data_6FKD # _model_server_result.job_id -pe4fNUOoGJgZ9xEgQ9Dqg _model_server_result.datetime_utc '2024-11-23 05:00:30' _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 6fkd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":407}' # _entry.id 6FKD # _exptl.entry_id 6FKD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 292.369 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'octyl beta-D-glucopyranoside' _entity.pdbx_number_of_molecules 5 _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 6FKD _cell.length_a 243.431 _cell.length_b 243.431 _cell.length_c 111.782 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6FKD _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 ? 4 D N N ? 4 E N N ? 4 F N N ? 4 G N N ? 4 H N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type 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 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 2 5 3 MAN BMA 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 B NAG 1 B 1 NAG A 400 NAG 2 n B NAG 2 B 2 NAG A 401 NAG 2 n B BMA 3 B 3 BMA A 402 BMA 2 n B MAN 4 B 4 MAN A 403 MAN 2 n B MAN 5 B 5 MAN A 404 MAN # 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 3 A CYS 2 1_555 A SG CYS 283 A CYS 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf2 A SG CYS 111 A CYS 110 1_555 A SG CYS 188 A CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? covale ? covale1 A C ACE 1 A ACE 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale2 A ND2 ASN 16 A ASN 15 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale3 A SG CYS 323 A CYS 322 1_555 C C1 PLM . A PLM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.724 ? covale ? covale4 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale5 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale6 B O3 BMA . B BMA 3 1_555 B C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale7 B O6 BMA . B BMA 3 1_555 B C1 MAN . B MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? # _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 100 n n C1 C2 BOG sing 101 n n C1 O5 BOG sing 102 n n C1 H1 BOG sing 103 n n O1 C1' BOG sing 104 n n C2 O2 BOG sing 105 n n C2 C3 BOG sing 106 n n C2 H2 BOG sing 107 n n O2 HO2 BOG sing 108 n n C3 O3 BOG sing 109 n n C3 C4 BOG sing 110 n n C3 H3 BOG sing 111 n n O3 HO3 BOG sing 112 n n C4 O4 BOG sing 113 n n C4 C5 BOG sing 114 n n C4 H4 BOG sing 115 n n O4 HO4 BOG sing 116 n n C5 O5 BOG sing 117 n n C5 C6 BOG sing 118 n n C5 H5 BOG sing 119 n n C6 O6 BOG sing 120 n n C6 H61 BOG sing 121 n n C6 H62 BOG sing 122 n n O6 HO6 BOG sing 123 n n C1' C2' BOG sing 124 n n C1' "H1'1" BOG sing 125 n n C1' "H1'2" BOG sing 126 n n C2' C3' BOG sing 127 n n C2' "H2'1" BOG sing 128 n n C2' "H2'2" BOG sing 129 n n C3' C4' BOG sing 130 n n C3' "H3'1" BOG sing 131 n n C3' "H3'2" BOG sing 132 n n C4' C5' BOG sing 133 n n C4' "H4'1" BOG sing 134 n n C4' "H4'2" BOG sing 135 n n C5' C6' BOG sing 136 n n C5' "H5'1" BOG sing 137 n n C5' "H5'2" BOG sing 138 n n C6' C7' BOG sing 139 n n C6' "H6'1" BOG sing 140 n n C6' "H6'2" BOG sing 141 n n C7' C8' BOG sing 142 n n C7' "H7'1" BOG sing 143 n n C7' "H7'2" BOG sing 144 n n C8' "H8'1" BOG sing 145 n n C8' "H8'2" BOG sing 146 n n C8' "H8'3" BOG sing 147 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 6FKD _atom_sites.fract_transf_matrix[1][1] 0.004108 _atom_sites.fract_transf_matrix[1][2] 0.002372 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004743 _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] 0.008946 _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 3 PLM A 1 401 1322 PLM P1L . D 4 BOG A 1 407 500 BOG BOG . E 4 BOG A 1 408 501 BOG BOG . F 4 BOG A 1 409 502 BOG BOG . G 4 BOG A 1 410 503 BOG BOG . H 4 BOG A 1 411 504 BOG BOG . I 5 DL2 A 1 412 600 DL2 L0R . J 6 HOH A 1 501 1006 HOH HOH . J 6 HOH A 2 502 1000 HOH HOH . J 6 HOH A 3 503 1004 HOH HOH . J 6 HOH A 4 504 1011 HOH HOH . J 6 HOH A 5 505 1002 HOH HOH . J 6 HOH A 6 506 1015 HOH HOH . J 6 HOH A 7 507 1022 HOH HOH . J 6 HOH A 8 508 1001 HOH HOH . J 6 HOH A 9 509 1016 HOH HOH . J 6 HOH A 10 510 1012 HOH HOH . J 6 HOH A 11 511 1010 HOH HOH . J 6 HOH A 12 512 1007 HOH HOH . J 6 HOH A 13 513 1018 HOH HOH . J 6 HOH A 14 514 1023 HOH HOH . J 6 HOH A 15 515 1009 HOH HOH . J 6 HOH A 16 516 1003 HOH HOH . J 6 HOH A 17 517 1024 HOH HOH . J 6 HOH A 18 518 1013 HOH HOH . J 6 HOH A 19 519 1005 HOH HOH . J 6 HOH A 20 520 1014 HOH HOH . J 6 HOH A 21 521 1021 HOH HOH . J 6 HOH A 22 522 1017 HOH HOH . J 6 HOH A 23 523 1019 HOH HOH . J 6 HOH A 24 524 1008 HOH HOH . J 6 HOH A 25 525 1020 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 . . . D 4 -229.934 45.02 38.637 1 80.37 ? C1 BOG 407 A 1 HETATM 2 O O1 BOG . . . D 4 -230.634 44.15 39.525 1 85.87 ? O1 BOG 407 A 1 HETATM 3 C C2 BOG . . . D 4 -230.206 46.471 39.011 1 82.42 ? C2 BOG 407 A 1 HETATM 4 O O2 BOG . . . D 4 -231.609 46.72 38.908 1 80.4 ? O2 BOG 407 A 1 HETATM 5 C C3 BOG . . . D 4 -229.405 47.424 38.134 1 80.29 ? C3 BOG 407 A 1 HETATM 6 O O3 BOG . . . D 4 -229.546 48.758 38.635 1 92.12 ? O3 BOG 407 A 1 HETATM 7 C C4 BOG . . . D 4 -227.934 47.024 38.158 1 74.26 ? C4 BOG 407 A 1 HETATM 8 O O4 BOG . . . D 4 -227.203 47.772 37.183 1 68.21 ? O4 BOG 407 A 1 HETATM 9 C C5 BOG . . . D 4 -227.766 45.549 37.814 1 75.03 ? C5 BOG 407 A 1 HETATM 10 O O5 BOG . . . D 4 -228.536 44.74 38.699 1 71.69 ? O5 BOG 407 A 1 HETATM 11 C C6 BOG . . . D 4 -226.3 45.135 37.895 1 62.52 ? C6 BOG 407 A 1 HETATM 12 O O6 BOG . . . D 4 -225.927 45.063 39.275 1 68.7 ? O6 BOG 407 A 1 HETATM 13 C C1' BOG . . . D 4 -230.796 42.863 38.93 1 83.26 ? C1' BOG 407 A 1 HETATM 14 C C2' BOG . . . D 4 -231.866 42.063 39.659 1 73.85 ? C2' BOG 407 A 1 HETATM 15 C C3' BOG . . . D 4 -231.99 40.673 39.038 1 80.74 ? C3' BOG 407 A 1 HETATM 16 C C4' BOG . . . D 4 -232.954 39.786 39.824 1 77.67 ? C4' BOG 407 A 1 HETATM 17 C C5' BOG . . . D 4 -232.909 38.344 39.324 1 88.67 ? C5' BOG 407 A 1 HETATM 18 C C6' BOG . . . D 4 -233.826 37.442 40.149 1 90.16 ? C6' BOG 407 A 1 HETATM 19 C C7' BOG . . . D 4 -235.282 37.89 40.063 1 83.46 ? C7' BOG 407 A 1 HETATM 20 C C8' BOG . . . D 4 -236.069 37.369 41.244 1 69.68 ? C8' BOG 407 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #