data_5URZ # _model_server_result.job_id 8gLy4zwjaUXbZu7NindvSw _model_server_result.datetime_utc '2024-11-06 01:40:13' _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 5urz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":201}' # _entry.id 5URZ # _exptl.entry_id 5URZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 292.369 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'octyl beta-D-glucopyranoside' _entity.pdbx_number_of_molecules 1 _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 5URZ _cell.length_a 123.051 _cell.length_b 123.051 _cell.length_c 46.87 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5URZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 FUC NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 1 FUC NAG 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 L 2 NAG 2 n C FUC 2 C 2 FUC L 4 FUC 2 n C FUC 3 C 3 FUC L 3 FUC # 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 21 A CYS 8 1_555 A SG CYS 82 A CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf2 A SG CYS 29 A CYS 16 1_555 A SG CYS 75 A CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf3 A SG CYS 66 A CYS 53 1_555 A SG CYS 104 A CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf4 A SG CYS 93 A CYS 80 1_555 A SG CYS 135 A CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf5 A SG CYS 97 A CYS 84 1_555 A SG CYS 121 A CYS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf6 B SG CYS 21 B CYS 8 1_555 B SG CYS 82 B CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf7 B SG CYS 29 B CYS 16 1_555 B SG CYS 75 B CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf8 B SG CYS 66 B CYS 53 1_555 B SG CYS 104 B CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? disulf ? disulf9 B SG CYS 93 B CYS 80 1_555 B SG CYS 135 B CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf10 B SG CYS 97 B CYS 84 1_555 B SG CYS 121 B CYS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? covale ? covale1 A ND2 ASN 35 A ASN 22 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.283 ? covale ? covale2 C O4 NAG . C NAG 1 1_555 C C1 FUC . C FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.468 ? covale ? covale3 C O6 NAG . C NAG 1 1_555 C C1 FUC . C FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? # _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 5URZ _atom_sites.fract_transf_matrix[1][1] 0.008127 _atom_sites.fract_transf_matrix[1][2] 0.004692 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009384 _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] 0.021336 _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 3 BOG B 1 201 1 BOG BOG . E 4 HOH A 1 301 93 HOH HOH . E 4 HOH A 2 302 72 HOH HOH . E 4 HOH A 3 303 34 HOH HOH . E 4 HOH A 4 304 43 HOH HOH . E 4 HOH A 5 305 22 HOH HOH . E 4 HOH A 6 306 17 HOH HOH . E 4 HOH A 7 307 63 HOH HOH . E 4 HOH A 8 308 49 HOH HOH . E 4 HOH A 9 309 41 HOH HOH . E 4 HOH A 10 310 19 HOH HOH . E 4 HOH A 11 311 36 HOH HOH . E 4 HOH A 12 312 23 HOH HOH . E 4 HOH A 13 313 70 HOH HOH . E 4 HOH A 14 314 27 HOH HOH . E 4 HOH A 15 315 55 HOH HOH . E 4 HOH A 16 316 38 HOH HOH . E 4 HOH A 17 317 94 HOH HOH . E 4 HOH A 18 318 8 HOH HOH . E 4 HOH A 19 319 31 HOH HOH . E 4 HOH A 20 320 33 HOH HOH . E 4 HOH A 21 321 18 HOH HOH . E 4 HOH A 22 322 48 HOH HOH . E 4 HOH A 23 323 6 HOH HOH . E 4 HOH A 24 324 86 HOH HOH . E 4 HOH A 25 325 57 HOH HOH . E 4 HOH A 26 326 13 HOH HOH . E 4 HOH A 27 327 1 HOH HOH . E 4 HOH A 28 328 67 HOH HOH . E 4 HOH A 29 329 40 HOH HOH . E 4 HOH A 30 330 64 HOH HOH . E 4 HOH A 31 331 89 HOH HOH . E 4 HOH A 32 332 9 HOH HOH . E 4 HOH A 33 333 7 HOH HOH . E 4 HOH A 34 334 24 HOH HOH . E 4 HOH A 35 335 12 HOH HOH . E 4 HOH A 36 336 14 HOH HOH . E 4 HOH A 37 337 80 HOH HOH . E 4 HOH A 38 338 75 HOH HOH . E 4 HOH A 39 339 52 HOH HOH . E 4 HOH A 40 340 11 HOH HOH . E 4 HOH A 41 341 62 HOH HOH . E 4 HOH A 42 342 35 HOH HOH . E 4 HOH A 43 343 73 HOH HOH . E 4 HOH A 44 344 25 HOH HOH . E 4 HOH A 45 345 76 HOH HOH . E 4 HOH A 46 346 15 HOH HOH . E 4 HOH A 47 347 51 HOH HOH . E 4 HOH A 48 348 3 HOH HOH . E 4 HOH A 49 349 97 HOH HOH . E 4 HOH A 50 350 74 HOH HOH . E 4 HOH A 51 351 88 HOH HOH . E 4 HOH A 52 352 69 HOH HOH . E 4 HOH A 53 353 32 HOH HOH . E 4 HOH A 54 354 83 HOH HOH . E 4 HOH A 55 355 66 HOH HOH . E 4 HOH A 56 356 4 HOH HOH . E 4 HOH A 57 357 87 HOH HOH . E 4 HOH A 58 358 91 HOH HOH . E 4 HOH A 59 359 60 HOH HOH . E 4 HOH A 60 360 85 HOH HOH . E 4 HOH A 61 361 90 HOH HOH . E 4 HOH A 62 362 58 HOH HOH . F 4 HOH B 1 301 79 HOH HOH . F 4 HOH B 2 302 59 HOH HOH . F 4 HOH B 3 303 65 HOH HOH . F 4 HOH B 4 304 39 HOH HOH . F 4 HOH B 5 305 53 HOH HOH . F 4 HOH B 6 306 5 HOH HOH . F 4 HOH B 7 307 20 HOH HOH . F 4 HOH B 8 308 44 HOH HOH . F 4 HOH B 9 309 16 HOH HOH . F 4 HOH B 10 310 50 HOH HOH . F 4 HOH B 11 311 30 HOH HOH . F 4 HOH B 12 312 28 HOH HOH . F 4 HOH B 13 313 46 HOH HOH . F 4 HOH B 14 314 71 HOH HOH . F 4 HOH B 15 315 68 HOH HOH . F 4 HOH B 16 316 29 HOH HOH . F 4 HOH B 17 317 2 HOH HOH . F 4 HOH B 18 318 77 HOH HOH . F 4 HOH B 19 319 10 HOH HOH . F 4 HOH B 20 320 21 HOH HOH . F 4 HOH B 21 321 84 HOH HOH . F 4 HOH B 22 322 45 HOH HOH . F 4 HOH B 23 323 95 HOH HOH . F 4 HOH B 24 324 47 HOH HOH . F 4 HOH B 25 325 61 HOH HOH . F 4 HOH B 26 326 37 HOH HOH . F 4 HOH B 27 327 54 HOH HOH . F 4 HOH B 28 328 42 HOH HOH . F 4 HOH B 29 329 56 HOH HOH . F 4 HOH B 30 330 26 HOH HOH . F 4 HOH B 31 331 81 HOH HOH . F 4 HOH B 32 332 82 HOH HOH . F 4 HOH B 33 333 78 HOH HOH . F 4 HOH B 34 334 96 HOH HOH . F 4 HOH B 35 335 92 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 3 -40.105 64.162 14.835 1 87.09 ? C1 BOG 201 B 1 HETATM 2 O O1 BOG . . . D 3 -40.422 63.341 13.743 1 76.85 ? O1 BOG 201 B 1 HETATM 3 C C2 BOG . . . D 3 -40.584 65.547 14.514 1 94.59 ? C2 BOG 201 B 1 HETATM 4 O O2 BOG . . . D 3 -39.593 66.073 13.664 1 94 ? O2 BOG 201 B 1 HETATM 5 C C3 BOG . . . D 3 -40.697 66.492 15.704 1 101.96 ? C3 BOG 201 B 1 HETATM 6 O O3 BOG . . . D 3 -42.059 66.895 15.878 1 104.05 ? O3 BOG 201 B 1 HETATM 7 C C4 BOG . . . D 3 -40.215 65.95 17.042 1 99.34 ? C4 BOG 201 B 1 HETATM 8 O O4 BOG . . . D 3 -38.809 66.032 17.197 1 97.26 ? O4 BOG 201 B 1 HETATM 9 C C5 BOG . . . D 3 -40.618 64.494 17.198 1 92.62 ? C5 BOG 201 B 1 HETATM 10 O O5 BOG . . . D 3 -40.824 63.767 15.979 1 88.48 ? O5 BOG 201 B 1 HETATM 11 C C6 BOG . . . D 3 -41.885 64.477 18.044 1 85.86 ? C6 BOG 201 B 1 HETATM 12 O O6 BOG . . . D 3 -41.757 65.343 19.173 1 84.3 ? O6 BOG 201 B 1 HETATM 13 C C1' BOG . . . D 3 -39.593 63.577 12.629 1 62.25 ? C1' BOG 201 B 1 HETATM 14 C C2' BOG . . . D 3 -39.754 62.443 11.65 1 52.47 ? C2' BOG 201 B 1 HETATM 15 C C3' BOG . . . D 3 -38.486 61.648 11.545 1 50.97 ? C3' BOG 201 B 1 HETATM 16 C C4' BOG . . . D 3 -38.604 60.674 10.399 1 58.95 ? C4' BOG 201 B 1 HETATM 17 C C5' BOG . . . D 3 -37.261 60.136 9.933 0.5 62.24 ? C5' BOG 201 B 1 HETATM 18 C C6' BOG . . . D 3 -36.658 61.001 8.84 0.5 64.18 ? C6' BOG 201 B 1 HETATM 19 C C7' BOG . . . D 3 -35.581 60.302 8.024 0.5 64.59 ? C7' BOG 201 B 1 HETATM 20 C C8' BOG . . . D 3 -34.594 61.291 7.455 0.5 71.9 ? C8' BOG 201 B 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #