data_5JRN # _model_server_result.job_id bvUFSkfuTcPGeVxqJ-Cu_g _model_server_result.datetime_utc '2024-11-29 07:46:29' _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 5jrn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":208}' # _entry.id 5JRN # _exptl.entry_id 5JRN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 164.156 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'methyl beta-D-xylopyranoside' _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 90 _cell.entry_id 5JRN _cell.length_a 105.7 _cell.length_b 36.1 _cell.length_c 48.8 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JRN _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id I _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C6 H12 O5' _chem_comp.formula_weight 164.156 _chem_comp.id 6MJ _chem_comp.mon_nstd_flag n _chem_comp.name 'methyl beta-D-xylopyranoside' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 'methyl beta-D-xyloside;methyl D-xyloside;methyl xyloside' # 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 O2 C2 6MJ sing 1 n n O3 C3 6MJ sing 2 n n C2 C3 6MJ sing 3 n n C2 C1 6MJ sing 4 n n O1 C01 6MJ sing 5 n n O1 C1 6MJ sing 6 n n C3 C4 6MJ sing 7 n n C1 O5 6MJ sing 8 n n C4 O4 6MJ sing 9 n n C4 C5 6MJ sing 10 n n O5 C5 6MJ sing 11 n n C01 H1A 6MJ sing 12 n n C01 H2A 6MJ sing 13 n n C01 H3A 6MJ sing 14 n n C1 H1 6MJ sing 15 n n C2 H2 6MJ sing 16 n n C3 H3 6MJ sing 17 n n C4 H4 6MJ sing 18 n n C5 H51 6MJ sing 19 n n C5 H52 6MJ sing 20 n n O4 HO4 6MJ sing 21 n n O3 HO3 6MJ sing 22 n n O2 HO2 6MJ sing 23 n n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version 6MJ DXylp[1Me]b 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 6MJ 1-methyl-b-D-xylopyranose 'COMMON NAME' GMML 1 # _atom_sites.entry_id 5JRN _atom_sites.fract_transf_matrix[1][1] 0.009461 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.027701 _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] 0.020492 _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 B 2 GOL A 1 201 1 GOL GOL . C 2 GOL A 1 202 2 GOL GOL . D 2 GOL A 1 203 3 GOL GOL . E 2 GOL A 1 204 4 GOL GOL . F 2 GOL A 1 205 5 GOL GOL . G 2 GOL A 1 206 7 GOL GOL . H 2 GOL A 1 207 8 GOL GOL . I 3 6MJ A 1 208 1 6MJ MBX . J 4 HOH A 1 301 14 HOH HOH . J 4 HOH A 2 302 20 HOH HOH . J 4 HOH A 3 303 5 HOH HOH . J 4 HOH A 4 304 9 HOH HOH . J 4 HOH A 5 305 1 HOH HOH . J 4 HOH A 6 306 23 HOH HOH . J 4 HOH A 7 307 18 HOH HOH . J 4 HOH A 8 308 4 HOH HOH . J 4 HOH A 9 309 16 HOH HOH . J 4 HOH A 10 310 15 HOH HOH . J 4 HOH A 11 311 22 HOH HOH . J 4 HOH A 12 312 11 HOH HOH . J 4 HOH A 13 313 8 HOH HOH . J 4 HOH A 14 314 19 HOH HOH . J 4 HOH A 15 315 17 HOH HOH . J 4 HOH A 16 316 2 HOH HOH . J 4 HOH A 17 317 10 HOH HOH . J 4 HOH A 18 318 3 HOH HOH . J 4 HOH A 19 319 7 HOH HOH . J 4 HOH A 20 320 6 HOH HOH . J 4 HOH A 21 321 13 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 C01 6MJ . . . I 3 16.614 32.45 22.554 1 79.53 ? C01 6MJ 208 A 1 HETATM 2 O O1 6MJ . . . I 3 15.645 31.439 22.42 1 79.43 ? O1 6MJ 208 A 1 HETATM 3 C C1 6MJ . . . I 3 14.506 31.634 23.21 1 80.96 ? C1 6MJ 208 A 1 HETATM 4 C C2 6MJ . . . I 3 13.319 31.931 22.25 1 79.28 ? C2 6MJ 208 A 1 HETATM 5 C C3 6MJ . . . I 3 11.973 31.823 22.984 1 80.95 ? C3 6MJ 208 A 1 HETATM 6 C C4 6MJ . . . I 3 11.871 30.441 23.657 1 81.56 ? C4 6MJ 208 A 1 HETATM 7 C C5 6MJ . . . I 3 13.09 30.234 24.586 1 82.12 ? C5 6MJ 208 A 1 HETATM 8 O O5 6MJ . . . I 3 14.339 30.483 23.986 1 81.76 ? O5 6MJ 208 A 1 HETATM 9 O O4 6MJ . . . I 3 10.702 30.437 24.419 1 81.4 ? O4 6MJ 208 A 1 HETATM 10 O O3 6MJ . . . I 3 10.953 31.888 22.033 1 78.05 ? O3 6MJ 208 A 1 HETATM 11 O O2 6MJ . . . I 3 13.462 33.269 21.876 1 80.37 ? O2 6MJ 208 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 11 #