data_6G9X
#
_model_server_result.job_id            ymcnwsSZ4nd4j7PEHqWXCQ 
_model_server_result.datetime_utc      '2024-11-27 17:10:31' 
_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          6g9x 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"U","auth_seq_id":507}' 
#
_entry.id    6G9X 
#
_exptl.entry_id    6G9X 
_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    6 
_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            6G9X 
_cell.length_a            106.765 
_cell.length_b            200.539 
_cell.length_c            64.561 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6G9X 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    'P 2 2ab' 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
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,X 1 1 
B,O,P,Q,R,S,T,U,V,W,Y 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
? 5 K N N 
? 5 L N N 
? 5 M N N 
? 5 U N N 
? 5 V N N 
? 5 W 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 SG CYS 56 A CYS 56 1_555 D HG HG . A HG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? 
metalc ? metalc2 A SG CYS 57 A CYS 57 1_555 G HG HG . A HG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? 
metalc ? metalc3 A O CYS 362 A CYS 362 1_555 C HG HG . A HG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? 
metalc ? metalc4 A O GLY 366 A GLY 366 1_555 G HG HG . A HG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.022 ? 
metalc ? metalc5 A SG CYS 389 A CYS 389 1_555 E HG HG . A HG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? 
metalc ? metalc6 E HG HG . A HG 503 1_555 L O2 BNG . A BNG 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.958 ? 
metalc ? metalc7 L O3 BNG . A BNG 510 1_555 N HG HG . A HG 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? 
metalc ? metalc8 B SG CYS 56 B CYS 56 1_555 P HG HG . B HG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? 
metalc ? metalc9 B SG CYS 57 B CYS 57 1_555 R HG HG . B HG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.519 ? 
metalc ? metalc10 B O CYS 362 B CYS 362 1_555 O HG HG . B HG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? 
metalc ? metalc11 B O GLY 366 B GLY 366 1_555 R HG HG . B HG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.099 ? 
metalc ? metalc12 B SG CYS 389 B CYS 389 1_555 Q HG HG . B HG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? 
metalc ? metalc13 B SG CYS 394 B CYS 394 1_555 S HG HG . B HG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.782 ? 
#
_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                     6G9X 
_atom_sites.fract_transf_matrix[1][1]    0.009366 
_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]    0.004987 
_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]    0.015489 
_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 HG A 1 501 1 HG HG . 
D 2 HG A 1 502 3 HG HG . 
E 2 HG A 1 503 5 HG HG . 
F 2 HG A 1 504 7 HG HG . 
G 2 HG A 1 505 9 HG HG . 
H 2 HG A 1 506 12 HG HG . 
I 3 JKE A 1 507 1 JKE JKE . 
J 4 EPE A 1 508 1 EPE EPE . 
K 5 BNG A 1 509 3 BNG BNG . 
L 5 BNG A 1 510 4 BNG BNG . 
M 5 BNG A 1 511 6 BNG BNG . 
N 2 HG A 1 512 8 HG HG . 
O 2 HG B 1 501 2 HG HG . 
P 2 HG B 1 502 4 HG HG . 
Q 2 HG B 1 503 6 HG HG . 
R 2 HG B 1 504 10 HG HG . 
S 2 HG B 1 505 11 HG HG . 
T 3 JKE B 1 506 2 JKE JKE . 
U 5 BNG B 1 507 1 BNG BNG . 
V 5 BNG B 1 508 2 BNG BNG . 
W 5 BNG B 1 509 5 BNG BNG . 
X 6 HOH A 1 601 1 HOH HOH . 
Y 6 HOH B 1 601 2 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 . . . U 5 138.316 31.335 62.371 1 120.57 ? C1 BNG 507 B 1 
HETATM 2 C C2 BNG . . . U 5 139.533 31.689 63.215 1 118.91 ? C2 BNG 507 B 1 
HETATM 3 C C3 BNG . . . U 5 139.098 31.546 64.627 1 119.49 ? C3 BNG 507 B 1 
HETATM 4 C C4 BNG . . . U 5 137.936 32.448 64.995 1 110.91 ? C4 BNG 507 B 1 
HETATM 5 C C5 BNG . . . U 5 136.84 32.622 63.894 1 110.83 ? C5 BNG 507 B 1 
HETATM 6 C C6 BNG . . . U 5 136.102 33.944 64.031 1 98.84 ? C6 BNG 507 B 1 
HETATM 7 C C1' BNG . . . U 5 138.757 32.151 60.193 1 103.11 ? C1' BNG 507 B 1 
HETATM 8 C C2' BNG . . . U 5 138.517 31.642 58.742 1 85.29 ? C2' BNG 507 B 1 
HETATM 9 C C3' BNG . . . U 5 139.354 32.502 57.776 1 72.97 ? C3' BNG 507 B 1 
HETATM 10 C C4' BNG . . . U 5 139.355 33.992 58.259 1 71.36 ? C4' BNG 507 B 1 
HETATM 11 C C5' BNG . . . U 5 138.196 34.773 57.585 1 69.88 ? C5' BNG 507 B 1 
HETATM 12 C C6' BNG . . . U 5 136.969 34.852 58.569 1 61.51 ? C6' BNG 507 B 1 
HETATM 13 C C7' BNG . . . U 5 135.674 35.234 57.779 1 53.69 ? C7' BNG 507 B 1 
HETATM 14 C C8' BNG . . . U 5 134.654 35.898 58.761 1 58.71 ? C8' BNG 507 B 1 
HETATM 15 C C9' BNG . . . U 5 134.788 35.334 60.206 1 60.94 ? C9' BNG 507 B 1 
HETATM 16 O O1 BNG . . . U 5 138.648 31.05 61.074 1 117.46 ? O1 BNG 507 B 1 
HETATM 17 O O2 BNG . . . U 5 140.658 30.827 62.948 1 115.37 ? O2 BNG 507 B 1 
HETATM 18 O O3 BNG . . . U 5 140.253 31.774 65.494 1 121.84 ? O3 BNG 507 B 1 
HETATM 19 O O4 BNG . . . U 5 137.349 31.961 66.221 1 97.39 ? O4 BNG 507 B 1 
HETATM 20 O O5 BNG . . . U 5 137.298 32.437 62.495 1 120.02 ? O5 BNG 507 B 1 
HETATM 21 O O6 BNG . . . U 5 136.35 34.895 63.017 1 86.22 ? O6 BNG 507 B 1 
#
_model_server_stats.io_time_ms              21 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           291 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           21 
#