data_5D65 # _model_server_result.job_id R2cPexdTc7zYVLRIYgQ_ZA _model_server_result.datetime_utc '2024-11-22 18:36:02' _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":"Q","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 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description alpha-D-glucopyranose _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 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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id Q _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 GLC _chem_comp.mon_nstd_flag . _chem_comp.name alpha-D-glucopyranose _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms alpha-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 C1 C2 GLC sing 107 n n C1 O1 GLC sing 108 n n C1 O5 GLC sing 109 n n C1 H1 GLC sing 110 n n C2 C3 GLC sing 111 n n C2 O2 GLC sing 112 n n C2 H2 GLC sing 113 n n C3 C4 GLC sing 114 n n C3 O3 GLC sing 115 n n C3 H3 GLC sing 116 n n C4 C5 GLC sing 117 n n C4 O4 GLC sing 118 n n C4 H4 GLC sing 119 n n C5 C6 GLC sing 120 n n C5 O5 GLC sing 121 n n C5 H5 GLC sing 122 n n C6 O6 GLC sing 123 n n C6 H61 GLC sing 124 n n C6 H62 GLC sing 125 n n O1 HO1 GLC sing 126 n n O2 HO2 GLC sing 127 n n O3 HO3 GLC sing 128 n n O4 HO4 GLC sing 129 n n O6 HO6 GLC sing 130 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 GLC DGlcpa 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 GLC a-D-glucopyranose 'COMMON NAME' GMML 1 GLC a-D-Glcp 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 GLC 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 C1 GLC . . . Q 5 21.192 69.14 62.137 1 124.94 ? C1 GLC 101 E 1 HETATM 2 C C2 GLC . . . Q 5 21.862 69.05 63.491 1 122.06 ? C2 GLC 101 E 1 HETATM 3 C C3 GLC . . . Q 5 20.965 69.488 64.624 1 122.64 ? C3 GLC 101 E 1 HETATM 4 C C4 GLC . . . Q 5 20.433 70.853 64.286 1 113.75 ? C4 GLC 101 E 1 HETATM 5 C C5 GLC . . . Q 5 19.503 70.72 63.103 1 114.18 ? C5 GLC 101 E 1 HETATM 6 C C6 GLC . . . Q 5 19.367 72.081 62.439 1 122.22 ? C6 GLC 101 E 1 HETATM 7 O O1 GLC . . . Q 5 21.089 67.787 61.726 1 133.51 ? O1 GLC 101 E 1 HETATM 8 O O2 GLC . . . Q 5 22.232 67.689 63.686 1 121.09 ? O2 GLC 101 E 1 HETATM 9 O O3 GLC . . . Q 5 21.731 69.579 65.823 1 123.63 ? O3 GLC 101 E 1 HETATM 10 O O4 GLC . . . Q 5 19.705 71.379 65.387 1 106.82 ? O4 GLC 101 E 1 HETATM 11 O O5 GLC . . . Q 5 19.873 69.695 62.16 1 114.89 ? O5 GLC 101 E 1 HETATM 12 O O6 GLC . . . Q 5 19.084 73.045 63.456 1 129.72 ? O6 GLC 101 E 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 12 #