data_5WBE # _model_server_result.job_id j1HLdDnc6URDJsJKYSZfVA _model_server_result.datetime_utc '2024-11-19 13:36:32' _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 5wbe # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":704}' # _entry.id 5WBE # _exptl.entry_id 5WBE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 292.369 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'octyl beta-D-glucopyranoside' _entity.pdbx_number_of_molecules 3 _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 120 _cell.entry_id 5WBE _cell.length_a 180.925 _cell.length_b 180.925 _cell.length_c 104.248 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WBE _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _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 _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 ? 5 J N N ? 5 N N N ? 5 O N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 MAN NAG C1 O1 . O4 HO4 . sing 4 ? 3 4 3 MAN MAN C1 O1 . O6 HO6 . sing 5 ? 3 5 4 MAN MAN C1 O1 . O6 HO6 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n C NAG 1 C 1 NAG C 661 NAG 2 n C NAG 2 C 2 NAG C 662 NAG 3 n D NAG 1 D 1 NAG C 671 NAG 3 n D NAG 2 D 2 NAG C 672 NAG 3 n D MAN 3 D 3 MAN C 673 MAN 3 n D MAN 4 D 4 MAN C 674 MAN 3 n D MAN 5 D 5 MAN C 675 MAN 2 n E NAG 1 E 1 NAG C 681 NAG 2 n E NAG 2 E 2 NAG C 682 NAG 2 n F NAG 1 F 1 NAG D 1661 NAG 2 n F NAG 2 F 2 NAG D 1662 NAG 3 n G NAG 1 G 1 NAG D 1671 NAG 3 n G NAG 2 G 2 NAG D 1672 NAG 3 n G MAN 3 G 3 MAN D 1673 MAN 3 n G MAN 4 G 4 MAN D 1674 MAN 3 n G MAN 5 G 5 MAN D 1675 MAN 2 n H NAG 1 H 1 NAG D 1681 NAG 2 n H NAG 2 H 2 NAG D 1682 NAG # 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 36 A CYS 36 1_555 A SG CYS 47 A CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf2 A SG CYS 37 A CYS 37 1_555 A SG CYS 159 A CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 A SG CYS 41 A CYS 41 1_555 A SG CYS 57 A CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 59 A CYS 59 1_555 A SG CYS 69 A CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf5 A SG CYS 569 A CYS 569 1_555 A SG CYS 575 A CYS 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 B SG CYS 36 B CYS 36 1_555 B SG CYS 47 B CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf7 B SG CYS 37 B CYS 37 1_555 B SG CYS 159 B CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 B SG CYS 41 B CYS 41 1_555 B SG CYS 57 B CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf9 B SG CYS 59 B CYS 59 1_555 B SG CYS 69 B CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf10 B SG CYS 569 B CYS 569 1_555 B SG CYS 575 B CYS 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 68 A ASN 68 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale2 A ND2 ASN 144 A ASN 144 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 A ND2 ASN 410 A ASN 410 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale4 B ND2 ASN 68 B ASN 68 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale5 B ND2 ASN 144 B ASN 144 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale6 B ND2 ASN 410 B ASN 410 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale7 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale8 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale9 D O4 NAG . D NAG 2 1_555 D C1 MAN . D MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale10 D O6 MAN . D MAN 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale11 D O6 MAN . D MAN 4 1_555 D C1 MAN . D MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale12 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale13 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale14 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale15 G O4 NAG . G NAG 2 1_555 G C1 MAN . G MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale16 G O6 MAN . G MAN 3 1_555 G C1 MAN . G MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale17 G O6 MAN . G MAN 4 1_555 G C1 MAN . G MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale18 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? metalc ? metalc1 A NE2 HIS 388 A HIS 388 1_555 I FE HEM . A HEM 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.566 ? metalc ? metalc2 B NE2 HIS 388 B HIS 388 1_555 L FE HEM . B HEM 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.487 ? # _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 114 n n C1 C2 BOG sing 115 n n C1 O5 BOG sing 116 n n C1 H1 BOG sing 117 n n O1 C1' BOG sing 118 n n C2 O2 BOG sing 119 n n C2 C3 BOG sing 120 n n C2 H2 BOG sing 121 n n O2 HO2 BOG sing 122 n n C3 O3 BOG sing 123 n n C3 C4 BOG sing 124 n n C3 H3 BOG sing 125 n n O3 HO3 BOG sing 126 n n C4 O4 BOG sing 127 n n C4 C5 BOG sing 128 n n C4 H4 BOG sing 129 n n O4 HO4 BOG sing 130 n n C5 O5 BOG sing 131 n n C5 C6 BOG sing 132 n n C5 H5 BOG sing 133 n n C6 O6 BOG sing 134 n n C6 H61 BOG sing 135 n n C6 H62 BOG sing 136 n n O6 HO6 BOG sing 137 n n C1' C2' BOG sing 138 n n C1' "H1'1" BOG sing 139 n n C1' "H1'2" BOG sing 140 n n C2' C3' BOG sing 141 n n C2' "H2'1" BOG sing 142 n n C2' "H2'2" BOG sing 143 n n C3' C4' BOG sing 144 n n C3' "H3'1" BOG sing 145 n n C3' "H3'2" BOG sing 146 n n C4' C5' BOG sing 147 n n C4' "H4'1" BOG sing 148 n n C4' "H4'2" BOG sing 149 n n C5' C6' BOG sing 150 n n C5' "H5'1" BOG sing 151 n n C5' "H5'2" BOG sing 152 n n C6' C7' BOG sing 153 n n C6' "H6'1" BOG sing 154 n n C6' "H6'2" BOG sing 155 n n C7' C8' BOG sing 156 n n C7' "H7'1" BOG sing 157 n n C7' "H7'2" BOG sing 158 n n C8' "H8'1" BOG sing 159 n n C8' "H8'2" BOG sing 160 n n C8' "H8'3" BOG sing 161 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 5WBE _atom_sites.fract_transf_matrix[1][1] 0.005527 _atom_sites.fract_transf_matrix[1][2] 0.003191 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006382 _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] 0.009593 _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 4 HEM A 1 801 801 HEM HEM . J 5 BOG A 1 802 751 BOG BOG . K 6 63X A 1 803 1 63X MOF . L 4 HEM B 1 701 601 HEM HEM . M 6 63X B 1 702 2 63X MOF . N 5 BOG B 1 703 1751 BOG BOG . O 5 BOG B 1 704 1750 BOG BOG . P 7 HOH A 1 901 15 HOH HOH . P 7 HOH A 2 902 11 HOH HOH . P 7 HOH A 3 903 16 HOH HOH . P 7 HOH A 4 904 26 HOH HOH . P 7 HOH A 5 905 5 HOH HOH . P 7 HOH A 6 906 34 HOH HOH . P 7 HOH A 7 907 23 HOH HOH . P 7 HOH A 8 908 35 HOH HOH . P 7 HOH A 9 909 30 HOH HOH . P 7 HOH A 10 910 29 HOH HOH . P 7 HOH A 11 911 32 HOH HOH . P 7 HOH A 12 912 39 HOH HOH . P 7 HOH A 13 913 31 HOH HOH . P 7 HOH A 14 914 6 HOH HOH . P 7 HOH A 15 915 13 HOH HOH . P 7 HOH A 16 916 22 HOH HOH . P 7 HOH A 17 917 25 HOH HOH . P 7 HOH A 18 918 7 HOH HOH . P 7 HOH A 19 919 17 HOH HOH . P 7 HOH A 20 920 27 HOH HOH . Q 7 HOH B 1 801 8 HOH HOH . Q 7 HOH B 2 802 14 HOH HOH . Q 7 HOH B 3 803 18 HOH HOH . Q 7 HOH B 4 804 1 HOH HOH . Q 7 HOH B 5 805 10 HOH HOH . Q 7 HOH B 6 806 3 HOH HOH . Q 7 HOH B 7 807 2 HOH HOH . Q 7 HOH B 8 808 33 HOH HOH . Q 7 HOH B 9 809 4 HOH HOH . Q 7 HOH B 10 810 28 HOH HOH . Q 7 HOH B 11 811 12 HOH HOH . Q 7 HOH B 12 812 19 HOH HOH . Q 7 HOH B 13 813 38 HOH HOH . Q 7 HOH B 14 814 21 HOH HOH . Q 7 HOH B 15 815 24 HOH HOH . Q 7 HOH B 16 816 36 HOH HOH . Q 7 HOH B 17 817 9 HOH HOH . Q 7 HOH B 18 818 37 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 . . . O 5 50.537 154.482 -29.048 1 84.73 ? C1 BOG 704 B 1 HETATM 2 O O1 BOG . . . O 5 51.875 154.075 -29.161 1 84.99 ? O1 BOG 704 B 1 HETATM 3 C C2 BOG . . . O 5 50.409 156.048 -28.843 1 84.8 ? C2 BOG 704 B 1 HETATM 4 O O2 BOG . . . O 5 51.129 156.48 -27.678 1 85.19 ? O2 BOG 704 B 1 HETATM 5 C C3 BOG . . . O 5 48.897 156.426 -28.736 1 84.85 ? C3 BOG 704 B 1 HETATM 6 O O3 BOG . . . O 5 48.782 157.839 -28.548 1 84.85 ? O3 BOG 704 B 1 HETATM 7 C C4 BOG . . . O 5 48.156 155.941 -30.049 1 84.73 ? C4 BOG 704 B 1 HETATM 8 O O4 BOG . . . O 5 46.75 156.28 -29.99 1 84.66 ? O4 BOG 704 B 1 HETATM 9 C C5 BOG . . . O 5 48.296 154.468 -30.217 1 84.54 ? C5 BOG 704 B 1 HETATM 10 O O5 BOG . . . O 5 49.762 154.055 -30.271 1 84.44 ? O5 BOG 704 B 1 HETATM 11 C C6 BOG . . . O 5 47.593 153.955 -31.524 1 84.41 ? C6 BOG 704 B 1 HETATM 12 O O6 BOG . . . O 5 47.73 152.544 -31.761 1 84.31 ? O6 BOG 704 B 1 HETATM 13 C C1' BOG . . . O 5 52.289 152.883 -28.464 1 85.76 ? C1' BOG 704 B 1 HETATM 14 C C2' BOG . . . O 5 53.768 152.668 -28.747 1 86.39 ? C2' BOG 704 B 1 HETATM 15 C C3' BOG . . . O 5 54.358 151.857 -27.807 1 87.17 ? C3' BOG 704 B 1 HETATM 16 C C4' BOG . . . O 5 55.808 152.264 -27.556 1 88.05 ? C4' BOG 704 B 1 HETATM 17 C C5' BOG . . . O 5 56.536 151.23 -26.687 1 88.64 ? C5' BOG 704 B 1 HETATM 18 C C6' BOG . . . O 5 57.093 151.85 -25.404 1 89.11 ? C6' BOG 704 B 1 HETATM 19 C C7' BOG . . . O 5 57.737 150.902 -24.646 1 89.48 ? C7' BOG 704 B 1 HETATM 20 C C8' BOG . . . O 5 58.281 151.536 -23.375 1 89.52 ? C8' BOG 704 B 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 251 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 20 #