data_3ZYJ # _model_server_result.job_id GqXIQChlE6xgEXAV5k6YIQ _model_server_result.datetime_utc '2025-03-03 07:33:02' _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 3zyj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":1373}' # _entry.id 3ZYJ # _exptl.entry_id 3ZYJ _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 beta-D-mannopyranose _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 3ZYJ _cell.length_a 184.42 _cell.length_b 204.43 _cell.length_c 288.07 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ZYJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 22 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'F 2 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,I 1 1 C,D,J,K,L,M,N,O,P 2 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 N _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 metalc ? metalc1 B O LEU 105 B LEU 105 1_555 I CA CA . B CA 1373 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc2 B OE2 GLU 110 B GLU 110 1_555 I CA CA . B CA 1373 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.172 ? metalc ? metalc3 B O THR 116 B THR 126 1_555 I CA CA . B CA 1373 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.787 ? metalc ? metalc4 B OG1 THR 116 B THR 126 1_555 I CA CA . B CA 1373 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.776 ? metalc ? metalc5 B O SER 289 B SER 299 1_555 I CA CA . B CA 1373 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.836 ? metalc ? metalc6 D O LEU 105 D LEU 105 1_555 P CA CA . D CA 1375 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc7 D OE2 GLU 110 D GLU 110 1_555 P CA CA . D CA 1375 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc8 D OG1 THR 116 D THR 126 1_555 P CA CA . D CA 1375 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? metalc ? metalc9 D O THR 116 D THR 126 1_555 P CA CA . D CA 1375 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.866 ? metalc ? metalc10 D O SER 289 D SER 299 1_555 P CA CA . D CA 1375 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.05 ? metalc ? metalc11 D OD1 ASP 290 D ASP 300 1_555 P CA CA . D CA 1375 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.714 ? # _chem_comp.formula 'C6 H12 O6' _chem_comp.formula_weight 180.156 _chem_comp.id BMA _chem_comp.mon_nstd_flag . _chem_comp.name beta-D-mannopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms beta-D-mannose;D-mannose;mannose # 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 BMA sing 70 n n C1 O1 BMA sing 71 n n C1 O5 BMA sing 72 n n C1 H1 BMA sing 73 n n C2 C3 BMA sing 74 n n C2 O2 BMA sing 75 n n C2 H2 BMA sing 76 n n C3 C4 BMA sing 77 n n C3 O3 BMA sing 78 n n C3 H3 BMA sing 79 n n C4 C5 BMA sing 80 n n C4 O4 BMA sing 81 n n C4 H4 BMA sing 82 n n C5 C6 BMA sing 83 n n C5 O5 BMA sing 84 n n C5 H5 BMA sing 85 n n C6 O6 BMA sing 86 n n C6 H61 BMA sing 87 n n C6 H62 BMA sing 88 n n O1 HO1 BMA sing 89 n n O2 HO2 BMA sing 90 n n O3 HO3 BMA sing 91 n n O4 HO4 BMA sing 92 n n O6 HO6 BMA 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 BMA DManpb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 BMA b-D-mannopyranose 'COMMON NAME' GMML 1 BMA b-D-Manp 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 BMA Man 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 3ZYJ _atom_sites.fract_transf_matrix[1][1] 0.005422 _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] 0.004892 _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] 0.003471 _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 E 3 NAG A 1 1445 1445 NAG NAG . F 3 NAG B 1 1370 1370 NAG NAG . G 3 NAG B 1 1371 1371 NAG NAG . H 3 NAG B 1 1372 1372 NAG NAG . I 4 CA B 1 1373 1373 CA CA . J 3 NAG C 1 1445 1445 NAG NAG . K 3 NAG D 1 1370 1370 NAG NAG . L 3 NAG D 1 1371 1371 NAG NAG . M 3 NAG D 1 1372 1372 NAG NAG . N 5 BMA D 1 1373 1373 BMA BMA . O 6 MAN D 1 1374 1374 MAN MAN . P 4 CA D 1 1375 1375 CA CA . # 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 BMA . . . N 5 9.357 20.242 4.157 1 108.62 ? C1 BMA 1373 D 1 HETATM 2 C C2 BMA . . . N 5 9.266 19.975 2.652 1 108.71 ? C2 BMA 1373 D 1 HETATM 3 C C3 BMA . . . N 5 10.536 20.54 2.014 1 108.76 ? C3 BMA 1373 D 1 HETATM 4 C C4 BMA . . . N 5 10.599 22.036 2.337 1 108.69 ? C4 BMA 1373 D 1 HETATM 5 C C5 BMA . . . N 5 10.602 22.212 3.862 1 108.35 ? C5 BMA 1373 D 1 HETATM 6 C C6 BMA . . . N 5 10.652 23.71 4.18 1 108.07 ? C6 BMA 1373 D 1 HETATM 7 O O2 BMA . . . N 5 8.112 20.628 2.117 1 108.73 ? O2 BMA 1373 D 1 HETATM 8 O O3 BMA . . . N 5 10.516 20.332 0.6 1 108.77 ? O3 BMA 1373 D 1 HETATM 9 O O4 BMA . . . N 5 11.786 22.596 1.772 1 108.82 ? O4 BMA 1373 D 1 HETATM 10 O O5 BMA . . . N 5 9.407 21.652 4.424 1 108.39 ? O5 BMA 1373 D 1 HETATM 11 O O6 BMA . . . N 5 10.653 23.903 5.596 1 107.84 ? O6 BMA 1373 D 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 11 #