data_3BKD
#
_model_server_result.job_id            9sAb1J8d9R4F4aekVqCzag 
_model_server_result.datetime_utc      '2024-11-16 23:32:08' 
_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          3bkd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"U","auth_seq_id":701}' 
#
_entry.id    3BKD 
#
_exptl.entry_id    3BKD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              292.369 
_entity.id                          2 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            'octyl 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          103.53 
_cell.angle_gamma         90 
_cell.entry_id            3BKD 
_cell.length_a            38.753 
_cell.length_b            56.557 
_cell.length_c            56.009 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3BKD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
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 tetrameric 4 author_and_software_defined_assembly 1 
PISA tetrameric 4 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
E,F,G,H,Q,R,S,T,U,V,AA,BA,CA,DA 1 1 
A,B,C,D,I,J,K,L,M,N,O,P,W,X,Y,Z 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
? 2 I N N 
? 2 M N N 
? 2 P N N 
? 2 Q N N 
? 2 U N N 
? 2 V 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 C ILE 11 A ILE 32 1_555 A N MSE 12 A MSE 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 
covale ? covale2 A C MSE 12 A MSE 33 1_555 A N GLY 13 A GLY 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale3 A C LEU 25 A LEU 46 1_555 A N NH2 26 A NH2 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.268 ? 
covale ? covale4 B C ILE 11 B ILE 32 1_555 B N MSE 12 B MSE 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.348 ? 
covale ? covale5 B C MSE 12 B MSE 33 1_555 B N GLY 13 B GLY 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
covale ? covale6 B C LEU 25 B LEU 46 1_555 B N NH2 26 B NH2 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.264 ? 
covale ? covale7 C C ILE 11 C ILE 32 1_555 C N MSE 12 C MSE 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? 
covale ? covale8 C C MSE 12 C MSE 33 1_555 C N GLY 13 C GLY 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale9 C C LEU 25 C LEU 46 1_555 C N NH2 26 C NH2 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.262 ? 
covale ? covale10 D C ILE 11 D ILE 32 1_555 D N MSE 12 D MSE 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? 
covale ? covale11 D C MSE 12 D MSE 33 1_555 D N GLY 13 D GLY 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale12 D C LEU 25 D LEU 46 1_555 D N NH2 26 D NH2 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.26 ? 
covale ? covale13 E C ILE 11 E ILE 32 1_555 E N MSE 12 E MSE 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? 
covale ? covale14 E C MSE 12 E MSE 33 1_555 E N GLY 13 E GLY 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale15 E C LEU 25 E LEU 46 1_555 E N NH2 26 E NH2 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.268 ? 
covale ? covale16 F C ILE 11 F ILE 32 1_555 F N MSE 12 F MSE 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? 
covale ? covale17 F C MSE 12 F MSE 33 1_555 F N GLY 13 F GLY 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? 
covale ? covale18 F C LEU 25 F LEU 46 1_555 F N NH2 26 F NH2 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.266 ? 
covale ? covale19 G C ILE 11 G ILE 32 1_555 G N MSE 12 G MSE 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale20 G C MSE 12 G MSE 33 1_555 G N GLY 13 G GLY 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? 
covale ? covale21 G C LEU 25 G LEU 46 1_555 G N NH2 26 G NH2 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.268 ? 
covale ? covale22 H C ILE 11 H ILE 32 1_555 H N MSE 12 H MSE 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? 
covale ? covale23 H C MSE 12 H MSE 33 1_555 H N GLY 13 H GLY 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? 
covale ? covale24 H C LEU 25 H LEU 46 1_555 H N NH2 26 H NH2 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.262 ? 
#
_chem_comp.formula           'C14 H28 O6' 
_chem_comp.formula_weight    292.369 
_chem_comp.id                BOG 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              'octyl beta-D-glucopyranoside' 
_chem_comp.type              d-saccharide 
_chem_comp.pdbx_synonyms     'Beta-Octylglucoside;octyl beta-D-glucoside;octyl D-glucoside;octyl 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 O1 BOG sing 54 n n 
C1 C2 BOG sing 55 n n 
C1 O5 BOG sing 56 n n 
C1 H1 BOG sing 57 n n 
O1 C1' BOG sing 58 n n 
C2 O2 BOG sing 59 n n 
C2 C3 BOG sing 60 n n 
C2 H2 BOG sing 61 n n 
O2 HO2 BOG sing 62 n n 
C3 O3 BOG sing 63 n n 
C3 C4 BOG sing 64 n n 
C3 H3 BOG sing 65 n n 
O3 HO3 BOG sing 66 n n 
C4 O4 BOG sing 67 n n 
C4 C5 BOG sing 68 n n 
C4 H4 BOG sing 69 n n 
O4 HO4 BOG sing 70 n n 
C5 O5 BOG sing 71 n n 
C5 C6 BOG sing 72 n n 
C5 H5 BOG sing 73 n n 
C6 O6 BOG sing 74 n n 
C6 H61 BOG sing 75 n n 
C6 H62 BOG sing 76 n n 
O6 HO6 BOG sing 77 n n 
C1' C2' BOG sing 78 n n 
C1' "H1'1" BOG sing 79 n n 
C1' "H1'2" BOG sing 80 n n 
C2' C3' BOG sing 81 n n 
C2' "H2'1" BOG sing 82 n n 
C2' "H2'2" BOG sing 83 n n 
C3' C4' BOG sing 84 n n 
C3' "H3'1" BOG sing 85 n n 
C3' "H3'2" BOG sing 86 n n 
C4' C5' BOG sing 87 n n 
C4' "H4'1" BOG sing 88 n n 
C4' "H4'2" BOG sing 89 n n 
C5' C6' BOG sing 90 n n 
C5' "H5'1" BOG sing 91 n n 
C5' "H5'2" BOG sing 92 n n 
C6' C7' BOG sing 93 n n 
C6' "H6'1" BOG sing 94 n n 
C6' "H6'2" BOG sing 95 n n 
C7' C8' BOG sing 96 n n 
C7' "H7'1" BOG sing 97 n n 
C7' "H7'2" BOG sing 98 n n 
C8' "H8'1" BOG sing 99 n n 
C8' "H8'2" BOG sing 100 n n 
C8' "H8'3" BOG sing 101 n n 
#
_pdbx_chem_comp_identifier.comp_id            BOG 
_pdbx_chem_comp_identifier.identifier         b-octylglucoside 
_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                     3BKD 
_atom_sites.fract_transf_matrix[1][1]    0.025804 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.006209 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.017681 
_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]    0.018364 
_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
I 2 BOG A 1 302 302 BOG BOG . 
J 3 CL A 1 101 101 CL CL . 
K 4 PEG A 1 401 401 PEG PEG . 
L 4 PEG A 1 803 803 PEG PEG . 
M 2 BOG B 1 301 301 BOG BOG . 
N 4 PEG B 1 402 402 PEG PEG . 
O 4 PEG B 1 403 403 PEG PEG . 
P 2 BOG C 1 303 303 BOG BOG . 
Q 2 BOG E 1 702 702 BOG BOG . 
R 3 CL E 1 501 501 CL CL . 
S 4 PEG E 1 801 801 PEG PEG . 
T 4 PEG E 1 802 802 PEG PEG . 
U 2 BOG G 1 701 701 BOG BOG . 
V 2 BOG G 1 703 703 BOG BOG . 
W 5 HOH A 1 804 205 HOH HOH . 
W 5 HOH A 2 805 207 HOH HOH . 
W 5 HOH A 3 806 210 HOH HOH . 
W 5 HOH A 4 807 216 HOH HOH . 
W 5 HOH A 5 808 221 HOH HOH . 
W 5 HOH A 6 809 613 HOH HOH . 
X 5 HOH B 1 404 203 HOH HOH . 
X 5 HOH B 2 405 209 HOH HOH . 
X 5 HOH B 3 406 211 HOH HOH . 
X 5 HOH B 4 407 215 HOH HOH . 
Y 5 HOH C 1 304 202 HOH HOH . 
Y 5 HOH C 2 305 206 HOH HOH . 
Y 5 HOH C 3 306 212 HOH HOH . 
Y 5 HOH C 4 307 218 HOH HOH . 
Z 5 HOH D 1 48 201 HOH HOH . 
Z 5 HOH D 2 49 204 HOH HOH . 
Z 5 HOH D 3 50 208 HOH HOH . 
Z 5 HOH D 4 51 213 HOH HOH . 
Z 5 HOH D 5 52 217 HOH HOH . 
Z 5 HOH D 6 53 219 HOH HOH . 
Z 5 HOH D 7 54 220 HOH HOH . 
AA 5 HOH E 1 803 214 HOH HOH . 
AA 5 HOH E 2 804 601 HOH HOH . 
AA 5 HOH E 3 805 607 HOH HOH . 
AA 5 HOH E 4 806 610 HOH HOH . 
AA 5 HOH E 5 807 615 HOH HOH . 
AA 5 HOH E 6 808 618 HOH HOH . 
BA 5 HOH F 1 48 603 HOH HOH . 
BA 5 HOH F 2 49 609 HOH HOH . 
BA 5 HOH F 3 50 617 HOH HOH . 
CA 5 HOH G 1 704 602 HOH HOH . 
CA 5 HOH G 2 705 605 HOH HOH . 
CA 5 HOH G 3 706 606 HOH HOH . 
CA 5 HOH G 4 707 614 HOH HOH . 
DA 5 HOH H 1 48 604 HOH HOH . 
DA 5 HOH H 2 49 608 HOH HOH . 
DA 5 HOH H 3 50 611 HOH HOH . 
DA 5 HOH H 4 51 612 HOH HOH . 
DA 5 HOH H 5 52 616 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 BOG . . . U 2 -0.045 5.143 -25.696 0.8 56.39 ? C1 BOG 701 G 1 
HETATM 2 O O1 BOG . . . U 2 0.693 4.379 -24.741 0.8 57.39 ? O1 BOG 701 G 1 
HETATM 3 C C2 BOG . . . U 2 -0.428 6.486 -25.077 0.8 56.24 ? C2 BOG 701 G 1 
HETATM 4 O O2 BOG . . . U 2 0.706 7.348 -25.229 0.8 56.33 ? O2 BOG 701 G 1 
HETATM 5 C C3 BOG . . . U 2 -1.717 7.146 -25.627 0.8 56.27 ? C3 BOG 701 G 1 
HETATM 6 O O3 BOG . . . U 2 -1.471 8.494 -26.053 0.8 56.72 ? O3 BOG 701 G 1 
HETATM 7 C C4 BOG . . . U 2 -2.484 6.399 -26.734 0.8 56.49 ? C4 BOG 701 G 1 
HETATM 8 O O4 BOG . . . U 2 -2.765 7.302 -27.808 0.8 56.83 ? O4 BOG 701 G 1 
HETATM 9 C C5 BOG . . . U 2 -1.713 5.197 -27.264 0.8 56.56 ? C5 BOG 701 G 1 
HETATM 10 O O5 BOG . . . U 2 -1.216 4.469 -26.145 0.8 56.68 ? O5 BOG 701 G 1 
HETATM 11 C C6 BOG . . . U 2 -2.531 4.311 -28.189 0.8 56.96 ? C6 BOG 701 G 1 
HETATM 12 O O6 BOG . . . U 2 -2.036 4.514 -29.52 0.8 57.14 ? O6 BOG 701 G 1 
HETATM 13 C C1' BOG . . . U 2 1.148 3.127 -25.248 0.8 57.65 ? C1' BOG 701 G 1 
HETATM 14 C C2' BOG . . . U 2 2.67 3.066 -25.202 0.8 57.77 ? C2' BOG 701 G 1 
HETATM 15 C C3' BOG . . . U 2 3.144 1.622 -25.061 0.8 58.07 ? C3' BOG 701 G 1 
HETATM 16 C C4' BOG . . . U 2 4.604 1.468 -25.474 0.8 58.59 ? C4' BOG 701 G 1 
HETATM 17 C C5' BOG . . . U 2 5.557 1.77 -24.322 0.8 59.03 ? C5' BOG 701 G 1 
HETATM 18 C C6' BOG . . . U 2 6.23 0.498 -23.814 0.8 59.89 ? C6' BOG 701 G 1 
HETATM 19 C C7' BOG . . . U 2 7.243 0.804 -22.715 0.8 59.82 ? C7' BOG 701 G 1 
HETATM 20 C C8' BOG . . . U 2 6.98 -0.022 -21.473 0.8 60.18 ? C8' BOG 701 G 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           266 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           20 
#