sing 148 n n C4' C5' BOG sing 149 n n C4' "H4'1" BOG sing 150 n n C4' "H4'2" BOG sing 151 n n C5' C6' BOG sing 152 n n C5' "H5'1" BOG sing 153 n n C5' "H5'2" BOG sing 154 n n C6' C7' BOG sing 155 n n C6' "H6'1" BOG sing 156 n n C6' "H6'2" BOG sing 157 n n C7' C8' BOG sing 158 n n C7' "H7'1" BOG sing 159 n n C7' "H7'2" BOG sing 160 n n C8' "H8'1" BOG sing 161 n n C8' "H8'2" BOG sing 162 n n C8' "H8'3" BOG sing 163 n n # _pdbx_chem_comp_identifier.comp_id BOG _pdbx_chem_comp_identifier.identifier b-octylglucoside _pdbx_chem_comp_identifier.type 'IUPAC CARBOHYDRATE SYMBOL' _pdbx_chem_comp_identifier.program PDB-CARE _pdbx_chem_comp_identifier.program_version 1 # _atom_sites.entry_id 4YL3 _atom_sites.fract_transf_matrix[1][1] 0.013083 _atom_sites.fract_transf_matrix[1][2] 0.007554 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015107 _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] 0.008113 _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 4U9 A 1 201 1 4U9 4U9 . C 3 GSH A 1 202 1 GSH GTT . D 4 BOG A 1 203 2 BOG BOG . E 4 BOG A 1 204 3 BOG BOG . F 5 PG4 A 1 205 4 PG4 PG4 . G 6 HOH A 1 301 58 HOH HOH . G 6 HOH A 2 302 124 HOH HOH . G 6 HOH A 3 303 90 HOH HOH . G 6 HOH A 4 304 1 HOH HOH . G 6 HOH A 5 305 69 HOH HOH . G 6 HOH A 6 306 18 HOH HOH . G 6 HOH A 7 307 22 HOH HOH . G 6 HOH A 8 308 26 HOH HOH . G 6 HOH A 9 309 24 HOH HOH . G 6 HOH A 10 310 35 HOH HOH . G 6 HOH A 11 311 108 HOH HOH . G 6 HOH A 12 312 17 HOH HOH . G 6 HOH A 13 313 23 HOH HOH . G 6 HOH A 14 314 72 HOH HOH . G 6 HOH A 15 315 29 HOH HOH . G 6 HOH A 16 316 10 HOH HOH . G 6 HOH A 17 317 51 HOH HOH . G 6 HOH A 18 318 73 HOH HOH . G 6 HOH A 19 319 82 HOH HOH . G 6 HOH A 20 320 36 HOH HOH . G 6 HOH A 21 321 27 HOH HOH . G 6 HOH A 22 322 5 HOH HOH . G 6 HOH A 23 323 7 HOH HOH . G 6 HOH A 24 324 61 HOH HOH . G 6 HOH A 25 325 55 HOH HOH . G 6 HOH A 26 326 70 HOH HOH . G 6 HOH A 27 327 43 HOH HOH . G 6 HOH A 28 328 13 HOH HOH . G 6 HOH A 29 329 85 HOH HOH . G 6 HOH A 30 330 42 HOH HOH . G 6 HOH A 31 331 99 HOH HOH . G 6 HOH A 32 332 80 HOH HOH . G 6 HOH A 33 333 8 HOH HOH . G 6 HOH A 34 334 6 HOH HOH . G 6 HOH A 35 335 30 HOH HOH . G 6 HOH A 36 336 53 HOH HOH . G 6 HOH A 37 337 19 HOH HOH . G 6 HOH A 38 338 16 HOH HOH . G 6 HOH A 39 339 49 HOH HOH . G 6 HOH A 40 340 75 HOH HOH . G 6 HOH A 41 341 84 HOH HOH . G 6 HOH A 42 342 20 HOH HOH . G 6 HOH A 43 343 9 HOH HOH . G 6 HOH A 44 344 50 HOH HOH . G 6 HOH A 45 345 39 HOH HOH . G 6 HOH A 46 346 138 HOH HOH . G 6 HOH A 47 347 4 HOH HOH . G 6 HOH A 48 348 44 HOH HOH . G 6 HOH A 49 349 38 HOH HOH . G 6 HOH A 50 350 33 HOH HOH . G 6 HOH A 51 351 41 HOH HOH . G 6 HOH A 52 352 11 HOH HOH . G 6 HOH A 53 353 54 HOH HOH . G 6 HOH A 54 354 21 HOH HOH . G 6 HOH A 55 355 37 HOH HOH . G 6 HOH A 56 356 47 HOH HOH . G 6 HOH A 57 357 12 HOH HOH . G 6 HOH A 58 358 64 HOH HOH . G 6 HOH A 59 359 59 HOH HOH . G 6 HOH A 60 360 52 HOH HOH . G 6 HOH A 61 361 15 HOH HOH . G 6 HOH A 62 362 31 HOH HOH . G 6 HOH A 63 363 67 HOH HOH . G 6 HOH A 64 364 81 HOH HOH . G 6 HOH A 65 365 71 HOH HOH . G 6 HOH A 66 366 40 HOH HOH . G 6 HOH A 67 367 28 HOH HOH . G 6 HOH A 68 368 77 HOH HOH . G 6 HOH A 69 369 107 HOH HOH . G 6 HOH A 70 370 126 HOH HOH . G 6 HOH A 71 371 125 HOH HOH . G 6 HOH A 72 372 62 HOH HOH . G 6 HOH A 73 373 25 HOH HOH . G 6 HOH A 74 374 101 HOH HOH . G 6 HOH A 75 375 79 HOH HOH . G 6 HOH A 76 376 60 HOH HOH . G 6 HOH A 77 377 129 HOH HOH . G 6 HOH A 78 378 86 HOH HOH . G 6 HOH A 79 379 78 HOH HOH . G 6 HOH A 80 380 76 HOH HOH . G 6 HOH A 81 381 14 HOH HOH . G 6 HOH A 82 382 48 HOH HOH . G 6 HOH A 83 383 32 HOH HOH . G 6 HOH A 84 384 46 HOH HOH . G 6 HOH A 85 385 45 HOH HOH . G 6 HOH A 86 386 57 HOH HOH . G 6 HOH A 87 387 66 HOH HOH . G 6 HOH A 88 388 98 HOH HOH . G 6 HOH A 89 389 127 HOH HOH . G 6 HOH A 90 390 97 HOH HOH . G 6 HOH A 91 391 110 HOH HOH . G 6 HOH A 92 392 133 HOH HOH . G 6 HOH A 93 393 115 HOH HOH . G 6 HOH A 94 394 122 HOH HOH . G 6 HOH A 95 395 106 HOH HOH . G 6 HOH A 96 396 94 HOH HOH . G 6 HOH A 97 397 100 HOH HOH . G 6 HOH A 98 398 102 HOH HOH . G 6 HOH A 99 399 56 HOH HOH . G 6 HOH A 100 400 63 HOH HOH . G 6 HOH A 101 401 136 HOH HOH . G 6 HOH A 102 402 140 HOH HOH . G 6 HOH A 103 403 134 HOH HOH . G 6 HOH A 104 404 68 HOH HOH . G 6 HOH A 105 405 103 HOH HOH . G 6 HOH A 106 406 131 HOH HOH . G 6 HOH A 107 407 111 HOH HOH . G 6 HOH A 108 408 88 HOH HOH . G 6 HOH A 109 409 95 HOH HOH . G 6 HOH A 110 410 83 HOH HOH . G 6 HOH A 111 411 2 HOH HOH . G 6 HOH A 112 412 117 HOH HOH . G 6 HOH A 113 413 89 HOH HOH . G 6 HOH A 114 414 92 HOH HOH . G 6 HOH A 115 415 74 HOH HOH . G 6 HOH A 116 416 112 HOH HOH . G 6 HOH A 117 417 128 HOH HOH . G 6 HOH A 118 418 137 HOH HOH . G 6 HOH A 119 419 109 HOH HOH . G 6 HOH A 120 420 34 HOH HOH . G 6 HOH A 121 421 120 HOH HOH . G 6 HOH A 122 422 104 HOH HOH . G 6 HOH A 123 423 116 HOH HOH . G 6 HOH A 124 424 93 HOH HOH . G 6 HOH A 125 425 123 HOH HOH . G 6 HOH A 126 426 139 HOH HOH . G 6 HOH A 127 427 114 HOH HOH . G 6 HOH A 128 428 65 HOH HOH . G 6 HOH A 129 429 3 HOH HOH . G 6 HOH A 130 430 130 HOH HOH . G 6 HOH A 131 431 87 HOH HOH . G 6 HOH A 132 432 96 HOH HOH . G 6 HOH A 133 433 119 HOH HOH . G 6 HOH A 134 434 113 HOH HOH . G 6 HOH A 135 435 91 HOH HOH . G 6 HOH A 136 436 105 HOH HOH . G 6 HOH A 137 437 118 HOH HOH . G 6 HOH A 138 438 121 HOH HOH . G 6 HOH A 139 439 135 HOH HOH . G 6 HOH A 140 440 132 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 C1 BOG . . . D 4 10.041 19.941 9.932 1 42.45 ? C1 BOG 203 A 1 HETATM 2 O O1 BOG . . . D 4 9.989 19.185 11.142 1 39.19 ? O1 BOG 203 A 1 HETATM 3 C C2 BOG . . . D 4 10.087 19.002 8.726 1 38.62 ? C2 BOG 203 A 1 HETATM 4 O O2 BOG . . . D 4 11.293 18.237 8.756 1 33.53 ? O2 BOG 203 A 1 HETATM 5 C C3 BOG . . . D 4 10.038 19.792 7.418 1 36.63 ? C3 BOG 203 A 1 HETATM 6 O O3 BOG . . . D 4 9.927 18.895 6.307 1 34.41 ? O3 BOG 203 A 1 HETATM 7 C C4 BOG . . . D 4 8.871 20.775 7.411 1 38.25 ? C4 BOG 203 A 1 HETATM 8 O O4 BOG . . . D 4 8.971 21.615 6.254 1 35.09 ? O4 BOG 203 A 1 HETATM 9 C C5 BOG . . . D 4 8.874 21.62 8.687 1 41.54 ? C5 BOG 203 A 1 HETATM 10 O O5 BOG . . . D 4 8.88 20.773 9.842 1 44.72 ? O5 BOG 203 A 1 HETATM 11 C C6 BOG . . . D 4 7.662 22.538 8.765 1 34.42 ? C6 BOG 203 A 1 HETATM 12 O O6 BOG . . . D 4 6.469 21.787 9.014 1 34.88 ? O6 BOG 203 A 1 HETATM 13 C C1' BOG . . . D 4 10.496 19.915 12.261 1 49.9 ? C1' BOG 203 A 1 HETATM 14 C C2' BOG . . . D 4 10.002 19.269 13.551 1 47.72 ? C2' BOG 203 A 1 HETATM 15 C C3' BOG . . . D 4 10.643 19.927 14.769 1 56.68 ? C3' BOG 203 A 1 HETATM 16 C C4' BOG . . . D 4 10.23 19.217 16.053 1 58.65 ? C4' BOG 203 A 1 HETATM 17 C C5' BOG . . . D 4 9.235 20.055 16.849 1 63.35 ? C5' BOG 203 A 1 HETATM 18 C C6' BOG . . . D 4 9.87 20.601 18.123 1 65.18 ? C6' BOG 203 A 1 HETATM 19 C C7' BOG . . . D 4 9.261 19.953 19.361 1 62.52 ? C7' BOG 203 A 1 HETATM 20 C C8' BOG . . . D 4 10.337 19.561 20.35 1 66.34 ? C8' BOG 203 A 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 339 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 20 #