data_6YVR
#
_model_server_result.job_id            ZncM1aLIzQQS6m6KXo613g 
_model_server_result.datetime_utc      '2025-09-07 21:43:07' 
_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          6yvr 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":4003}' 
#
_entry.id    6YVR 
#
_exptl.entry_id    6YVR 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              306.395 
_entity.id                          3 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            'nonyl beta-D-glucopyranoside' 
_entity.pdbx_number_of_molecules    8 
_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            6YVR 
_cell.length_a            89.886 
_cell.length_b            114.001 
_cell.length_c            195.424 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6YVR 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_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
? 3 E N N 
? 3 F N N 
? 3 G N N 
? 3 H N N 
? 3 I N N 
? 3 J N N 
? 3 K N N 
? 3 L 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
disulf ? disulf1 A SG CYS 97 AAA CYS 142 1_555 A SG CYS 180 AAA CYS 225 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
disulf ? disulf2 B SG CYS 97 BBB CYS 142 1_555 B SG CYS 180 BBB CYS 225 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? 
#
_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                     6YVR 
_atom_sites.fract_transf_matrix[1][1]    0.011125 
_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]    0.008772 
_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]    0.005117 
_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 3 BNG AAA 1 4001 4001 BNG BNG . 
F 3 BNG AAA 1 4002 4002 BNG BNG . 
G 3 BNG AAA 1 4003 4003 BNG BNG . 
H 3 BNG BBB 1 4001 4001 BNG BNG . 
I 3 BNG BBB 1 4002 4002 BNG BNG . 
J 3 BNG BBB 1 4003 4003 BNG BNG . 
K 3 BNG BBB 1 4004 4007 BNG BNG . 
L 3 BNG BBB 1 4005 4008 BNG BNG . 
M 4 HOH AAA 1 4101 2007 HOH HOH . 
M 4 HOH AAA 2 4102 2013 HOH HOH . 
M 4 HOH AAA 3 4103 2014 HOH HOH . 
M 4 HOH AAA 4 4104 2101 HOH HOH . 
M 4 HOH AAA 5 4105 2010 HOH HOH . 
M 4 HOH AAA 6 4106 2006 HOH HOH . 
M 4 HOH AAA 7 4107 2002 HOH HOH . 
M 4 HOH AAA 8 4108 2001 HOH HOH . 
M 4 HOH AAA 9 4109 2103 HOH HOH . 
M 4 HOH AAA 10 4110 2009 HOH HOH . 
M 4 HOH AAA 11 4111 2004 HOH HOH . 
M 4 HOH AAA 12 4112 2011 HOH HOH . 
M 4 HOH AAA 13 4113 2019 HOH HOH . 
M 4 HOH AAA 14 4114 2016 HOH HOH . 
M 4 HOH AAA 15 4115 2015 HOH HOH . 
M 4 HOH AAA 16 4116 2020 HOH HOH . 
M 4 HOH AAA 17 4117 2012 HOH HOH . 
M 4 HOH AAA 18 4118 2008 HOH HOH . 
M 4 HOH AAA 19 4119 2017 HOH HOH . 
M 4 HOH AAA 20 4120 2005 HOH HOH . 
M 4 HOH AAA 21 4121 2102 HOH HOH . 
N 4 HOH BBB 1 4101 2010 HOH HOH . 
N 4 HOH BBB 2 4102 2007 HOH HOH . 
N 4 HOH BBB 3 4103 2207 HOH HOH . 
N 4 HOH BBB 4 4104 2014 HOH HOH . 
N 4 HOH BBB 5 4105 2006 HOH HOH . 
N 4 HOH BBB 6 4106 2009 HOH HOH . 
N 4 HOH BBB 7 4107 2003 HOH HOH . 
N 4 HOH BBB 8 4108 2011 HOH HOH . 
N 4 HOH BBB 9 4109 2208 HOH HOH . 
N 4 HOH BBB 10 4110 2015 HOH HOH . 
N 4 HOH BBB 11 4111 2002 HOH HOH . 
N 4 HOH BBB 12 4112 2004 HOH HOH . 
N 4 HOH BBB 13 4113 2020 HOH HOH . 
N 4 HOH BBB 14 4114 2003 HOH HOH . 
N 4 HOH BBB 15 4115 2008 HOH HOH . 
N 4 HOH BBB 16 4116 2202 HOH HOH . 
N 4 HOH BBB 17 4117 2205 HOH HOH . 
N 4 HOH BBB 18 4118 2019 HOH HOH . 
N 4 HOH BBB 19 4119 2001 HOH HOH . 
N 4 HOH BBB 20 4120 2206 HOH HOH . 
N 4 HOH BBB 21 4121 2016 HOH HOH . 
N 4 HOH BBB 22 4122 2012 HOH HOH . 
N 4 HOH BBB 23 4123 2203 HOH HOH . 
N 4 HOH BBB 24 4124 2017 HOH HOH . 
N 4 HOH BBB 25 4125 2005 HOH HOH . 
N 4 HOH BBB 26 4126 2204 HOH HOH . 
N 4 HOH BBB 27 4127 2201 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 . . . G 3 19.434 -14.243 -7.594 1 125.97 ? C1 BNG 4003 AAA 1 
HETATM 2 C C2 BNG . . . G 3 17.917 -14.08 -7.452 1 120.75 ? C2 BNG 4003 AAA 1 
HETATM 3 C C3 BNG . . . G 3 17.407 -14.906 -6.276 1 122.47 ? C3 BNG 4003 AAA 1 
HETATM 4 C C4 BNG . . . G 3 17.898 -16.354 -6.347 1 123.07 ? C4 BNG 4003 AAA 1 
HETATM 5 C C5 BNG . . . G 3 19.391 -16.474 -6.707 1 112.03 ? C5 BNG 4003 AAA 1 
HETATM 6 C C6 BNG . . . G 3 19.803 -17.914 -7.052 1 100.94 ? C6 BNG 4003 AAA 1 
HETATM 7 C C1' BNG . . . G 3 20.853 -13.847 -9.589 1 106.06 ? C1' BNG 4003 AAA 1 
HETATM 8 C C2' BNG . . . G 3 20.217 -13.738 -10.971 1 93.3 ? C2' BNG 4003 AAA 1 
HETATM 9 C C3' BNG . . . G 3 21.253 -13.764 -12.088 1 92.62 ? C3' BNG 4003 AAA 1 
HETATM 10 C C4' BNG . . . G 3 20.581 -14.09 -13.419 1 86.18 ? C4' BNG 4003 AAA 1 
HETATM 11 C C5' BNG . . . G 3 21.589 -14.259 -14.553 1 88.62 ? C5' BNG 4003 AAA 1 
HETATM 12 C C6' BNG . . . G 3 21.038 -15.187 -15.632 1 86.72 ? C6' BNG 4003 AAA 1 
HETATM 13 C C7' BNG . . . G 3 19.831 -14.552 -16.325 1 84.57 ? C7' BNG 4003 AAA 1 
HETATM 14 C C8' BNG . . . G 3 19.42 -15.305 -17.587 1 76.61 ? C8' BNG 4003 AAA 1 
HETATM 15 C C9' BNG . . . G 3 17.92 -15.253 -17.763 1 73.45 ? C9' BNG 4003 AAA 1 
HETATM 16 O O1 BNG . . . G 3 19.895 -13.365 -8.637 1 118.85 ? O1 BNG 4003 AAA 1 
HETATM 17 O O2 BNG . . . G 3 17.553 -12.704 -7.256 1 118.97 ? O2 BNG 4003 AAA 1 
HETATM 18 O O3 BNG . . . G 3 15.971 -14.894 -6.28 1 113.52 ? O3 BNG 4003 AAA 1 
HETATM 19 O O4 BNG . . . G 3 17.631 -16.978 -5.08 1 94.3 ? O4 BNG 4003 AAA 1 
HETATM 20 O O5 BNG . . . G 3 19.719 -15.632 -7.826 1 119.11 ? O5 BNG 4003 AAA 1 
HETATM 21 O O6 BNG . . . G 3 18.914 -18.914 -6.509 1 65.78 ? O6 BNG 4003 AAA 1 
HETATM 22 H H1 BNG . . . G 3 19.896 -13.937 -6.645 1 122 ? H1 BNG 4003 AAA 1 
HETATM 23 H H2 BNG . . . G 3 17.441 -14.455 -8.368 1 121.47 ? H2 BNG 4003 AAA 1 
HETATM 24 H H3 BNG . . . G 3 17.779 -14.456 -5.344 1 120.27 ? H3 BNG 4003 AAA 1 
HETATM 25 H H4 BNG . . . G 3 17.318 -16.865 -7.128 1 114.01 ? H4 BNG 4003 AAA 1 
HETATM 26 H H5 BNG . . . G 3 19.977 -16.156 -5.833 1 112.98 ? H5 BNG 4003 AAA 1 
HETATM 27 H H61 BNG . . . G 3 20.807 -18.091 -6.661 1 93.05 ? H61 BNG 4003 AAA 1 
HETATM 28 H H62 BNG . . . G 3 19.85 -18.021 -8.138 1 93.13 ? H62 BNG 4003 AAA 1 
HETATM 29 H "H1'1" BNG . . . G 3 21.144 -14.879 -9.389 1 105.61 ? "H1'1" BNG 4003 AAA 1 
HETATM 30 H "H1'2" BNG . . . G 3 21.751 -13.227 -9.549 1 105.55 ? "H1'2" BNG 4003 AAA 1 
HETATM 31 H "H2'1" BNG . . . G 3 19.648 -12.807 -11.032 1 95.85 ? "H2'1" BNG 4003 AAA 1 
HETATM 32 H "H2'2" BNG . . . G 3 19.515 -14.563 -11.106 1 95.82 ? "H2'2" BNG 4003 AAA 1 
HETATM 33 H "H3'1" BNG . . . G 3 22.012 -14.517 -11.863 1 90.96 ? "H3'1" BNG 4003 AAA 1 
HETATM 34 H "H3'2" BNG . . . G 3 21.748 -12.793 -12.154 1 91.08 ? "H3'2" BNG 4003 AAA 1 
HETATM 35 H "H4'1" BNG . . . G 3 19.885 -13.289 -13.675 1 88.13 ? "H4'1" BNG 4003 AAA 1 
HETATM 36 H "H4'2" BNG . . . G 3 20.002 -15.009 -13.312 1 88.14 ? "H4'2" BNG 4003 AAA 1 
HETATM 37 H "H5'1" BNG . . . G 3 22.522 -14.667 -14.162 1 87.4 ? "H5'1" BNG 4003 AAA 1 
HETATM 38 H "H5'2" BNG . . . G 3 21.809 -13.283 -14.99 1 87.47 ? "H5'2" BNG 4003 AAA 1 
HETATM 39 H "H6'1" BNG . . . G 3 20.741 -16.137 -15.183 1 86.51 ? "H6'1" BNG 4003 AAA 1 
HETATM 40 H "H6'2" BNG . . . G 3 21.815 -15.399 -16.365 1 86.25 ? "H6'2" BNG 4003 AAA 1 
HETATM 41 H "H7'1" BNG . . . G 3 20.07 -13.52 -16.588 1 83.05 ? "H7'1" BNG 4003 AAA 1 
HETATM 42 H "H7'2" BNG . . . G 3 18.99 -14.529 -15.63 1 83.02 ? "H7'2" BNG 4003 AAA 1 
HETATM 43 H "H8'1" BNG . . . G 3 19.745 -16.346 -17.517 1 77.61 ? "H8'1" BNG 4003 AAA 1 
HETATM 44 H "H8'2" BNG . . . G 3 19.907 -14.857 -18.456 1 77.6 ? "H8'2" BNG 4003 AAA 1 
HETATM 45 H "H9'1" BNG . . . G 3 17.653 -15.743 -18.662 1 74.36 ? "H9'1" BNG 4003 AAA 1 
HETATM 46 H "H9'2" BNG . . . G 3 17.451 -15.736 -16.945 1 74.37 ? "H9'2" BNG 4003 AAA 1 
HETATM 47 H "H9'3" BNG . . . G 3 17.605 -14.243 -17.804 1 74.36 ? "H9'3" BNG 4003 AAA 1 
HETATM 48 H HO2 BNG . . . G 3 17.94 -12.1 -7.915 0 58.22 ? HO2 BNG 4003 AAA 1 
HETATM 49 H HO3 BNG . . . G 3 15.828 -13.835 -5.956 0 58.22 ? HO3 BNG 4003 AAA 1 
HETATM 50 H HO4 BNG . . . G 3 16.829 -16.846 -4.788 0 58.22 ? HO4 BNG 4003 AAA 1 
HETATM 51 H HO6 BNG . . . G 3 18.229 -18.422 -6.079 0 58.22 ? HO6 BNG 4003 AAA 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           308 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           51 
#