data_6YU2 # _model_server_result.job_id uRMNnGvr-oZBrYCak64rmg _model_server_result.datetime_utc '2024-10-14 09:17:25' _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 6yu2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":501}' # _entry.id 6YU2 # _exptl.entry_id 6YU2 _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 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 96.14 _cell.angle_gamma 90 _cell.entry_id 6YU2 _cell.length_a 43.95 _cell.length_b 97.29 _cell.length_c 110.94 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YU2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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,F,G,H,O 1 1 B,I,J,K,L,M,N,P 2 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 ? 2 C N N ? 2 D N N ? 2 E N N ? 2 I N N ? 2 J N N ? 2 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 O GLY 26 A GLY 24 1_555 F NA NA . A NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc2 A O ALA 28 A ALA 26 1_555 G NA NA . A NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc3 A O VAL 29 A VAL 27 1_555 F NA NA . A NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc4 A OD1 ASN 33 A ASN 31 1_555 G NA NA . A NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc5 A O THR 233 A THR 231 1_555 G NA NA . A NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? metalc ? metalc6 A OG1 THR 233 A THR 231 1_555 G NA NA . A NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc7 A OD1 ASP 265 A ASP 263 1_555 G NA NA . A NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc8 A O ALA 322 A ALA 320 1_555 F NA NA . A NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? metalc ? metalc9 A OG SER 325 A SER 323 1_555 F NA NA . A NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc10 A OG SER 326 A SER 324 1_555 F NA NA . A NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc11 G NA NA . A NA 505 1_555 H OXT ILE . A ILE 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc12 B O GLY 26 B GLY 24 1_555 L NA NA . B NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc13 B O ALA 28 B ALA 26 1_555 M NA NA . B NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? metalc ? metalc14 B O VAL 29 B VAL 27 1_555 L NA NA . B NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc15 B OD1 ASN 33 B ASN 31 1_555 M NA NA . B NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc16 B O THR 233 B THR 231 1_555 M NA NA . B NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc17 B OG1 THR 233 B THR 231 1_555 M NA NA . B NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc18 B OD1 ASP 265 B ASP 263 1_555 M NA NA . B NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc19 B O ALA 322 B ALA 320 1_555 L NA NA . B NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc20 B OG SER 325 B SER 323 1_555 L NA NA . B NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc21 B OG SER 326 B SER 324 1_555 L NA NA . B NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc22 M NA NA . B NA 505 1_555 N O ILE . B ILE 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? # _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 6YU2 _atom_sites.fract_transf_matrix[1][1] 0.022753 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002447 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010279 _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] 0.009066 _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 1 501 1 BOG BOG . D 2 BOG A 1 502 4 BOG BOG . E 2 BOG A 1 503 5 BOG BOG . F 3 NA A 1 504 1 NA NA . G 3 NA A 1 505 3 NA NA . H 4 ILE A 1 506 2 ILE ILE . I 2 BOG B 1 501 2 BOG BOG . J 2 BOG B 1 502 3 BOG BOG . K 2 BOG B 1 503 6 BOG BOG . L 3 NA B 1 504 2 NA NA . M 3 NA B 1 505 4 NA NA . N 4 ILE B 1 506 3 ILE ILE . O 5 HOH A 1 601 14 HOH HOH . O 5 HOH A 2 602 8 HOH HOH . O 5 HOH A 3 603 6 HOH HOH . O 5 HOH A 4 604 18 HOH HOH . O 5 HOH A 5 605 21 HOH HOH . O 5 HOH A 6 606 1 HOH HOH . O 5 HOH A 7 607 13 HOH HOH . O 5 HOH A 8 608 7 HOH HOH . O 5 HOH A 9 609 9 HOH HOH . O 5 HOH A 10 610 20 HOH HOH . O 5 HOH A 11 611 19 HOH HOH . O 5 HOH A 12 612 15 HOH HOH . O 5 HOH A 13 613 16 HOH HOH . P 5 HOH B 1 601 12 HOH HOH . P 5 HOH B 2 602 10 HOH HOH . P 5 HOH B 3 603 4 HOH HOH . P 5 HOH B 4 604 5 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 . . . I 2 -5.05 1.293 1.353 1 59.49 ? C1 BOG 501 B 1 HETATM 2 O O1 BOG . . . I 2 -5.436 -0.016 1.325 1 60.58 ? O1 BOG 501 B 1 HETATM 3 C C2 BOG . . . I 2 -4.089 1.527 0.194 1 59.22 ? C2 BOG 501 B 1 HETATM 4 O O2 BOG . . . I 2 -2.844 0.88 0.512 1 59.22 ? O2 BOG 501 B 1 HETATM 5 C C3 BOG . . . I 2 -3.797 2.959 -0.096 1 61.01 ? C3 BOG 501 B 1 HETATM 6 O O3 BOG . . . I 2 -3.339 3.036 -1.477 1 64.59 ? O3 BOG 501 B 1 HETATM 7 C C4 BOG . . . I 2 -4.947 3.911 0.064 1 61.27 ? C4 BOG 501 B 1 HETATM 8 O O4 BOG . . . I 2 -4.404 5.218 0.255 1 61.15 ? O4 BOG 501 B 1 HETATM 9 C C5 BOG . . . I 2 -5.862 3.591 1.251 1 61.51 ? C5 BOG 501 B 1 HETATM 10 O O5 BOG . . . I 2 -6.259 2.173 1.268 1 61.17 ? O5 BOG 501 B 1 HETATM 11 C C6 BOG . . . I 2 -7.087 4.448 1.175 1 61.01 ? C6 BOG 501 B 1 HETATM 12 O O6 BOG . . . I 2 -6.892 5.626 1.916 1 59.69 ? O6 BOG 501 B 1 HETATM 13 C C1' BOG . . . I 2 -4.806 -0.832 2.303 1 59.07 ? C1' BOG 501 B 1 HETATM 14 C C2' BOG . . . I 2 -5.197 -2.305 2.076 1 58.93 ? C2' BOG 501 B 1 HETATM 15 C C3' BOG . . . I 2 -4.224 -3.229 2.829 1 58.55 ? C3' BOG 501 B 1 HETATM 16 C C4' BOG . . . I 2 -4.837 -3.642 4.18 1 58.23 ? C4' BOG 501 B 1 HETATM 17 C C5' BOG . . . I 2 -4.238 -4.975 4.625 1 57.3 ? C5' BOG 501 B 1 HETATM 18 C C6' BOG . . . I 2 -4.982 -5.49 5.856 1 56.84 ? C6' BOG 501 B 1 HETATM 19 C C7' BOG . . . I 2 -4.382 -6.819 6.311 1 55.82 ? C7' BOG 501 B 1 HETATM 20 C C8' BOG . . . I 2 -3.667 -6.633 7.65 1 55.82 ? C8' BOG 501 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 20 #