data_3EH5
#
_model_server_result.job_id            a-Q5AObVIr9VHkn8cGkdOw 
_model_server_result.datetime_utc      '2025-07-14 02:19:43' 
_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          3eh5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":806}' 
#
_entry.id    3EH5 
#
_exptl.entry_id    3EH5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              306.395 
_entity.id                          7 
_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            3EH5 
_cell.length_a            115.631 
_cell.length_b            115.631 
_cell.length_c            149.169 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3EH5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 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
PISA trimeric 3 software_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
? monomeric 1 author_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H,I,J,K,L,M,N 1 1 
A,D,E,F,G,H,I,L 2 1 
B,J,M 3 1 
C,K,N 4 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
? 7 G N N 
? 7 H N N 
? 7 I N N 
? 7 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 NE2 HIS 128 A HIS 72 1_555 E FE HEM . A HEM 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? 
metalc ? metalc2 A ND1 HIS 289 A HIS 233 1_555 D CU CU1 . A CU1 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? 
metalc ? metalc3 A NE2 HIS 338 A HIS 282 1_555 D CU CU1 . A CU1 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? 
metalc ? metalc4 A NE2 HIS 339 A HIS 283 1_555 D CU CU1 . A CU1 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc5 A NE2 HIS 440 A HIS 384 1_555 F FE HAS . A HAS 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? 
metalc ? metalc6 A NE2 HIS 442 A HIS 386 1_555 E FE HEM . A HEM 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
metalc ? metalc7 B ND1 HIS 112 B HIS 114 1_555 J CU2 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? 
metalc ? metalc8 B ND1 HIS 155 B HIS 157 1_555 J CU1 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
#
_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                     3EH5 
_atom_sites.fract_transf_matrix[1][1]    0.008648 
_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]    0.008648 
_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]    0.006704 
_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
D 4 CU1 A 1 803 803 CU1 CU1 . 
E 5 HEM A 1 800 800 HEM HEM . 
F 6 HAS A 1 801 801 HAS HAS . 
G 7 BNG A 1 805 805 BNG BNG . 
H 7 BNG A 1 806 806 BNG BNG . 
I 7 BNG A 1 807 807 BNG BNG . 
J 8 CUA B 1 802 802 CUA CUA . 
K 7 BNG C 1 804 804 BNG BNG . 
L 9 HOH A 1 563 1 HOH HOH . 
L 9 HOH A 2 564 2 HOH HOH . 
L 9 HOH A 3 565 3 HOH HOH . 
L 9 HOH A 4 566 4 HOH HOH . 
L 9 HOH A 5 567 5 HOH HOH . 
L 9 HOH A 6 568 6 HOH HOH . 
L 9 HOH A 7 569 7 HOH HOH . 
L 9 HOH A 8 570 8 HOH HOH . 
L 9 HOH A 9 571 9 HOH HOH . 
L 9 HOH A 10 572 10 HOH HOH . 
L 9 HOH A 11 573 11 HOH HOH . 
L 9 HOH A 12 574 13 HOH HOH . 
L 9 HOH A 13 575 15 HOH HOH . 
L 9 HOH A 14 576 16 HOH HOH . 
L 9 HOH A 15 577 17 HOH HOH . 
L 9 HOH A 16 578 19 HOH HOH . 
L 9 HOH A 17 579 20 HOH HOH . 
L 9 HOH A 18 580 21 HOH HOH . 
L 9 HOH A 19 581 22 HOH HOH . 
L 9 HOH A 20 582 23 HOH HOH . 
L 9 HOH A 21 583 24 HOH HOH . 
L 9 HOH A 22 584 25 HOH HOH . 
L 9 HOH A 23 585 27 HOH HOH . 
L 9 HOH A 24 586 28 HOH HOH . 
L 9 HOH A 25 587 30 HOH HOH . 
L 9 HOH A 26 588 31 HOH HOH . 
L 9 HOH A 27 589 32 HOH HOH . 
L 9 HOH A 28 590 33 HOH HOH . 
L 9 HOH A 29 591 34 HOH HOH . 
L 9 HOH A 30 592 35 HOH HOH . 
L 9 HOH A 31 593 36 HOH HOH . 
L 9 HOH A 32 594 37 HOH HOH . 
L 9 HOH A 33 595 38 HOH HOH . 
L 9 HOH A 34 596 39 HOH HOH . 
L 9 HOH A 35 597 40 HOH HOH . 
L 9 HOH A 36 598 41 HOH HOH . 
L 9 HOH A 37 599 42 HOH HOH . 
L 9 HOH A 38 600 44 HOH HOH . 
L 9 HOH A 39 601 45 HOH HOH . 
L 9 HOH A 40 602 46 HOH HOH . 
L 9 HOH A 41 603 47 HOH HOH . 
L 9 HOH A 42 604 51 HOH HOH . 
L 9 HOH A 43 605 52 HOH HOH . 
L 9 HOH A 44 606 57 HOH HOH . 
L 9 HOH A 45 607 58 HOH HOH . 
L 9 HOH A 46 608 59 HOH HOH . 
L 9 HOH A 47 609 60 HOH HOH . 
L 9 HOH A 48 610 61 HOH HOH . 
L 9 HOH A 49 611 62 HOH HOH . 
L 9 HOH A 50 612 63 HOH HOH . 
L 9 HOH A 51 613 64 HOH HOH . 
L 9 HOH A 52 614 66 HOH HOH . 
L 9 HOH A 53 615 67 HOH HOH . 
L 9 HOH A 54 616 72 HOH HOH . 
L 9 HOH A 55 617 75 HOH HOH . 
L 9 HOH A 56 618 76 HOH HOH . 
L 9 HOH A 57 619 77 HOH HOH . 
L 9 HOH A 58 620 78 HOH HOH . 
L 9 HOH A 59 621 79 HOH HOH . 
L 9 HOH A 60 622 80 HOH HOH . 
L 9 HOH A 61 623 81 HOH HOH . 
L 9 HOH A 62 624 82 HOH HOH . 
L 9 HOH A 63 625 83 HOH HOH . 
M 9 HOH B 1 169 12 HOH HOH . 
M 9 HOH B 2 170 14 HOH HOH . 
M 9 HOH B 3 171 26 HOH HOH . 
M 9 HOH B 4 172 29 HOH HOH . 
M 9 HOH B 5 173 43 HOH HOH . 
M 9 HOH B 6 174 48 HOH HOH . 
M 9 HOH B 7 175 49 HOH HOH . 
M 9 HOH B 8 176 50 HOH HOH . 
M 9 HOH B 9 177 53 HOH HOH . 
M 9 HOH B 10 178 54 HOH HOH . 
M 9 HOH B 11 179 55 HOH HOH . 
M 9 HOH B 12 180 56 HOH HOH . 
M 9 HOH B 13 181 65 HOH HOH . 
M 9 HOH B 14 182 68 HOH HOH . 
M 9 HOH B 15 183 69 HOH HOH . 
M 9 HOH B 16 184 70 HOH HOH . 
M 9 HOH B 17 185 71 HOH HOH . 
M 9 HOH B 18 186 73 HOH HOH . 
M 9 HOH B 19 187 74 HOH HOH . 
N 9 HOH C 1 35 18 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 . . . H 7 -41.404 13.278 -17.1 1 143.83 ? C1 BNG 806 A 1 
HETATM 2 C C2 BNG . . . H 7 -39.924 13.251 -16.654 1 141.75 ? C2 BNG 806 A 1 
HETATM 3 C C3 BNG . . . H 7 -39.537 14.126 -15.421 1 141.18 ? C3 BNG 806 A 1 
HETATM 4 C C4 BNG . . . H 7 -40.377 15.439 -15.309 1 140.69 ? C4 BNG 806 A 1 
HETATM 5 C C5 BNG . . . H 7 -41.861 15.119 -15.533 1 142.16 ? C5 BNG 806 A 1 
HETATM 6 C C6 BNG . . . H 7 -42.736 16.358 -15.397 1 142.11 ? C6 BNG 806 A 1 
HETATM 7 C C1' BNG . . . H 7 -42.081 11.677 -18.808 1 142.28 ? C1' BNG 806 A 1 
HETATM 8 C C2' BNG . . . H 7 -43.41 11.87 -19.55 1 142.58 ? C2' BNG 806 A 1 
HETATM 9 C C3' BNG . . . H 7 -43.688 10.787 -20.6 1 142.06 ? C3' BNG 806 A 1 
HETATM 10 C C4' BNG . . . H 7 -44.515 11.331 -21.768 1 141.38 ? C4' BNG 806 A 1 
HETATM 11 C C5' BNG . . . H 7 -44.706 10.3 -22.883 1 141.35 ? C5' BNG 806 A 1 
HETATM 12 C C6' BNG . . . H 7 -46.176 9.889 -23.039 1 139.76 ? C6' BNG 806 A 1 
HETATM 13 C C7' BNG . . . H 7 -46.339 8.417 -23.45 1 138.35 ? C7' BNG 806 A 1 
HETATM 14 C C8' BNG . . . H 7 -46.352 7.425 -22.28 1 136.3 ? C8' BNG 806 A 1 
HETATM 15 C C9' BNG . . . H 7 -47.756 7.037 -21.857 1 134.3 ? C9' BNG 806 A 1 
HETATM 16 O O1 BNG . . . H 7 -41.472 12.943 -18.507 1 143.13 ? O1 BNG 806 A 1 
HETATM 17 O O2 BNG . . . H 7 -39.625 11.865 -16.425 1 139.1 ? O2 BNG 806 A 1 
HETATM 18 O O3 BNG . . . H 7 -38.086 14.286 -15.353 1 134.03 ? O3 BNG 806 A 1 
HETATM 19 O O4 BNG . . . H 7 -40.253 16.134 -14.049 1 136.31 ? O4 BNG 806 A 1 
HETATM 20 O O5 BNG . . . H 7 -42.057 14.547 -16.842 1 144.89 ? O5 BNG 806 A 1 
HETATM 21 O O6 BNG . . . H 7 -44.095 15.966 -15.612 1 141.95 ? O6 BNG 806 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           237 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           21 
#