data_5U6X # _model_server_result.job_id os-fzgMpqsSvETQlfrJG3Q _model_server_result.datetime_utc '2024-11-19 15:37:59' _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 5u6x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":703}' # _entry.id 5U6X # _exptl.entry_id 5U6X _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 292.369 _entity.id 6 _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 5U6X _cell.length_a 181.463 _cell.length_b 181.463 _cell.length_c 103.5 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5U6X _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 _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 ? 6 K N N ? 6 N N N ? 6 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 E 661 NAG 2 n C NAG 2 C 2 NAG E 662 NAG 3 n D NAG 1 D 1 NAG E 671 NAG 3 n D NAG 2 D 2 NAG E 672 NAG 3 n D MAN 3 D 3 MAN E 673 MAN 3 n D MAN 4 D 4 MAN E 674 MAN 3 n D MAN 5 D 5 MAN E 675 MAN 2 n E NAG 1 E 1 NAG E 681 NAG 2 n E NAG 2 E 2 NAG E 682 NAG 2 n F NAG 1 F 1 NAG H 1661 NAG 2 n F NAG 2 F 2 NAG H 1662 NAG 3 n G NAG 1 G 1 NAG H 1671 NAG 3 n G NAG 2 G 2 NAG H 1672 NAG 3 n G MAN 3 G 3 MAN H 1673 MAN 3 n G MAN 4 G 4 MAN H 1674 MAN 3 n G MAN 5 G 5 MAN H 1675 MAN 2 n H NAG 1 H 1 NAG H 1681 NAG 2 n H NAG 2 H 2 NAG H 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf2 A SG CYS 37 A CYS 37 1_555 A SG CYS 159 A CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? disulf ? disulf3 A SG CYS 41 A CYS 41 1_555 A SG CYS 57 A CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf6 B SG CYS 36 B CYS 36 1_555 B SG CYS 47 B CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf7 B SG CYS 37 B CYS 37 1_555 B SG CYS 159 B CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? disulf ? disulf8 B SG CYS 41 B CYS 41 1_555 B SG CYS 57 B CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf9 B SG CYS 59 B CYS 59 1_555 B SG CYS 69 B CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf10 B SG CYS 569 B CYS 569 1_555 B SG CYS 575 B CYS 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? covale ? covale1 A ND2 ASN 68 A ASN 68 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.47 ? covale ? covale2 A ND2 ASN 144 A ASN 144 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale3 A ND2 ASN 410 A ASN 410 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale4 B ND2 ASN 68 B ASN 68 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.468 ? covale ? covale5 B ND2 ASN 144 B ASN 144 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale6 B ND2 ASN 410 B ASN 410 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale7 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale8 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale9 D O4 NAG . D NAG 2 1_555 D C1 MAN . D MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale10 D O6 MAN . D MAN 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale11 D O6 MAN . D MAN 4 1_555 D C1 MAN . D MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale14 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale15 G O4 NAG . G NAG 2 1_555 G C1 MAN . G MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale16 G O6 MAN . G MAN 3 1_555 G C1 MAN . G MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale17 G O6 MAN . G MAN 4 1_555 G C1 MAN . G MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale18 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? metalc ? metalc1 A NE2 HIS 388 A HIS 388 1_555 I FE HEM . A HEM 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.724 ? metalc ? metalc2 B NE2 HIS 388 B HIS 388 1_555 L FE HEM . B HEM 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.621 ? # _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 70 n n C1 C2 BOG sing 71 n n C1 O5 BOG sing 72 n n C1 H1 BOG sing 73 n n O1 C1' BOG sing 74 n n C2 O2 BOG sing 75 n n C2 C3 BOG sing 76 n n C2 H2 BOG sing 77 n n O2 HO2 BOG sing 78 n n C3 O3 BOG sing 79 n n C3 C4 BOG sing 80 n n C3 H3 BOG sing 81 n n O3 HO3 BOG sing 82 n n C4 O4 BOG sing 83 n n C4 C5 BOG sing 84 n n C4 H4 BOG sing 85 n n O4 HO4 BOG sing 86 n n C5 O5 BOG sing 87 n n C5 C6 BOG sing 88 n n C5 H5 BOG sing 89 n n C6 O6 BOG sing 90 n n C6 H61 BOG sing 91 n n C6 H62 BOG sing 92 n n O6 HO6 BOG sing 93 n n C1' C2' BOG sing 94 n n C1' "H1'1" BOG sing 95 n n C1' "H1'2" BOG sing 96 n n C2' C3' BOG sing 97 n n C2' "H2'1" BOG sing 98 n n C2' "H2'2" BOG sing 99 n n C3' C4' BOG sing 100 n n C3' "H3'1" BOG sing 101 n n C3' "H3'2" BOG sing 102 n n C4' C5' BOG sing 103 n n C4' "H4'1" BOG sing 104 n n C4' "H4'2" BOG sing 105 n n C5' C6' BOG sing 106 n n C5' "H5'1" BOG sing 107 n n C5' "H5'2" BOG sing 108 n n C6' C7' BOG sing 109 n n C6' "H6'1" BOG sing 110 n n C6' "H6'2" BOG sing 111 n n C7' C8' BOG sing 112 n n C7' "H7'1" BOG sing 113 n n C7' "H7'2" BOG sing 114 n n C8' "H8'1" BOG sing 115 n n C8' "H8'2" BOG sing 116 n n C8' "H8'3" BOG sing 117 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 5U6X _atom_sites.fract_transf_matrix[1][1] 0.005511 _atom_sites.fract_transf_matrix[1][2] 0.003182 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006363 _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] 0.009662 _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 1 701 2 HEM HEM . J 5 P6A A 1 702 1 P6A P6 . K 6 BOG A 1 703 751 BOG BOG . L 4 HEM B 1 701 1 HEM HEM . M 5 P6A B 1 702 1 P6A P6 . N 6 BOG B 1 703 1750 BOG BOG . O 6 BOG B 1 704 1751 BOG BOG . # 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 . . . N 6 50.501 155.798 -29.177 1 94.99 ? C1 BOG 703 B 1 HETATM 2 O O1 BOG . . . N 6 51.861 155.462 -29.44 1 83.81 ? O1 BOG 703 B 1 HETATM 3 C C2 BOG . . . N 6 50.392 157.291 -28.893 1 106.28 ? C2 BOG 703 B 1 HETATM 4 O O2 BOG . . . N 6 51.134 157.607 -27.71 1 110.54 ? O2 BOG 703 B 1 HETATM 5 C C3 BOG . . . N 6 48.938 157.708 -28.707 1 104.62 ? C3 BOG 703 B 1 HETATM 6 O O3 BOG . . . N 6 48.852 159.137 -28.67 1 98.27 ? O3 BOG 703 B 1 HETATM 7 C C4 BOG . . . N 6 48.068 157.176 -29.84 1 100.89 ? C4 BOG 703 B 1 HETATM 8 O O4 BOG . . . N 6 46.688 157.388 -29.522 1 96.8 ? O4 BOG 703 B 1 HETATM 9 C C5 BOG . . . N 6 48.315 155.689 -30.065 1 93.99 ? C5 BOG 703 B 1 HETATM 10 O O5 BOG . . . N 6 49.703 155.47 -30.312 1 94.31 ? O5 BOG 703 B 1 HETATM 11 C C6 BOG . . . N 6 47.501 155.173 -31.246 1 85.25 ? C6 BOG 703 B 1 HETATM 12 O O6 BOG . . . N 6 47.611 153.747 -31.314 1 78.36 ? O6 BOG 703 B 1 HETATM 13 C C1' BOG . . . N 6 52.354 154.488 -28.522 1 79.33 ? C1' BOG 703 B 1 HETATM 14 C C2' BOG . . . N 6 53.843 154.271 -28.761 1 71.52 ? C2' BOG 703 B 1 HETATM 15 C C3' BOG . . . N 6 54.415 153.264 -27.771 1 75 ? C3' BOG 703 B 1 HETATM 16 C C4' BOG . . . N 6 55.937 153.239 -27.836 1 70.55 ? C4' BOG 703 B 1 HETATM 17 C C5' BOG . . . N 6 56.508 152.206 -26.872 1 62.58 ? C5' BOG 703 B 1 HETATM 18 C C6' BOG . . . N 6 57.003 152.868 -25.591 1 63.05 ? C6' BOG 703 B 1 HETATM 19 C C7' BOG . . . N 6 57.678 151.853 -24.677 1 63.66 ? C7' BOG 703 B 1 HETATM 20 C C8' BOG . . . N 6 58.262 152.529 -23.455 1 70.56 ? C8' BOG 703 B 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 52 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 20 #