data_1QD3 # _model_server_result.job_id GowDYcsQKgQrUe2lH7NIFA _model_server_result.datetime_utc '2024-11-12 20:54:41' _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 1qd3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":47}' # _entry.id 1QD3 # _exptl.entry_id 1QD3 _exptl.method 'SOLUTION NMR' # _entity.details ? _entity.formula_weight 162.187 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-DEOXYSTREPTAMINE _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 1QD3 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1QD3 _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 4 _struct_asym.id D _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 RIB _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 RIB 1 B 1 RIB ? 48 RIB 2 n B IDG 2 B 2 IDG ? 49 IDG # 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 O1 BDG . A BDG 46 1_555 D C4 CYY . A CYY 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale2 D O5 CYY . A CYY 47 1_555 B C1 RIB . B RIB 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale3 B O3 RIB . B RIB 1 1_555 B C1 IDG . B IDG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 sing hydrog WATSON-CRICK hydrog1 A N1 G 1 A G 17 1_555 A N3 C 29 A C 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 G 1 A G 17 1_555 A O2 C 29 A C 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 G 1 A G 17 1_555 A N4 C 29 A C 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N3 C 2 A C 18 1_555 A N1 G 28 A G 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N4 C 2 A C 18 1_555 A O6 G 28 A G 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O2 C 2 A C 18 1_555 A N2 G 28 A G 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N3 C 3 A C 19 1_555 A N1 G 27 A G 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N4 C 3 A C 19 1_555 A O6 G 27 A G 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O2 C 3 A C 19 1_555 A N2 G 27 A G 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 A 4 A A 20 1_555 A N3 U 26 A U 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N6 A 4 A A 20 1_555 A O4 U 26 A U 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N1 G 5 A G 21 1_555 A N3 C 25 A C 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N2 G 5 A G 21 1_555 A O2 C 25 A C 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A O6 G 5 A G 21 1_555 A N4 C 25 A C 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N1 A 6 A A 22 1_555 A N3 U 24 A U 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N6 A 6 A A 22 1_555 A O4 U 24 A U 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N1 G 10 A G 26 1_555 A N3 C 23 A C 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N2 G 10 A G 26 1_555 A O2 C 23 A C 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A O6 G 10 A G 26 1_555 A N4 C 23 A C 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N1 A 11 A A 27 1_555 A N3 U 22 A U 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N6 A 11 A A 27 1_555 A O4 U 22 A U 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N1 G 12 A G 28 1_555 A N3 C 21 A C 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N2 G 12 A G 28 1_555 A O2 C 21 A C 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A O6 G 12 A G 28 1_555 A N4 C 21 A C 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N3 C 13 A C 29 1_555 A N1 G 20 A G 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A N4 C 13 A C 29 1_555 A O6 G 20 A G 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A O2 C 13 A C 29 1_555 A N2 G 20 A G 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-G PAIR' hydrog28 A O2 C 14 A C 30 1_555 A N1 G 18 A G 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C6 H14 N2 O3' _chem_comp.formula_weight 162.187 _chem_comp.id CYY _chem_comp.mon_nstd_flag . _chem_comp.name 2-DEOXYSTREPTAMINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 CYY sing 102 n n C1 C6 CYY sing 103 n n C1 N1 CYY sing 104 n n C1 H1 CYY sing 105 n n C2 C3 CYY sing 106 n n C2 H21 CYY sing 107 n n C2 H22 CYY sing 108 n n C3 C4 CYY sing 109 n n C3 N3 CYY sing 110 n n C3 H3 CYY sing 111 n n C4 C5 CYY sing 112 n n C4 O4 CYY sing 113 n n C4 H4 CYY sing 114 n n C5 C6 CYY sing 115 n n C5 O5 CYY sing 116 n n C5 H5 CYY sing 117 n n C6 O6 CYY sing 118 n n C6 H6 CYY sing 119 n n N1 HN11 CYY sing 120 n n N1 HN12 CYY sing 121 n n N3 HN31 CYY sing 122 n n N3 HN32 CYY sing 123 n n O4 HO4 CYY sing 124 n n O5 HO5 CYY sing 125 n n O6 HO6 CYY sing 126 n n # _atom_sites.entry_id 1QD3 _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 46 46 BDG BDG . D 4 CYY A 1 47 47 CYY CYY . # 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 CYY . . . D 4 8.865 0.191 -2.354 1 0.2 ? C1 CYY 47 A 1 HETATM 2 C C2 CYY . . . D 4 9.841 0.671 -1.298 1 0.23 ? C2 CYY 47 A 1 HETATM 3 C C3 CYY . . . D 4 9.102 1.076 -0.036 1 0.22 ? C3 CYY 47 A 1 HETATM 4 C C4 CYY . . . D 4 8.325 -0.083 0.59 1 0.17 ? C4 CYY 47 A 1 HETATM 5 C C5 CYY . . . D 4 7.439 -0.788 -0.463 1 0.15 ? C5 CYY 47 A 1 HETATM 6 C C6 CYY . . . D 4 8.066 -1.002 -1.847 1 0.16 ? C6 CYY 47 A 1 HETATM 7 N N1 CYY . . . D 4 9.595 -0.184 -3.55 1 0.22 ? N1 CYY 47 A 1 HETATM 8 N N3 CYY . . . D 4 10.053 1.623 0.912 1 0.29 ? N3 CYY 47 A 1 HETATM 9 O O5 CYY . . . D 4 6.909 -2.039 0.04 1 0.16 ? O5 CYY 47 A 1 HETATM 10 O O6 CYY . . . D 4 7.052 -1.336 -2.789 1 0.18 ? O6 CYY 47 A 1 HETATM 11 H H1 CYY . . . D 4 8.165 1.002 -2.585 1 0.24 ? H1 CYY 47 A 1 HETATM 12 H H21 CYY . . . D 4 10.384 1.544 -1.688 1 0.28 ? H21 CYY 47 A 1 HETATM 13 H H22 CYY . . . D 4 10.58 -0.104 -1.052 1 0.26 ? H22 CYY 47 A 1 HETATM 14 H H3 CYY . . . D 4 8.302 1.779 -0.293 1 0.24 ? H3 CYY 47 A 1 HETATM 15 H H4 CYY . . . D 4 9.044 -0.789 1.014 1 0.2 ? H4 CYY 47 A 1 HETATM 16 H H5 CYY . . . D 4 6.562 -0.144 -0.617 1 0.17 ? H5 CYY 47 A 1 HETATM 17 H H6 CYY . . . D 4 8.73 -1.82 -1.808 1 0.19 ? H6 CYY 47 A 1 HETATM 18 H HN11 CYY . . . D 4 9.496 -1.089 -3.916 1 0.25 ? HN11 CYY 47 A 1 HETATM 19 H HN12 CYY . . . D 4 10.538 0.069 -3.645 1 0.3 ? HN12 CYY 47 A 1 HETATM 20 H HN31 CYY . . . D 4 10.981 1.306 0.909 1 0.43 ? HN31 CYY 47 A 1 HETATM 21 H HN32 CYY . . . D 4 10.074 2.592 1.061 1 0.39 ? HN32 CYY 47 A 1 HETATM 22 H HO6 CYY . . . D 4 6.876 -0.609 -3.408 1 0.4 ? HO6 CYY 47 A 1 # _model_server_stats.io_time_ms 79 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 4602 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 22 #