data_6YU7 # _model_server_result.job_id xJ2Ng14x38QlO0mXtoGpTw _model_server_result.datetime_utc '2024-11-22 18:15:21' _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 6yu7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":507}' # _entry.id 6YU7 # _exptl.entry_id 6YU7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 306.395 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'nonyl 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 96.8 _cell.angle_gamma 90 _cell.entry_id 6YU7 _cell.length_a 44.1 _cell.length_b 49.9 _cell.length_c 110.3 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YU7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 3 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 H N N ? 5 I 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 E NA NA . A NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc2 A O ALA 28 A ALA 26 1_555 F NA NA . A NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc3 A O VAL 29 A VAL 27 1_555 E NA NA . A NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc4 A OD1 ASN 33 A ASN 31 1_555 F NA NA . A NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc5 A O THR 233 A THR 231 1_555 F NA NA . A NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc6 A OG1 THR 233 A THR 231 1_555 F NA NA . A NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc7 A OD1 ASP 265 A ASP 263 1_555 F NA NA . A NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc8 A O ALA 322 A ALA 320 1_555 E NA NA . A NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc9 A OG SER 325 A SER 323 1_555 E NA NA . A NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc10 A OG SER 326 A SER 324 1_555 E NA NA . A NA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc11 E NA NA . A NA 504 1_555 J O HOH . A HOH 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? metalc ? metalc12 F NA NA . A NA 505 1_555 G OXT TYR . A TYR 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? # _chem_comp.formula 'C15 H30 O6' _chem_comp.formula_weight 306.395 _chem_comp.id BNG _chem_comp.mon_nstd_flag n _chem_comp.name 'nonyl beta-D-glucopyranoside' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 'Beta-NONYLGLUCOSIDE;nonyl beta-D-glucoside;nonyl D-glucoside;nonyl 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 C2 BNG sing 70 n n C1 O1 BNG sing 71 n n C1 O5 BNG sing 72 n n C1 H1 BNG sing 73 n n C2 C3 BNG sing 74 n n C2 O2 BNG sing 75 n n C2 H2 BNG sing 76 n n C3 C4 BNG sing 77 n n C3 O3 BNG sing 78 n n C3 H3 BNG sing 79 n n C4 C5 BNG sing 80 n n C4 O4 BNG sing 81 n n C4 H4 BNG sing 82 n n C5 C6 BNG sing 83 n n C5 O5 BNG sing 84 n n C5 H5 BNG sing 85 n n C6 O6 BNG sing 86 n n C6 H61 BNG sing 87 n n C6 H62 BNG sing 88 n n C1' C2' BNG sing 89 n n C1' O1 BNG sing 90 n n C1' "H1'1" BNG sing 91 n n C1' "H1'2" BNG sing 92 n n C2' C3' BNG sing 93 n n C2' "H2'1" BNG sing 94 n n C2' "H2'2" BNG sing 95 n n C3' C4' BNG sing 96 n n C3' "H3'1" BNG sing 97 n n C3' "H3'2" BNG sing 98 n n C4' C5' BNG sing 99 n n C4' "H4'1" BNG sing 100 n n C4' "H4'2" BNG sing 101 n n C5' C6' BNG sing 102 n n C5' "H5'1" BNG sing 103 n n C5' "H5'2" BNG sing 104 n n C6' C7' BNG sing 105 n n C6' "H6'1" BNG sing 106 n n C6' "H6'2" BNG sing 107 n n C7' C8' BNG sing 108 n n C7' "H7'1" BNG sing 109 n n C7' "H7'2" BNG sing 110 n n C8' C9' BNG sing 111 n n C8' "H8'1" BNG sing 112 n n C8' "H8'2" BNG sing 113 n n C9' "H9'1" BNG sing 114 n n C9' "H9'2" BNG sing 115 n n C9' "H9'3" BNG sing 116 n n O2 HO2 BNG sing 117 n n O3 HO3 BNG sing 118 n n O4 HO4 BNG sing 119 n n O6 HO6 BNG sing 120 n n # _pdbx_chem_comp_identifier.comp_id BNG _pdbx_chem_comp_identifier.identifier b-nonylglucoside _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 6YU7 _atom_sites.fract_transf_matrix[1][1] 0.022676 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002704 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.02004 _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] 0.00913 _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 LMT A 1 501 501 LMT LMT . C 2 LMT A 1 502 601 LMT LMT . D 2 LMT A 1 503 701 LMT LMT . E 3 NA A 1 504 1 NA NA . F 3 NA A 1 505 2 NA NA . G 4 TYR A 1 506 601 TYR TYR . H 5 BNG A 1 507 1 BNG BNG . I 5 BNG A 1 508 2 BNG BNG . J 6 HOH A 1 601 9 HOH HOH . J 6 HOH A 2 602 25 HOH HOH . J 6 HOH A 3 603 58 HOH HOH . J 6 HOH A 4 604 16 HOH HOH . J 6 HOH A 5 605 46 HOH HOH . J 6 HOH A 6 606 42 HOH HOH . J 6 HOH A 7 607 50 HOH HOH . J 6 HOH A 8 608 40 HOH HOH . J 6 HOH A 9 609 12 HOH HOH . J 6 HOH A 10 610 64 HOH HOH . J 6 HOH A 11 611 10 HOH HOH . J 6 HOH A 12 612 44 HOH HOH . J 6 HOH A 13 613 32 HOH HOH . J 6 HOH A 14 614 21 HOH HOH . J 6 HOH A 15 615 43 HOH HOH . J 6 HOH A 16 616 6 HOH HOH . J 6 HOH A 17 617 41 HOH HOH . J 6 HOH A 18 618 18 HOH HOH . J 6 HOH A 19 619 14 HOH HOH . J 6 HOH A 20 620 33 HOH HOH . J 6 HOH A 21 621 54 HOH HOH . J 6 HOH A 22 622 35 HOH HOH . J 6 HOH A 23 623 7 HOH HOH . J 6 HOH A 24 624 38 HOH HOH . J 6 HOH A 25 625 20 HOH HOH . J 6 HOH A 26 626 15 HOH HOH . J 6 HOH A 27 627 49 HOH HOH . J 6 HOH A 28 628 30 HOH HOH . J 6 HOH A 29 629 3 HOH HOH . J 6 HOH A 30 630 60 HOH HOH . J 6 HOH A 31 631 53 HOH HOH . J 6 HOH A 32 632 57 HOH HOH . J 6 HOH A 33 633 34 HOH HOH . J 6 HOH A 34 634 8 HOH HOH . J 6 HOH A 35 635 61 HOH HOH . J 6 HOH A 36 636 24 HOH HOH . J 6 HOH A 37 637 2 HOH HOH . J 6 HOH A 38 638 37 HOH HOH . J 6 HOH A 39 639 19 HOH HOH . J 6 HOH A 40 640 17 HOH HOH . J 6 HOH A 41 641 59 HOH HOH . J 6 HOH A 42 642 23 HOH HOH . J 6 HOH A 43 643 5 HOH HOH . J 6 HOH A 44 644 62 HOH HOH . J 6 HOH A 45 645 45 HOH HOH . J 6 HOH A 46 646 51 HOH HOH . J 6 HOH A 47 647 11 HOH HOH . J 6 HOH A 48 648 22 HOH HOH . J 6 HOH A 49 649 36 HOH HOH . J 6 HOH A 50 650 4 HOH HOH . J 6 HOH A 51 651 52 HOH HOH . J 6 HOH A 52 652 26 HOH HOH . J 6 HOH A 53 653 31 HOH HOH . J 6 HOH A 54 654 56 HOH HOH . J 6 HOH A 55 655 47 HOH HOH . J 6 HOH A 56 656 13 HOH HOH . J 6 HOH A 57 657 66 HOH HOH . J 6 HOH A 58 658 63 HOH HOH . J 6 HOH A 59 659 27 HOH HOH . J 6 HOH A 60 660 65 HOH HOH . J 6 HOH A 61 661 48 HOH HOH . J 6 HOH A 62 662 55 HOH HOH . J 6 HOH A 63 663 1 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 BNG . . . H 5 62.003 45.263 141.516 1 45.36 ? C1 BNG 507 A 1 HETATM 2 C C2 BNG . . . H 5 62.661 46.068 140.394 1 44.23 ? C2 BNG 507 A 1 HETATM 3 C C3 BNG . . . H 5 63.664 47.027 140.936 1 49.45 ? C3 BNG 507 A 1 HETATM 4 C C4 BNG . . . H 5 63.037 47.942 141.941 1 59.09 ? C4 BNG 507 A 1 HETATM 5 C C5 BNG . . . H 5 62.382 47.134 143.075 1 52.55 ? C5 BNG 507 A 1 HETATM 6 C C6 BNG . . . H 5 61.683 48.042 143.993 1 58.84 ? C6 BNG 507 A 1 HETATM 7 C C1' BNG . . . H 5 60.727 43.33 141.842 1 40.65 ? C1' BNG 507 A 1 HETATM 8 C C2' BNG . . . H 5 60.071 42.26 141.01 1 37.75 ? C2' BNG 507 A 1 HETATM 9 C C3' BNG . . . H 5 61.108 41.099 140.747 1 42.33 ? C3' BNG 507 A 1 HETATM 10 C C4' BNG . . . H 5 60.594 40.243 139.545 1 46.33 ? C4' BNG 507 A 1 HETATM 11 C C5' BNG . . . H 5 61.636 39.17 139.181 1 36.1 ? C5' BNG 507 A 1 HETATM 12 C C6' BNG . . . H 5 60.891 37.917 138.617 1 35.86 ? C6' BNG 507 A 1 HETATM 13 C C7' BNG . . . H 5 61.606 37.413 137.319 1 36.37 ? C7' BNG 507 A 1 HETATM 14 C C8' BNG . . . H 5 60.823 36.231 136.738 1 32.97 ? C8' BNG 507 A 1 HETATM 15 C C9' BNG . . . H 5 61.109 36.114 135.2 1 28.69 ? C9' BNG 507 A 1 HETATM 16 O O1 BNG . . . H 5 61.036 44.467 140.993 1 43.22 ? O1 BNG 507 A 1 HETATM 17 O O2 BNG . . . H 5 63.326 45.13 139.539 1 53.67 ? O2 BNG 507 A 1 HETATM 18 O O3 BNG . . . H 5 64.242 47.802 139.858 1 48.1 ? O3 BNG 507 A 1 HETATM 19 O O4 BNG . . . H 5 64.049 48.799 142.494 1 58.82 ? O4 BNG 507 A 1 HETATM 20 O O5 BNG . . . H 5 61.401 46.149 142.563 1 49.44 ? O5 BNG 507 A 1 HETATM 21 O O6 BNG . . . H 5 60.77 47.297 144.733 1 58.78 ? O6 BNG 507 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #