data_3NK5 # _model_server_result.job_id qFuH5q8NTkkApKdysU5E1g _model_server_result.datetime_utc '2025-04-06 04:18:19' _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 3nk5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":233}' # _entry.id 3NK5 # _exptl.entry_id 3NK5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 292.369 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'octyl beta-D-glucopyranoside' _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 3NK5 _cell.length_a 92.424 _cell.length_b 92.424 _cell.length_c 78.819 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NK5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 75 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 4' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,G 1 1,2,3,4 B,F,H 2 1,5,6,7 # 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 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 5 'crystal symmetry operation' 2_465 -x-1,-y+1,z -1 0 0 0 -1 0 0 0 1 -92.424 92.424 0 6 'crystal symmetry operation' 3_565 -y,x+1,z 0 -1 0 1 0 0 0 0 1 0 92.424 0 7 'crystal symmetry operation' 4_455 y-1,-x,z 0 1 0 -1 0 0 0 0 1 -92.424 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N ? 2 E N N ? 2 F 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 70 n n C1 C2 BOG sing 71 n n C1 O5 BOG sing 72 n n C1 H1 BOG sing 73 n n O1 C1' BOG sing 74 n n C2 O2 BOG sing 75 n n C2 C3 BOG sing 76 n n C2 H2 BOG sing 77 n n O2 HO2 BOG sing 78 n n C3 O3 BOG sing 79 n n C3 C4 BOG sing 80 n n C3 H3 BOG sing 81 n n O3 HO3 BOG sing 82 n n C4 O4 BOG sing 83 n n C4 C5 BOG sing 84 n n C4 H4 BOG sing 85 n n O4 HO4 BOG sing 86 n n C5 O5 BOG sing 87 n n C5 C6 BOG sing 88 n n C5 H5 BOG sing 89 n n C6 O6 BOG sing 90 n n C6 H61 BOG sing 91 n n C6 H62 BOG sing 92 n n O6 HO6 BOG sing 93 n n C1' C2' BOG sing 94 n n C1' "H1'1" BOG sing 95 n n C1' "H1'2" BOG sing 96 n n C2' C3' BOG sing 97 n n C2' "H2'1" BOG sing 98 n n C2' "H2'2" BOG sing 99 n n C3' C4' BOG sing 100 n n C3' "H3'1" BOG sing 101 n n C3' "H3'2" BOG sing 102 n n C4' C5' BOG sing 103 n n C4' "H4'1" BOG sing 104 n n C4' "H4'2" BOG sing 105 n n C5' C6' BOG sing 106 n n C5' "H5'1" BOG sing 107 n n C5' "H5'2" BOG sing 108 n n C6' C7' BOG sing 109 n n C6' "H6'1" BOG sing 110 n n C6' "H6'2" BOG sing 111 n n C7' C8' BOG sing 112 n n C7' "H7'1" BOG sing 113 n n C7' "H7'2" BOG sing 114 n n C8' "H8'1" BOG sing 115 n n C8' "H8'2" BOG sing 116 n n C8' "H8'3" BOG sing 117 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 3NK5 _atom_sites.fract_transf_matrix[1][1] 0.01082 _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] 0.01082 _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] 0.012687 _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 C 2 BOG A 1 232 1 BOG BOG . D 2 BOG A 1 233 2 BOG BOG . E 2 BOG A 1 234 4 BOG BOG . F 2 BOG B 1 232 3 BOG BOG . G 3 HOH A 1 235 1 HOH HOH . G 3 HOH A 2 236 3 HOH HOH . G 3 HOH A 3 237 4 HOH HOH . G 3 HOH A 4 238 5 HOH HOH . G 3 HOH A 5 239 8 HOH HOH . G 3 HOH A 6 240 9 HOH HOH . G 3 HOH A 7 241 11 HOH HOH . G 3 HOH A 8 242 12 HOH HOH . G 3 HOH A 9 243 13 HOH HOH . G 3 HOH A 10 244 14 HOH HOH . G 3 HOH A 11 245 15 HOH HOH . G 3 HOH A 12 246 16 HOH HOH . G 3 HOH A 13 247 17 HOH HOH . G 3 HOH A 14 248 18 HOH HOH . G 3 HOH A 15 249 19 HOH HOH . G 3 HOH A 16 250 20 HOH HOH . G 3 HOH A 17 251 21 HOH HOH . G 3 HOH A 18 252 22 HOH HOH . G 3 HOH A 19 253 23 HOH HOH . G 3 HOH A 20 254 24 HOH HOH . G 3 HOH A 21 255 25 HOH HOH . G 3 HOH A 22 256 26 HOH HOH . G 3 HOH A 23 257 27 HOH HOH . G 3 HOH A 24 258 28 HOH HOH . G 3 HOH A 25 259 29 HOH HOH . G 3 HOH A 26 260 30 HOH HOH . G 3 HOH A 27 261 31 HOH HOH . G 3 HOH A 28 262 32 HOH HOH . G 3 HOH A 29 263 33 HOH HOH . G 3 HOH A 30 264 34 HOH HOH . G 3 HOH A 31 265 35 HOH HOH . G 3 HOH A 32 266 36 HOH HOH . G 3 HOH A 33 267 37 HOH HOH . G 3 HOH A 34 268 38 HOH HOH . G 3 HOH A 35 269 39 HOH HOH . G 3 HOH A 36 270 40 HOH HOH . G 3 HOH A 37 271 41 HOH HOH . G 3 HOH A 38 272 55 HOH HOH . G 3 HOH A 39 273 56 HOH HOH . G 3 HOH A 40 274 59 HOH HOH . G 3 HOH A 41 275 60 HOH HOH . G 3 HOH A 42 276 61 HOH HOH . G 3 HOH A 43 277 62 HOH HOH . G 3 HOH A 44 278 65 HOH HOH . G 3 HOH A 45 279 66 HOH HOH . G 3 HOH A 46 280 67 HOH HOH . G 3 HOH A 47 281 68 HOH HOH . G 3 HOH A 48 282 69 HOH HOH . G 3 HOH A 49 283 70 HOH HOH . G 3 HOH A 50 284 71 HOH HOH . G 3 HOH A 51 285 77 HOH HOH . G 3 HOH A 52 286 78 HOH HOH . G 3 HOH A 53 287 79 HOH HOH . G 3 HOH A 54 288 80 HOH HOH . G 3 HOH A 55 289 81 HOH HOH . G 3 HOH A 56 290 88 HOH HOH . G 3 HOH A 57 291 89 HOH HOH . G 3 HOH A 58 292 90 HOH HOH . G 3 HOH A 59 293 92 HOH HOH . G 3 HOH A 60 294 93 HOH HOH . G 3 HOH A 61 295 94 HOH HOH . G 3 HOH A 62 296 95 HOH HOH . G 3 HOH A 63 297 98 HOH HOH . G 3 HOH A 64 298 99 HOH HOH . G 3 HOH A 65 299 100 HOH HOH . G 3 HOH A 66 300 101 HOH HOH . G 3 HOH A 67 301 103 HOH HOH . G 3 HOH A 68 302 104 HOH HOH . G 3 HOH A 69 303 107 HOH HOH . G 3 HOH A 70 304 110 HOH HOH . G 3 HOH A 71 305 113 HOH HOH . G 3 HOH A 72 306 117 HOH HOH . G 3 HOH A 73 307 118 HOH HOH . G 3 HOH A 74 308 119 HOH HOH . G 3 HOH A 75 309 122 HOH HOH . G 3 HOH A 76 310 125 HOH HOH . G 3 HOH A 77 311 127 HOH HOH . G 3 HOH A 78 312 130 HOH HOH . G 3 HOH A 79 313 131 HOH HOH . G 3 HOH A 80 314 132 HOH HOH . H 3 HOH B 1 233 2 HOH HOH . H 3 HOH B 2 234 6 HOH HOH . H 3 HOH B 3 235 7 HOH HOH . H 3 HOH B 4 236 10 HOH HOH . H 3 HOH B 5 237 42 HOH HOH . H 3 HOH B 6 238 43 HOH HOH . H 3 HOH B 7 239 44 HOH HOH . H 3 HOH B 8 240 45 HOH HOH . H 3 HOH B 9 241 46 HOH HOH . H 3 HOH B 10 242 47 HOH HOH . H 3 HOH B 11 243 48 HOH HOH . H 3 HOH B 12 244 49 HOH HOH . H 3 HOH B 13 245 50 HOH HOH . H 3 HOH B 14 246 51 HOH HOH . H 3 HOH B 15 247 52 HOH HOH . H 3 HOH B 16 248 53 HOH HOH . H 3 HOH B 17 249 54 HOH HOH . H 3 HOH B 18 250 57 HOH HOH . H 3 HOH B 19 251 58 HOH HOH . H 3 HOH B 20 252 63 HOH HOH . H 3 HOH B 21 253 64 HOH HOH . H 3 HOH B 22 254 72 HOH HOH . H 3 HOH B 23 255 73 HOH HOH . H 3 HOH B 24 256 74 HOH HOH . H 3 HOH B 25 257 75 HOH HOH . H 3 HOH B 26 258 76 HOH HOH . H 3 HOH B 27 259 82 HOH HOH . H 3 HOH B 28 260 83 HOH HOH . H 3 HOH B 29 261 84 HOH HOH . H 3 HOH B 30 262 85 HOH HOH . H 3 HOH B 31 263 86 HOH HOH . H 3 HOH B 32 264 87 HOH HOH . H 3 HOH B 33 265 91 HOH HOH . H 3 HOH B 34 266 96 HOH HOH . H 3 HOH B 35 267 97 HOH HOH . H 3 HOH B 36 268 102 HOH HOH . H 3 HOH B 37 269 105 HOH HOH . H 3 HOH B 38 270 106 HOH HOH . H 3 HOH B 39 271 108 HOH HOH . H 3 HOH B 40 272 109 HOH HOH . H 3 HOH B 41 273 111 HOH HOH . H 3 HOH B 42 274 112 HOH HOH . H 3 HOH B 43 275 114 HOH HOH . H 3 HOH B 44 276 115 HOH HOH . H 3 HOH B 45 277 116 HOH HOH . H 3 HOH B 46 278 120 HOH HOH . H 3 HOH B 47 279 121 HOH HOH . H 3 HOH B 48 280 123 HOH HOH . H 3 HOH B 49 281 124 HOH HOH . H 3 HOH B 50 282 126 HOH HOH . H 3 HOH B 51 283 128 HOH HOH . H 3 HOH B 52 284 129 HOH HOH . H 3 HOH B 53 285 133 HOH HOH . H 3 HOH B 54 286 134 HOH HOH . H 3 HOH B 55 287 135 HOH HOH . H 3 HOH B 56 288 136 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 2 -23.48 26.706 -2.063 1 65.16 ? C1 BOG 233 A 1 HETATM 2 O O1 BOG . . . D 2 -23.058 26.636 -3.442 1 66.49 ? O1 BOG 233 A 1 HETATM 3 C C2 BOG . . . D 2 -22.389 27.252 -1.115 1 63.58 ? C2 BOG 233 A 1 HETATM 4 O O2 BOG . . . D 2 -21.363 26.226 -0.952 1 59.91 ? O2 BOG 233 A 1 HETATM 5 C C3 BOG . . . D 2 -22.98 27.696 0.252 1 62.78 ? C3 BOG 233 A 1 HETATM 6 O O3 BOG . . . D 2 -22.03 28.422 1.053 1 62 ? O3 BOG 233 A 1 HETATM 7 C C4 BOG . . . D 2 -24.222 28.572 0.132 1 63.33 ? C4 BOG 233 A 1 HETATM 8 O O4 BOG . . . D 2 -24.901 28.798 1.381 1 61.14 ? O4 BOG 233 A 1 HETATM 9 C C5 BOG . . . D 2 -25.217 27.916 -0.788 1 65.48 ? C5 BOG 233 A 1 HETATM 10 O O5 BOG . . . D 2 -24.646 27.531 -2.043 1 66.75 ? O5 BOG 233 A 1 HETATM 11 C C6 BOG . . . D 2 -26.305 28.926 -1.093 1 67.93 ? C6 BOG 233 A 1 HETATM 12 O O6 BOG . . . D 2 -27.524 28.337 -0.672 1 72.74 ? O6 BOG 233 A 1 HETATM 13 C C1' BOG . . . D 2 -23.707 25.623 -4.242 1 65.61 ? C1' BOG 233 A 1 HETATM 14 C C2' BOG . . . D 2 -23.229 25.717 -5.704 1 65.77 ? C2' BOG 233 A 1 HETATM 15 C C3' BOG . . . D 2 -23.907 24.639 -6.588 1 67.48 ? C3' BOG 233 A 1 HETATM 16 C C4' BOG . . . D 2 -23.373 24.669 -8.031 1 68.93 ? C4' BOG 233 A 1 HETATM 17 C C5' BOG . . . D 2 -24.305 24.159 -9.148 1 69.48 ? C5' BOG 233 A 1 HETATM 18 C C6' BOG . . . D 2 -24.858 22.729 -8.955 1 70.35 ? C6' BOG 233 A 1 HETATM 19 C C7' BOG . . . D 2 -25.508 22.124 -10.229 1 71.1 ? C7' BOG 233 A 1 HETATM 20 C C8' BOG . . . D 2 -24.651 22.171 -11.504 1 70.15 ? C8' BOG 233 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #