data_6YU5 # _model_server_result.job_id 1OV-AWANb5rs8iUIhBWbLg _model_server_result.datetime_utc '2024-11-26 02:57:17' _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 6yu5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"X","auth_seq_id":504}' # _entry.id 6YU5 # _exptl.entry_id 6YU5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 306.395 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'nonyl beta-D-glucopyranoside' _entity.pdbx_number_of_molecules 20 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.02 _cell.angle_gamma 90 _cell.entry_id 6YU5 _cell.length_a 44.16 _cell.length_b 216.03 _cell.length_c 50.36 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YU5 _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,I,J,K,L,M,N,O,P,Q,R,S,T,EA 1 1 B,U,V,W,X,Y,Z,AA,BA,CA,DA,FA 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 ? 4 F N N ? 4 G N N ? 4 H N N ? 4 I N N ? 4 J N N ? 4 K N N ? 4 L N N ? 4 M N N ? 4 N N N ? 4 O N N ? 4 P N N ? 4 Q N N ? 4 R N N ? 4 X N N ? 4 Y N N ? 4 Z N N ? 4 AA N N ? 4 BA N N ? 4 CA N N ? 4 DA 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 D NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc2 A O ALA 28 A ALA 26 1_555 E NA NA . A NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc3 A O VAL 29 A VAL 27 1_555 D NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc4 A OD1 ASN 33 A ASN 31 1_555 E NA NA . A NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? metalc ? metalc5 A O THR 233 A THR 231 1_555 E NA NA . A NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc6 A OG1 THR 233 A THR 231 1_555 E NA NA . A NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc7 A OD1 ASP 265 A ASP 263 1_555 E NA NA . A NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc8 A O ALA 322 A ALA 320 1_555 D NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc9 A OG SER 325 A SER 323 1_555 D NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? metalc ? metalc10 A OG SER 326 A SER 324 1_555 D NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? metalc ? metalc11 C O VAL . A VAL 501 1_555 E NA NA . A NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc12 B O GLY 26 B GLY 24 1_555 W NA NA . B NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc13 B O ALA 28 B ALA 26 1_555 V NA NA . B NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.586 ? metalc ? metalc14 B O VAL 29 B VAL 27 1_555 W NA NA . B NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc15 B OD1 ASN 33 B ASN 31 1_555 V NA NA . B NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc16 B O THR 233 B THR 231 1_555 V NA NA . B NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc17 B OG1 THR 233 B THR 231 1_555 V NA NA . B NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc18 B OD1 ASP 265 B ASP 263 1_555 V NA NA . B NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc19 B O ALA 322 B ALA 320 1_555 W NA NA . B NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc20 B OG SER 325 B SER 323 1_555 W NA NA . B NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? metalc ? metalc21 B OG SER 326 B SER 324 1_555 W NA NA . B NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc22 U O VAL . B VAL 501 1_555 V NA NA . B NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? # _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 6YU5 _atom_sites.fract_transf_matrix[1][1] 0.022645 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000008 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004629 _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] 0.019857 _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 VAL A 1 501 2 VAL VAL . D 3 NA A 1 502 2 NA NA . E 3 NA A 1 503 4 NA NA . F 4 BNG A 1 504 2 BNG BNG . G 4 BNG A 1 505 4 BNG BNG . H 4 BNG A 1 506 5 BNG BNG . I 4 BNG A 1 507 8 BNG BNG . J 4 BNG A 1 508 9 BNG BNG . K 4 BNG A 1 509 10 BNG BNG . L 4 BNG A 1 510 14 BNG BNG . M 4 BNG A 1 511 20 BNG BNG . N 4 BNG A 1 512 21 BNG BNG . O 4 BNG A 1 513 22 BNG BNG . P 4 BNG A 1 514 26 BNG BNG . Q 4 BNG A 1 515 27 BNG BNG . R 4 BNG A 1 516 30 BNG BNG . S 5 LMT A 1 517 4 LMT LMT . T 5 LMT A 1 518 5 LMT LMT . U 2 VAL B 1 501 1 VAL VAL . V 3 NA B 1 502 1 NA NA . W 3 NA B 1 503 3 NA NA . X 4 BNG B 1 504 1 BNG BNG . Y 4 BNG B 1 505 13 BNG BNG . Z 4 BNG B 1 506 16 BNG BNG . AA 4 BNG B 1 507 19 BNG BNG . BA 4 BNG B 1 508 24 BNG BNG . CA 4 BNG B 1 509 28 BNG BNG . DA 4 BNG B 1 510 29 BNG BNG . EA 6 HOH A 1 601 48 HOH HOH . EA 6 HOH A 2 602 58 HOH HOH . EA 6 HOH A 3 603 24 HOH HOH . EA 6 HOH A 4 604 25 HOH HOH . EA 6 HOH A 5 605 112 HOH HOH . EA 6 HOH A 6 606 41 HOH HOH . EA 6 HOH A 7 607 2 HOH HOH . EA 6 HOH A 8 608 32 HOH HOH . EA 6 HOH A 9 609 86 HOH HOH . EA 6 HOH A 10 610 33 HOH HOH . EA 6 HOH A 11 611 45 HOH HOH . EA 6 HOH A 12 612 26 HOH HOH . EA 6 HOH A 13 613 46 HOH HOH . EA 6 HOH A 14 614 36 HOH HOH . EA 6 HOH A 15 615 1 HOH HOH . EA 6 HOH A 16 616 101 HOH HOH . EA 6 HOH A 17 617 34 HOH HOH . EA 6 HOH A 18 618 28 HOH HOH . EA 6 HOH A 19 619 61 HOH HOH . EA 6 HOH A 20 620 136 HOH HOH . EA 6 HOH A 21 621 30 HOH HOH . EA 6 HOH A 22 622 22 HOH HOH . EA 6 HOH A 23 623 35 HOH HOH . EA 6 HOH A 24 624 85 HOH HOH . EA 6 HOH A 25 625 128 HOH HOH . EA 6 HOH A 26 626 27 HOH HOH . EA 6 HOH A 27 627 82 HOH HOH . EA 6 HOH A 28 628 14 HOH HOH . EA 6 HOH A 29 629 76 HOH HOH . EA 6 HOH A 30 630 132 HOH HOH . EA 6 HOH A 31 631 100 HOH HOH . EA 6 HOH A 32 632 53 HOH HOH . EA 6 HOH A 33 633 115 HOH HOH . EA 6 HOH A 34 634 44 HOH HOH . EA 6 HOH A 35 635 102 HOH HOH . EA 6 HOH A 36 636 43 HOH HOH . EA 6 HOH A 37 637 79 HOH HOH . EA 6 HOH A 38 638 107 HOH HOH . FA 6 HOH B 1 601 131 HOH HOH . FA 6 HOH B 2 602 49 HOH HOH . FA 6 HOH B 3 603 40 HOH HOH . FA 6 HOH B 4 604 21 HOH HOH . FA 6 HOH B 5 605 52 HOH HOH . FA 6 HOH B 6 606 10 HOH HOH . FA 6 HOH B 7 607 69 HOH HOH . FA 6 HOH B 8 608 38 HOH HOH . FA 6 HOH B 9 609 12 HOH HOH . FA 6 HOH B 10 610 13 HOH HOH . FA 6 HOH B 11 611 18 HOH HOH . FA 6 HOH B 12 612 66 HOH HOH . FA 6 HOH B 13 613 94 HOH HOH . FA 6 HOH B 14 614 116 HOH HOH . FA 6 HOH B 15 615 39 HOH HOH . FA 6 HOH B 16 616 5 HOH HOH . FA 6 HOH B 17 617 93 HOH HOH . FA 6 HOH B 18 618 23 HOH HOH . FA 6 HOH B 19 619 92 HOH HOH . FA 6 HOH B 20 620 7 HOH HOH . FA 6 HOH B 21 621 54 HOH HOH . FA 6 HOH B 22 622 6 HOH HOH . FA 6 HOH B 23 623 65 HOH HOH . FA 6 HOH B 24 624 122 HOH HOH . FA 6 HOH B 25 625 104 HOH HOH . FA 6 HOH B 26 626 106 HOH HOH . FA 6 HOH B 27 627 73 HOH HOH . FA 6 HOH B 28 628 135 HOH HOH . FA 6 HOH B 29 629 4 HOH HOH . FA 6 HOH B 30 630 74 HOH HOH . FA 6 HOH B 31 631 17 HOH HOH . FA 6 HOH B 32 632 125 HOH HOH . FA 6 HOH B 33 633 134 HOH HOH . FA 6 HOH B 34 634 16 HOH HOH . FA 6 HOH B 35 635 51 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 . . . X 4 40.065 -76.526 -17.674 1 70.2 ? C1 BNG 504 B 1 HETATM 2 C C2 BNG . . . X 4 40.42 -77.65 -18.651 1 68.02 ? C2 BNG 504 B 1 HETATM 3 C C3 BNG . . . X 4 41.406 -77.113 -19.628 1 71.35 ? C3 BNG 504 B 1 HETATM 4 C C4 BNG . . . X 4 40.841 -75.962 -20.41 1 76.71 ? C4 BNG 504 B 1 HETATM 5 C C5 BNG . . . X 4 40.164 -74.883 -19.538 1 78.77 ? C5 BNG 504 B 1 HETATM 6 C C6 BNG . . . X 4 39.278 -74.073 -20.392 1 78.65 ? C6 BNG 504 B 1 HETATM 7 C C1' BNG . . . X 4 39.521 -76.272 -15.407 1 66.2 ? C1' BNG 504 B 1 HETATM 8 C C2' BNG . . . X 4 38.867 -77.023 -14.274 1 60.69 ? C2' BNG 504 B 1 HETATM 9 C C3' BNG . . . X 4 39.838 -78.154 -13.75 1 57.21 ? C3' BNG 504 B 1 HETATM 10 C C4' BNG . . . X 4 39.25 -78.742 -12.427 1 57.28 ? C4' BNG 504 B 1 HETATM 11 C C5' BNG . . . X 4 40.085 -79.956 -11.975 1 55.38 ? C5' BNG 504 B 1 HETATM 12 C C6' BNG . . . X 4 40.014 -80.071 -10.417 1 53.4 ? C6' BNG 504 B 1 HETATM 13 C C7' BNG . . . X 4 39.15 -81.312 -10.019 1 52.03 ? C7' BNG 504 B 1 HETATM 14 C C8' BNG . . . X 4 40.058 -82.409 -9.444 1 58.34 ? C8' BNG 504 B 1 HETATM 15 C C9' BNG . . . X 4 39.182 -83.613 -8.954 1 52.54 ? C9' BNG 504 B 1 HETATM 16 O O1 BNG . . . X 4 39.286 -76.979 -16.656 1 69.25 ? O1 BNG 504 B 1 HETATM 17 O O2 BNG . . . X 4 40.982 -78.767 -17.935 1 69.43 ? O2 BNG 504 B 1 HETATM 18 O O3 BNG . . . X 4 41.811 -78.161 -20.544 1 71.4 ? O3 BNG 504 B 1 HETATM 19 O O4 BNG . . . X 4 41.901 -75.339 -21.161 1 75.43 ? O4 BNG 504 B 1 HETATM 20 O O5 BNG . . . X 4 39.361 -75.425 -18.408 1 74.47 ? O5 BNG 504 B 1 HETATM 21 O O6 BNG . . . X 4 38.117 -74.788 -20.68 1 78.77 ? O6 BNG 504 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 140 _model_server_stats.query_time_ms 379 _model_server_stats.encode_time_ms 38 _model_server_stats.element_count 21 #