data_1NEM # _model_server_result.job_id dzwU7Yac27SOJYCJ4L77hQ _model_server_result.datetime_utc '2025-03-06 03:50:40' _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 1nem # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":27}' # _entry.id 1NEM # _exptl.entry_id 1NEM _exptl.method 'SOLUTION NMR' # _entity.details ? _entity.formula_weight 178.186 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2,6-diamino-2,6-dideoxy-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 90 _cell.entry_id 1NEM _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NEM _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 3 _struct_asym.id C _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 IDG _pdbx_entity_branch_link.comp_id_2 BDR _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 O3 _pdbx_entity_branch_link.leaving_atom_id_2 HO3 _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 B BDR 1 B 1 BDR ? 29 RIB 2 n B IDG 2 B 2 IDG ? 30 NED # 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 C C1 BDG . A BDG 27 1_555 D O4 NEB . A NEB 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.4 ? covale ? covale2 D O5 NEB . A NEB 28 1_555 B C1 BDR . B BDR 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale3 B O3 BDR . B BDR 1 1_555 B C1 IDG . B IDG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.399 ? hydrog WATSON-CRICK hydrog1 A N1 G 1 A G 4 1_555 A N3 C 23 A C 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 G 1 A G 4 1_555 A O2 C 23 A C 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 G 1 A G 4 1_555 A N4 C 23 A C 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 G 2 A G 5 1_555 A N3 C 22 A C 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N2 G 2 A G 5 1_555 A O2 C 22 A C 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O6 G 2 A G 5 1_555 A N4 C 22 A C 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-C PAIR' hydrog7 A N2 G 2 A G 5 1_555 A O2 C 23 A C 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N1 A 3 A A 6 1_555 A N3 U 21 A U 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N6 A 3 A A 6 1_555 A O4 U 21 A U 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N3 C 4 A C 7 1_555 A N1 G 20 A G 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N4 C 4 A C 7 1_555 A O6 G 20 A G 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O2 C 4 A C 7 1_555 A N2 G 20 A G 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N3 U 5 A U 8 1_555 A N1 A 19 A A 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A O4 U 5 A U 8 1_555 A N6 A 19 A A 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog15 A N1 G 6 A G 9 1_555 A O2 U 18 A U 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog16 A O6 G 6 A G 9 1_555 A N3 U 18 A U 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog17 A N1 G 7 A G 10 1_555 A O2 U 17 A U 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog18 A O6 G 7 A G 10 1_555 A N3 U 17 A U 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog19 A N1 G 8 A G 11 1_555 A O2 U 16 A U 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog20 A O6 G 8 A G 11 1_555 A N3 U 16 A U 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N3 C 9 A C 12 1_555 A N1 G 15 A G 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N4 C 9 A C 12 1_555 A O6 G 15 A G 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A O2 C 9 A C 12 1_555 A N2 G 15 A G 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog24 A N2 G 10 A G 13 1_555 A N7 A 14 A A 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog25 A N3 G 10 A G 13 1_555 A N6 A 14 A A 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C6 H14 N2 O4' _chem_comp.formula_weight 178.186 _chem_comp.id BDG _chem_comp.mon_nstd_flag . _chem_comp.name 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranose _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms O-2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSE;2,6-diamino-2,6-dideoxy-alpha-D-glucose;2,6-diamino-2,6-dideoxy-D-glucose;2,6-diamino-2,6-dideoxy-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 C5 O5 BDG sing 40 n n C5 C4 BDG sing 41 n n C5 C6 BDG sing 42 n n C5 H5 BDG sing 43 n n O5 C1 BDG sing 44 n n C1 O1 BDG sing 45 n n C1 C2 BDG sing 46 n n C1 H1 BDG sing 47 n n O1 HO1 BDG sing 48 n n C2 N2 BDG sing 49 n n C2 C3 BDG sing 50 n n C2 H2 BDG sing 51 n n N2 HN21 BDG sing 52 n n N2 HN22 BDG sing 53 n n C3 O3 BDG sing 54 n n C3 C4 BDG sing 55 n n C3 H3 BDG sing 56 n n O3 HO3 BDG sing 57 n n C4 O4 BDG sing 58 n n C4 H4 BDG sing 59 n n O4 HO4 BDG sing 60 n n C6 N6 BDG sing 61 n n C6 H61 BDG sing 62 n n C6 H62 BDG sing 63 n n N6 HN61 BDG sing 64 n n N6 HN62 BDG sing 65 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 BDG DGlcpN[6N]a 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 BDG a-D-GlcpN6N 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 # _atom_sites.entry_id 1NEM _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 3 BDG A 1 27 27 BDG BDG . D 4 NEB A 1 28 28 NEB NEB . # 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 C5 BDG . . . C 3 -3.661 -2.693 2.947 1 0.2 ? C5 BDG 27 A 1 HETATM 2 O O5 BDG . . . C 3 -2.454 -1.904 2.929 1 0.17 ? O5 BDG 27 A 1 HETATM 3 C C1 BDG . . . C 3 -1.605 -2.145 1.81 1 0.14 ? C1 BDG 27 A 1 HETATM 4 C C2 BDG . . . C 3 -1.205 -3.617 1.745 1 0.15 ? C2 BDG 27 A 1 HETATM 5 N N2 BDG . . . C 3 -0.401 -3.877 0.527 1 0.16 ? N2 BDG 27 A 1 HETATM 6 C C3 BDG . . . C 3 -2.447 -4.498 1.727 1 0.18 ? C3 BDG 27 A 1 HETATM 7 O O3 BDG . . . C 3 -2.062 -5.864 1.745 1 0.21 ? O3 BDG 27 A 1 HETATM 8 C C4 BDG . . . C 3 -3.316 -4.181 2.942 1 0.22 ? C4 BDG 27 A 1 HETATM 9 O O4 BDG . . . C 3 -4.511 -4.95 2.896 1 0.29 ? O4 BDG 27 A 1 HETATM 10 C C6 BDG . . . C 3 -4.452 -2.283 4.177 1 0.25 ? C6 BDG 27 A 1 HETATM 11 N N6 BDG . . . C 3 -5.036 -0.931 4.022 1 0.29 ? N6 BDG 27 A 1 HETATM 12 H H5 BDG . . . C 3 -4.263 -2.508 2.045 1 0.22 ? H5 BDG 27 A 1 HETATM 13 H H1 BDG . . . C 3 -0.723 -1.506 1.953 1 0.16 ? H1 BDG 27 A 1 HETATM 14 H H2 BDG . . . C 3 -0.619 -3.881 2.63 1 0.19 ? H2 BDG 27 A 1 HETATM 15 H HN21 BDG . . . C 3 0.524 -3.4 0.577 1 0.23 ? HN21 BDG 27 A 1 HETATM 16 H HN22 BDG . . . C 3 -0.23 -4.895 0.401 1 0.23 ? HN22 BDG 27 A 1 HETATM 17 H H3 BDG . . . C 3 -3.019 -4.277 0.821 1 0.18 ? H3 BDG 27 A 1 HETATM 18 H HO3 BDG . . . C 3 -1.466 -6.029 2.483 1 0.24 ? HO3 BDG 27 A 1 HETATM 19 H H4 BDG . . . C 3 -2.749 -4.428 3.854 1 0.26 ? H4 BDG 27 A 1 HETATM 20 H HO4 BDG . . . C 3 -4.274 -5.878 2.81 1 0.36 ? HO4 BDG 27 A 1 HETATM 21 H H61 BDG . . . C 3 -3.797 -2.287 5.059 1 0.31 ? H61 BDG 27 A 1 HETATM 22 H H62 BDG . . . C 3 -5.276 -2.989 4.356 1 0.29 ? H62 BDG 27 A 1 HETATM 23 H HN61 BDG . . . C 3 -5.709 -0.942 3.23 1 0.34 ? HN61 BDG 27 A 1 HETATM 24 H HN62 BDG . . . C 3 -5.517 -0.631 4.902 1 0.33 ? HN62 BDG 27 A 1 HETATM 25 H HN23 BDG . . . C 3 -0.889 -3.509 -0.318 1 0.2 ? HN23 BDG 27 A 1 HETATM 26 H HN63 BDG . . . C 3 -4.279 -0.24 3.842 1 0.35 ? HN63 BDG 27 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 4 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 2143 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #