data_4DXW # _model_server_result.job_id sro5i1t6CfKxkHw8_NBcnA _model_server_result.datetime_utc '2024-10-27 04:32:56' _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 4dxw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":302}' # _entry.id 4DXW # _exptl.entry_id 4DXW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 306.395 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'nonyl 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 4DXW _cell.length_a 163.437 _cell.length_b 163.437 _cell.length_c 61.071 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DXW _symmetry.cell_setting ? _symmetry.Int_Tables_number 77 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 42' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,K,L,M,N _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 ? 2 E N N ? 2 F 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 LYS 226 A LYS 226 1_555 G CA CA . A CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.997 ? metalc ? metalc2 L O HOH . A HOH 401 1_555 I CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc3 L O HOH . A HOH 402 1_555 I CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc4 L O HOH . A HOH 403 1_555 I CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc5 I CA CA . B CA 302 1_555 M O HOH . B HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc6 I CA CA . B CA 302 1_555 N O HOH . C HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc7 I CA CA . B CA 302 1_555 N O HOH . C HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.521 ? # _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 4DXW _atom_sites.fract_transf_matrix[1][1] 0.006119 _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] 0.006119 _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] 0.016374 _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 E 2 BNG A 1 301 300 BNG BNG . F 2 BNG A 1 302 300 BNG BNG . G 3 CA A 1 303 2 CA CA . H 4 PX4 B 1 301 1 PX4 PX4 . I 3 CA B 1 302 3 CA CA . J 2 BNG C 1 301 300 BNG BNG . K 2 BNG C 1 302 300 BNG BNG . L 5 HOH A 1 401 2 HOH HOH . L 5 HOH A 2 402 3 HOH HOH . L 5 HOH A 3 403 6 HOH HOH . M 5 HOH B 1 401 5 HOH HOH . N 5 HOH C 1 401 1 HOH HOH . N 5 HOH C 2 402 4 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 . . . F 2 34.307 -27.471 -5.742 1 83.24 ? C1 BNG 302 A 1 HETATM 2 C C2 BNG . . . F 2 33.135 -26.729 -6.374 1 85.25 ? C2 BNG 302 A 1 HETATM 3 C C3 BNG . . . F 2 32.32 -27.657 -7.267 1 86.27 ? C3 BNG 302 A 1 HETATM 4 C C4 BNG . . . F 2 33.223 -28.423 -8.226 1 86.01 ? C4 BNG 302 A 1 HETATM 5 C C5 BNG . . . F 2 34.391 -29.062 -7.485 1 83.96 ? C5 BNG 302 A 1 HETATM 6 C C6 BNG . . . F 2 35.335 -29.763 -8.454 1 84.05 ? C6 BNG 302 A 1 HETATM 7 C C1' BNG . . . F 2 35.83 -27.213 -3.956 1 80.78 ? C1' BNG 302 A 1 HETATM 8 C C2' BNG . . . F 2 36.25 -26.194 -2.903 1 80.6 ? C2' BNG 302 A 1 HETATM 9 C C3' BNG . . . F 2 36.192 -26.799 -1.505 1 79.18 ? C3' BNG 302 A 1 HETATM 10 C C4' BNG . . . F 2 36.83 -25.868 -0.481 1 78.93 ? C4' BNG 302 A 1 HETATM 11 C C5' BNG . . . F 2 37.559 -26.661 0.597 1 77.22 ? C5' BNG 302 A 1 HETATM 12 C C6' BNG . . . F 2 37.448 -25.971 1.952 1 77.23 ? C6' BNG 302 A 1 HETATM 13 C C7' BNG . . . F 2 38.693 -26.221 2.795 1 75.95 ? C7' BNG 302 A 1 HETATM 14 C C8' BNG . . . F 2 38.723 -25.3 4.009 1 76.3 ? C8' BNG 302 A 1 HETATM 15 C C9' BNG . . . F 2 39.164 -26.05 5.248 1 75.05 ? C9' BNG 302 A 1 HETATM 16 O O1 BNG . . . F 2 35.099 -26.555 -4.989 1 82.61 ? O1 BNG 302 A 1 HETATM 17 O O2 BNG . . . F 2 32.294 -26.199 -5.343 1 86.51 ? O2 BNG 302 A 1 HETATM 18 O O3 BNG . . . F 2 31.372 -26.887 -8.016 1 88.47 ? O3 BNG 302 A 1 HETATM 19 O O4 BNG . . . F 2 32.462 -29.441 -8.887 1 86.68 ? O4 BNG 302 A 1 HETATM 20 O O5 BNG . . . F 2 35.105 -28.058 -6.767 1 83.37 ? O5 BNG 302 A 1 HETATM 21 O O6 BNG . . . F 2 35.044 -29.344 -9.792 1 85.93 ? O6 BNG 302 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 21 #