data_4RI3 # _model_server_result.job_id BTli4EBdhQ12UPKxfE2CGA _model_server_result.datetime_utc '2024-11-08 16:12:57' _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 4ri3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":304}' # _entry.id 4RI3 # _exptl.entry_id 4RI3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 306.395 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'nonyl beta-D-glucopyranoside' _entity.pdbx_number_of_molecules 4 _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 4RI3 _cell.length_a 71.704 _cell.length_b 77.697 _cell.length_c 93.159 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4RI3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 ? 3 D N N ? 3 J N N ? 3 K N N ? 3 L N N # 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 covale ? covale1 A CD GLU 173 A GLU 173 1_555 C N1 DCW . A DCW 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.501 ? covale ? covale2 B CD GLU 173 B GLU 173 1_555 I N1 DCW . B DCW 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.561 ? metalc ? metalc1 A O ALA 6 A ALA 6 1_555 E HG HG . A HG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? metalc ? metalc2 A OH TYR 75 A TYR 75 1_555 F HG HG . A HG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.02 ? metalc ? metalc3 A OH TYR 75 A TYR 75 1_555 H HG HG . A HG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.171 ? metalc ? metalc4 A OE1 GLU 76 A GLU 76 1_555 H HG HG . A HG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.956 ? metalc ? metalc5 A NH2 ARG 101 A ARG 101 1_555 O HG HG . B HG 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.437 ? metalc ? metalc6 A O ILE 172 A ILE 172 1_555 M HG HG . B HG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.641 ? metalc ? metalc7 A O THR 206 A THR 206 1_555 G HG HG . A HG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.006 ? metalc ? metalc8 F HG HG . A HG 304 1_555 B O ILE 172 B ILE 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.739 ? metalc ? metalc9 G HG HG . A HG 305 1_555 B NH2 ARG 101 B ARG 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc10 B OH TYR 75 B TYR 75 1_555 N HG HG . B HG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? metalc ? metalc11 B OE1 GLU 76 B GLU 76 1_555 N HG HG . B HG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc12 B O THR 206 B THR 206 1_555 O HG HG . B HG 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? # _chem_comp.formula 'C15 H30 O6' _chem_comp.formula_weight 306.395 _chem_comp.id BNG _chem_comp.mon_nstd_flag n _chem_comp.name 'nonyl beta-D-glucopyranoside' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms ? # _pdbx_chem_comp_identifier.comp_id BNG _pdbx_chem_comp_identifier.identifier b-nonylglucoside _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 4RI3 _atom_sites.fract_transf_matrix[1][1] 0.013946 _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] 0.012871 _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] 0.010734 _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 2 DCW A 1 301 1 DCW DCW . D 3 BNG A 1 302 2 BNG BNG . E 4 HG A 1 303 1 HG HG . F 4 HG A 1 304 2 HG HG . G 4 HG A 1 305 4 HG HG . H 4 HG A 1 306 5 HG HG . I 2 DCW B 1 301 2 DCW DCW . J 3 BNG B 1 302 1 BNG BNG . K 3 BNG B 1 303 3 BNG BNG . L 3 BNG B 1 304 4 BNG BNG . M 4 HG B 1 305 3 HG HG . N 4 HG B 1 306 6 HG HG . O 4 HG B 1 307 7 HG HG . P 5 HOH A 1 401 1 HOH HOH . P 5 HOH A 2 402 2 HOH HOH . Q 5 HOH B 1 401 3 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 BNG . . . L 3 74.011 68.948 32.088 1 67.34 ? C1 BNG 304 B 1 HETATM 2 C C2 BNG . . . L 3 72.574 69.336 32.425 1 66.23 ? C2 BNG 304 B 1 HETATM 3 C C3 BNG . . . L 3 72.341 69.22 33.875 1 72.1 ? C3 BNG 304 B 1 HETATM 4 C C4 BNG . . . L 3 72.57 67.909 34.382 1 69.68 ? C4 BNG 304 B 1 HETATM 5 C C5 BNG . . . L 3 73.86 67.264 33.89 1 68.06 ? C5 BNG 304 B 1 HETATM 6 C C6 BNG . . . L 3 73.692 65.798 33.916 1 76.14 ? C6 BNG 304 B 1 HETATM 7 C C1' BNG . . . L 3 74.962 68.049 30.104 1 67.03 ? C1' BNG 304 B 1 HETATM 8 C C2' BNG . . . L 3 76.265 68.485 29.414 1 59.57 ? C2' BNG 304 B 1 HETATM 9 C C3' BNG . . . L 3 77.537 67.671 29.731 1 72.88 ? C3' BNG 304 B 1 HETATM 10 C C4' BNG . . . L 3 78.887 68.423 29.742 1 61.62 ? C4' BNG 304 B 1 HETATM 11 C C5' BNG . . . L 3 79.869 68.136 30.88 1 67.04 ? C5' BNG 304 B 1 HETATM 12 C C6' BNG . . . L 3 81.353 68.222 30.558 1 60.87 ? C6' BNG 304 B 1 HETATM 13 C C7' BNG . . . L 3 82.286 68.824 31.606 1 45.14 ? C7' BNG 304 B 1 HETATM 14 C C8' BNG . . . L 3 83.352 67.905 32.232 1 56.62 ? C8' BNG 304 B 1 HETATM 15 C C9' BNG . . . L 3 84.289 67.171 31.296 1 44.37 ? C9' BNG 304 B 1 HETATM 16 O O1 BNG . . . L 3 74.21 69.024 30.728 1 64.81 ? O1 BNG 304 B 1 HETATM 17 O O2 BNG . . . L 3 72.291 70.632 31.966 1 52.29 ? O2 BNG 304 B 1 HETATM 18 O O3 BNG . . . L 3 70.984 69.651 34.188 1 69.32 ? O3 BNG 304 B 1 HETATM 19 O O4 BNG . . . L 3 72.615 67.976 35.808 1 74.1 ? O4 BNG 304 B 1 HETATM 20 O O5 BNG . . . L 3 74.313 67.65 32.525 1 77.05 ? O5 BNG 304 B 1 HETATM 21 O O6 BNG . . . L 3 73.549 65.15 32.687 1 86.13 ? O6 BNG 304 B 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #