data_1VGO
#
_model_server_result.job_id            t3nyXFjMCIr1m56Q03tg7A 
_model_server_result.datetime_utc      '2024-11-02 05:28:13' 
_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          1vgo 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":302}' 
#
_entry.id    1VGO 
#
_exptl.entry_id    1VGO 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              306.395 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'nonyl beta-D-glucopyranoside' 
_entity.pdbx_number_of_molecules    12 
_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            1VGO 
_cell.length_a            122.88 
_cell.length_b            139.48 
_cell.length_c            108.1 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1VGO 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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,O,P,Q,R,S,T,U 
_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 C N N 
? 2 D N N 
? 2 E N N 
? 2 F N N 
? 2 G N N 
? 2 H N N 
? 2 I N N 
? 2 J N N 
? 2 K N N 
? 2 N N N 
? 2 O N N 
? 2 P 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
covale ? covale1 A NZ LYS 221 A LYS 221 1_555 M C15 RET . A RET 260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.354 ? 
covale ? covale2 B NZ LYS 221 B LYS 221 1_555 S C15 RET . B RET 261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.356 ? 
#
_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                     1VGO 
_atom_sites.fract_transf_matrix[1][1]    0.008138 
_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]    0.007169 
_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]    0.009251 
_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 BNG A 1 301 301 BNG BNG . 
D 2 BNG A 1 302 302 BNG BNG . 
E 2 BNG A 1 303 303 BNG BNG . 
F 2 BNG A 1 304 304 BNG BNG . 
G 2 BNG A 1 305 305 BNG BNG . 
H 2 BNG A 1 306 306 BNG BNG . 
I 2 BNG A 1 307 307 BNG BNG . 
J 2 BNG A 1 308 308 BNG BNG . 
K 2 BNG A 1 309 309 BNG BNG . 
L 3 SO4 A 1 400 400 SO4 SO4 . 
M 4 RET A 1 260 260 RET RET . 
N 2 BNG B 1 310 310 BNG BNG . 
O 2 BNG B 1 311 311 BNG BNG . 
P 2 BNG B 1 312 312 BNG BNG . 
Q 3 SO4 B 1 401 401 SO4 SO4 . 
R 3 SO4 B 1 402 402 SO4 SO4 . 
S 4 RET B 1 261 261 RET RET . 
T 5 HOH A 1 501 501 HOH HOH . 
T 5 HOH A 2 502 502 HOH HOH . 
T 5 HOH A 3 503 503 HOH HOH . 
T 5 HOH A 4 504 504 HOH HOH . 
T 5 HOH A 5 505 505 HOH HOH . 
T 5 HOH A 6 506 506 HOH HOH . 
T 5 HOH A 7 507 507 HOH HOH . 
T 5 HOH A 8 508 508 HOH HOH . 
T 5 HOH A 9 509 509 HOH HOH . 
T 5 HOH A 10 510 510 HOH HOH . 
T 5 HOH A 11 511 511 HOH HOH . 
T 5 HOH A 12 512 512 HOH HOH . 
T 5 HOH A 13 513 513 HOH HOH . 
T 5 HOH A 14 701 701 HOH HOH . 
T 5 HOH A 15 702 702 HOH HOH . 
T 5 HOH A 16 705 705 HOH HOH . 
U 5 HOH B 1 601 601 HOH HOH . 
U 5 HOH B 2 602 602 HOH HOH . 
U 5 HOH B 3 603 603 HOH HOH . 
U 5 HOH B 4 605 605 HOH HOH . 
U 5 HOH B 5 606 606 HOH HOH . 
U 5 HOH B 6 607 607 HOH HOH . 
U 5 HOH B 7 608 608 HOH HOH . 
U 5 HOH B 8 700 700 HOH HOH . 
U 5 HOH B 9 703 703 HOH HOH . 
U 5 HOH B 10 704 704 HOH HOH . 
U 5 HOH B 11 706 706 HOH HOH . 
U 5 HOH B 12 707 707 HOH HOH . 
U 5 HOH B 13 708 708 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 . . . D 2 23.351 0.062 73.291 1 116.3 ? C1 BNG 302 A 1 
HETATM 2 C C2 BNG . . . D 2 22.229 -0.695 74.178 1 116.63 ? C2 BNG 302 A 1 
HETATM 3 C C3 BNG . . . D 2 22.802 -0.849 75.662 1 117.14 ? C3 BNG 302 A 1 
HETATM 4 C C4 BNG . . . D 2 24.065 -1.695 75.622 1 118.29 ? C4 BNG 302 A 1 
HETATM 5 C C5 BNG . . . D 2 25.16 -0.953 74.702 1 118.61 ? C5 BNG 302 A 1 
HETATM 6 C C6 BNG . . . D 2 26.413 -1.802 74.643 1 119.36 ? C6 BNG 302 A 1 
HETATM 7 C C1' BNG . . . D 2 23.496 1.244 71.235 1 109.93 ? C1' BNG 302 A 1 
HETATM 8 C C2' BNG . . . D 2 22.897 1.395 69.794 1 106.85 ? C2' BNG 302 A 1 
HETATM 9 C C3' BNG . . . D 2 23.665 0.676 68.754 1 102.75 ? C3' BNG 302 A 1 
HETATM 10 C C4' BNG . . . D 2 22.995 0.878 67.386 1 98.9 ? C4' BNG 302 A 1 
HETATM 11 C C5' BNG . . . D 2 23.793 0.147 66.369 1 96.24 ? C5' BNG 302 A 1 
HETATM 12 C C6' BNG . . . D 2 22.931 -0.43 65.261 1 92.74 ? C6' BNG 302 A 1 
HETATM 13 C C7' BNG . . . D 2 23.819 -1.139 64.281 1 90.28 ? C7' BNG 302 A 1 
HETATM 14 C C8' BNG . . . D 2 23.042 -1.75 63.134 1 87.72 ? C8' BNG 302 A 1 
HETATM 15 C C9' BNG . . . D 2 24.03 -2.424 62.221 1 86.65 ? C9' BNG 302 A 1 
HETATM 16 O O1 BNG . . . D 2 22.834 0.215 71.932 1 113.69 ? O1 BNG 302 A 1 
HETATM 17 O O2 BNG . . . D 2 21.045 0.088 74.177 1 116.06 ? O2 BNG 302 A 1 
HETATM 18 O O3 BNG . . . D 2 21.823 -1.519 76.479 1 117.25 ? O3 BNG 302 A 1 
HETATM 19 O O4 BNG . . . D 2 24.638 -1.872 76.994 1 118.45 ? O4 BNG 302 A 1 
HETATM 20 O O5 BNG . . . D 2 24.566 -0.758 73.318 1 118.63 ? O5 BNG 302 A 1 
HETATM 21 O O6 BNG . . . D 2 27.434 -1.212 73.841 1 120.17 ? O6 BNG 302 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           281 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           21 
#