data_6JDA # _model_server_result.job_id ULCjUR6nkK-W9BM6fnTo-g _model_server_result.datetime_utc '2024-11-23 09:17:27' _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 6jda # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 6JDA # _exptl.entry_id 6JDA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-alpha-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 6JDA _cell.length_a 103.816 _cell.length_b 173.732 _cell.length_c 48.06 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6JDA _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_555 -x,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 24.03 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 A ND1 HIS 156 A HIS 156 1_555 C ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc2 A SG CYS 166 A CYS 166 1_555 C ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc3 A SG CYS 168 A CYS 168 1_555 C ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.495 ? metalc ? metalc4 A SG CYS 173 A CYS 173 1_555 C ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id BM3 _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-alpha-D-mannopyranose _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms N-acetyl-alpha-D-mannosamine;2-acetamido-2-deoxy-alpha-D-mannose;2-acetamido-2-deoxy-D-mannose;2-acetamido-2-deoxy-mannose;2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-MANNOPYRANOSE # 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 O1 BM3 sing 70 n n C1 C2 BM3 sing 71 n n C1 O5 BM3 sing 72 n n C1 H1 BM3 sing 73 n n O1 HO1 BM3 sing 74 n n C2 N2 BM3 sing 75 n n C2 C3 BM3 sing 76 n n C2 H2 BM3 sing 77 n n N2 C7 BM3 sing 78 n n N2 HN2 BM3 sing 79 n n C7 O7 BM3 doub 80 n n C7 C8 BM3 sing 81 n n C8 H81 BM3 sing 82 n n C8 H82 BM3 sing 83 n n C8 H83 BM3 sing 84 n n C3 O3 BM3 sing 85 n n C3 C4 BM3 sing 86 n n C3 H3 BM3 sing 87 n n O3 HO3 BM3 sing 88 n n C4 O4 BM3 sing 89 n n C4 C5 BM3 sing 90 n n C4 H4 BM3 sing 91 n n O4 HO4 BM3 sing 92 n n C5 C6 BM3 sing 93 n n C5 O5 BM3 sing 94 n n C5 H5 BM3 sing 95 n n C6 O6 BM3 sing 96 n n C6 H61 BM3 sing 97 n n C6 H62 BM3 sing 98 n n O6 HO6 BM3 sing 99 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 BM3 DManpNAca 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 BM3 N-acetyl-a-D-mannopyranosamine 'COMMON NAME' GMML 1 BM3 a-D-ManpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 BM3 ManNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 6JDA _atom_sites.fract_transf_matrix[1][1] 0.009632 _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] 0.005756 _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] 0.020807 _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 BM3 A 1 301 301 BM3 BM3 . C 3 ZN A 1 302 1 ZN ZN . D 4 GOL A 1 303 301 GOL GOL . E 5 HOH A 1 401 3 HOH HOH . E 5 HOH A 2 402 1 HOH HOH . E 5 HOH A 3 403 4 HOH HOH . E 5 HOH A 4 404 7 HOH HOH . E 5 HOH A 5 405 2 HOH HOH . E 5 HOH A 6 406 6 HOH HOH . E 5 HOH A 7 407 5 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 BM3 . . . B 2 15.005 56.829 17.316 1 49.1 ? C1 BM3 301 A 1 HETATM 2 O O1 BM3 . . . B 2 13.788 56.291 17.034 1 53.24 ? O1 BM3 301 A 1 HETATM 3 C C2 BM3 . . . B 2 14.777 57.959 18.311 1 53.12 ? C2 BM3 301 A 1 HETATM 4 N N2 BM3 . . . B 2 16.037 58.061 19.121 1 57.63 ? N2 BM3 301 A 1 HETATM 5 C C7 BM3 . . . B 2 16.009 57.852 20.577 1 57.11 ? C7 BM3 301 A 1 HETATM 6 O O7 BM3 . . . B 2 14.986 57.608 21.163 1 54.86 ? O7 BM3 301 A 1 HETATM 7 C C8 BM3 . . . B 2 17.344 57.966 21.329 1 55.66 ? C8 BM3 301 A 1 HETATM 8 C C3 BM3 . . . B 2 14.445 59.23 17.606 1 55.27 ? C3 BM3 301 A 1 HETATM 9 O O3 BM3 . . . B 2 14.189 60.342 18.507 1 50.86 ? O3 BM3 301 A 1 HETATM 10 C C4 BM3 . . . B 2 15.53 59.624 16.651 1 52.84 ? C4 BM3 301 A 1 HETATM 11 O O4 BM3 . . . B 2 15.258 60.95 16.17 1 48.55 ? O4 BM3 301 A 1 HETATM 12 C C5 BM3 . . . B 2 15.587 58.606 15.51 1 47.3 ? C5 BM3 301 A 1 HETATM 13 C C6 BM3 . . . B 2 16.715 58.977 14.574 1 50.44 ? C6 BM3 301 A 1 HETATM 14 O O6 BM3 . . . B 2 17.772 58.042 14.532 1 61.01 ? O6 BM3 301 A 1 HETATM 15 O O5 BM3 . . . B 2 15.698 57.214 16.018 1 52.42 ? O5 BM3 301 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 573 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 15 #