data_5D65 # _model_server_result.job_id X4AbXZxvaPPsrfilsUYOmQ _model_server_result.datetime_utc '2024-11-22 18:51:28' _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 5d65 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":101}' # _entry.id 5D65 # _exptl.entry_id 5D65 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 180.156 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description beta-D-glucopyranose _entity.pdbx_number_of_molecules 9 _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 5D65 _cell.length_a 181.061 _cell.length_b 181.061 _cell.length_c 77.378 _cell.Z_PDB 60 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5D65 _symmetry.cell_setting ? _symmetry.Int_Tables_number 180 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 62 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,R,S _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 H N N ? 3 I N N ? 3 J N N ? 3 K N N ? 3 L N N ? 3 N N N ? 3 O N N ? 3 P N N ? 3 R N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 SGN _pdbx_entity_branch_link.comp_id_2 IDS _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 F IDS 1 F 1 IDS B 104 IDS 2 n F SGN 2 F 2 SGN B 103 SGN 2 n G IDS 1 G 1 IDS B 106 IDS 2 n G SGN 2 G 2 SGN B 105 SGN # 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 11 A CYS 11 1_555 A SG CYS 35 A CYS 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 12 A CYS 12 1_555 A SG CYS 51 A CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 B SG CYS 11 B CYS 11 1_555 B SG CYS 35 B CYS 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf4 B SG CYS 12 B CYS 12 1_555 B SG CYS 51 B CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf5 C SG CYS 11 C CYS 11 1_555 C SG CYS 35 C CYS 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 C SG CYS 12 C CYS 12 1_555 C SG CYS 51 C CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 D SG CYS 11 D CYS 11 1_555 D SG CYS 35 D CYS 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf8 D SG CYS 12 D CYS 12 1_555 D SG CYS 51 D CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf9 E SG CYS 11 E CYS 11 1_555 E SG CYS 35 E CYS 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf10 E SG CYS 12 E CYS 12 1_555 E SG CYS 51 E CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 F O4 IDS . F IDS 1 1_555 F C1 SGN . F SGN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.36 ? covale ? covale2 G O4 IDS . G IDS 1 1_555 G C1 SGN . G SGN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? # _chem_comp.formula 'C6 H12 O6' _chem_comp.formula_weight 180.156 _chem_comp.id BGC _chem_comp.mon_nstd_flag . _chem_comp.name beta-D-glucopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms beta-D-glucose;D-glucose;glucose # 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 C2 C3 BGC sing 70 n n C2 C1 BGC sing 71 n n C2 O2 BGC sing 72 n n C2 H2 BGC sing 73 n n C3 C4 BGC sing 74 n n C3 O3 BGC sing 75 n n C3 H3 BGC sing 76 n n C4 C5 BGC sing 77 n n C4 O4 BGC sing 78 n n C4 H4 BGC sing 79 n n C5 C6 BGC sing 80 n n C5 O5 BGC sing 81 n n C5 H5 BGC sing 82 n n C6 O6 BGC sing 83 n n C6 H61 BGC sing 84 n n C6 H62 BGC sing 85 n n C1 O1 BGC sing 86 n n C1 O5 BGC sing 87 n n C1 H1 BGC sing 88 n n O1 HO1 BGC sing 89 n n O2 HO2 BGC sing 90 n n O3 HO3 BGC sing 91 n n O4 HO4 BGC sing 92 n n O6 HO6 BGC sing 93 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 BGC DGlcpb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 BGC b-D-glucopyranose 'COMMON NAME' GMML 1 BGC b-D-Glcp 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 BGC Glc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 5D65 _atom_sites.fract_transf_matrix[1][1] 0.005523 _atom_sites.fract_transf_matrix[1][2] 0.003189 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006377 _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] 0.012924 _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 H 3 BGC A 1 101 101 BGC BGC . I 3 BGC A 1 102 102 BGC BGC . J 3 BGC A 1 103 103 BGC BGC . K 3 BGC A 1 104 104 BGC BGC . L 3 BGC B 1 101 101 BGC BGC . M 4 CL B 1 102 102 CL CL . N 3 BGC C 1 101 101 BGC BGC . O 3 BGC D 1 101 101 BGC BGC . P 3 BGC D 1 102 102 BGC BGC . Q 5 GLC E 1 101 101 GLC GLC . R 3 BGC E 1 102 102 BGC BGC . S 4 CL E 1 103 103 CL CL . # 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 C2 BGC . . . L 3 27.591 98.501 57.653 1 111.41 ? C2 BGC 101 B 1 HETATM 2 C C3 BGC . . . L 3 28.849 97.82 58.181 1 107.95 ? C3 BGC 101 B 1 HETATM 3 C C4 BGC . . . L 3 30.087 98.679 57.944 1 112.14 ? C4 BGC 101 B 1 HETATM 4 C C5 BGC . . . L 3 30.095 99.247 56.529 1 116.79 ? C5 BGC 101 B 1 HETATM 5 C C6 BGC . . . L 3 31.445 99.025 55.858 1 108.01 ? C6 BGC 101 B 1 HETATM 6 C C1 BGC . . . L 3 27.787 98.977 56.216 1 117.84 ? C1 BGC 101 B 1 HETATM 7 O O1 BGC . . . L 3 26.819 98.38 55.382 1 111.75 ? O1 BGC 101 B 1 HETATM 8 O O2 BGC . . . L 3 27.266 99.598 58.476 1 108.94 ? O2 BGC 101 B 1 HETATM 9 O O3 BGC . . . L 3 29.015 96.572 57.548 1 100.77 ? O3 BGC 101 B 1 HETATM 10 O O4 BGC . . . L 3 30.115 99.736 58.877 1 115.95 ? O4 BGC 101 B 1 HETATM 11 O O5 BGC . . . L 3 29.08 98.632 55.763 1 119.43 ? O5 BGC 101 B 1 HETATM 12 O O6 BGC . . . L 3 31.411 99.545 54.547 1 108.15 ? O6 BGC 101 B 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 12 #