data_1PBR # _model_server_result.job_id SRIyLYCUMJW5VAp_W7schQ _model_server_result.datetime_utc '2024-12-06 07:43:58' _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 1pbr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":102}' # _entry.id 1PBR # _exptl.entry_id 1PBR _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 1PBR _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1PBR _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 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 ? 30 PA3 2 n B IDG 2 B 2 IDG ? 31 PA4 # 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 PA1 . A PA1 101 1_555 D O4 CYY . A CYY 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale2 D O5 CYY . A CYY 102 1_555 B C1 BDR . B BDR 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? covale ? covale3 B O3 BDR . B BDR 1 1_555 B C1 IDG . B IDG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? hydrog WATSON-CRICK hydrog1 A N1 G 1 A G 1 1_555 A N3 C 27 A C 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 G 1 A G 1 1_555 A O2 C 27 A C 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 G 1 A G 1 1_555 A N4 C 27 A C 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 G 2 A G 2 1_555 A N3 C 26 A C 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N2 G 2 A G 2 1_555 A O2 C 26 A C 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O6 G 2 A G 2 1_555 A N4 C 26 A C 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N3 C 3 A C 3 1_555 A N1 G 25 A G 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N4 C 3 A C 3 1_555 A O6 G 25 A G 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O2 C 3 A C 3 1_555 A N2 G 25 A G 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 G 4 A G 4 1_555 A N3 C 24 A C 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N2 G 4 A G 4 1_555 A O2 C 24 A C 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O6 G 4 A G 4 1_555 A N4 C 24 A C 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-C MISPAIR' hydrog13 A N3 U 5 A U 5 1_555 A O2 C 24 A C 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N3 C 6 A C 6 1_555 A N1 G 22 A G 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N4 C 6 A C 6 1_555 A O6 G 22 A G 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A O2 C 6 A C 6 1_555 A N2 G 22 A G 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-U MISPAIR' hydrog17 A N4 C 6 A C 6 1_555 A O4 U 23 A U 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N3 C 8 A C 8 1_555 A N1 G 19 A G 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N4 C 8 A C 8 1_555 A O6 G 19 A G 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A O2 C 8 A C 8 1_555 A N2 G 19 A G 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-A MISPAIR' hydrog21 A O2 C 8 A C 8 1_555 A N6 A 21 A A 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N1 A 9 A A 9 1_555 A N3 U 18 A U 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N6 A 9 A A 9 1_555 A O4 U 18 A U 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N3 C 10 A C 10 1_555 A N1 G 17 A G 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N4 C 10 A C 10 1_555 A O6 G 17 A G 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A O2 C 10 A C 10 1_555 A N2 G 17 A G 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A N3 C 11 A C 11 1_555 A N1 G 16 A G 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A N4 C 11 A C 11 1_555 A O6 G 16 A G 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A O2 C 11 A C 11 1_555 A N2 G 16 A G 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-G MISPAIR' hydrog30 A O2 U 12 A U 12 1_555 A N1 G 15 A G 15 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 96 n n C1 C6 CYY sing 97 n n C1 N1 CYY sing 98 n n C1 H1 CYY sing 99 n n C2 C3 CYY sing 100 n n C2 H21 CYY sing 101 n n C2 H22 CYY sing 102 n n C3 C4 CYY sing 103 n n C3 N3 CYY sing 104 n n C3 H3 CYY sing 105 n n C4 C5 CYY sing 106 n n C4 O4 CYY sing 107 n n C4 H4 CYY sing 108 n n C5 C6 CYY sing 109 n n C5 O5 CYY sing 110 n n C5 H5 CYY sing 111 n n C6 O6 CYY sing 112 n n C6 H6 CYY sing 113 n n N1 HN11 CYY sing 114 n n N1 HN12 CYY sing 115 n n N3 HN31 CYY sing 116 n n N3 HN32 CYY sing 117 n n O4 HO4 CYY sing 118 n n O5 HO5 CYY sing 119 n n O6 HO6 CYY sing 120 n n # _atom_sites.entry_id 1PBR _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 PA1 A 1 101 28 PA1 PA1 . D 4 CYY A 1 102 29 CYY PA2 . # 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 0.234 -5.603 41.991 1 0 ? C1 CYY 102 A 1 HETATM 2 C C2 CYY . . . D 4 -0.71 -4.949 43.042 1 0 ? C2 CYY 102 A 1 HETATM 3 C C3 CYY . . . D 4 0.105 -4.076 44.031 1 0 ? C3 CYY 102 A 1 HETATM 4 C C4 CYY . . . D 4 0.911 -2.98 43.263 1 0 ? C4 CYY 102 A 1 HETATM 5 C C5 CYY . . . D 4 1.804 -3.57 42.123 1 0 ? C5 CYY 102 A 1 HETATM 6 C C6 CYY . . . D 4 1.002 -4.515 41.181 1 0 ? C6 CYY 102 A 1 HETATM 7 N N1 CYY . . . D 4 -0.524 -6.518 41.118 1 0 ? N1 CYY 102 A 1 HETATM 8 N N3 CYY . . . D 4 -0.804 -3.48 45.035 1 0 ? N3 CYY 102 A 1 HETATM 9 O O4 CYY . . . D 4 1.764 -2.297 44.213 1 0 ? O4 CYY 102 A 1 HETATM 10 O O5 CYY . . . D 4 2.358 -2.48 41.328 1 0 ? O5 CYY 102 A 1 HETATM 11 O O6 CYY . . . D 4 1.915 -5.124 40.271 1 0 ? O6 CYY 102 A 1 HETATM 12 H H1 CYY . . . D 4 0.975 -6.223 42.532 1 0 ? H1 CYY 102 A 1 HETATM 13 H H21 CYY . . . D 4 -1.302 -5.725 43.561 1 0 ? H21 CYY 102 A 1 HETATM 14 H H22 CYY . . . D 4 -1.476 -4.304 42.571 1 0 ? H22 CYY 102 A 1 HETATM 15 H H3 CYY . . . D 4 0.817 -4.728 44.573 1 0 ? H3 CYY 102 A 1 HETATM 16 H H4 CYY . . . D 4 0.184 -2.274 42.809 1 0 ? H4 CYY 102 A 1 HETATM 17 H H5 CYY . . . D 4 2.609 -4.166 42.597 1 0 ? H5 CYY 102 A 1 HETATM 18 H H6 CYY . . . D 4 0.277 -3.918 40.59 1 0 ? H6 CYY 102 A 1 HETATM 19 H HN11 CYY . . . D 4 -1.211 -5.991 40.568 1 0 ? HN11 CYY 102 A 1 HETATM 20 H HN12 CYY . . . D 4 0.104 -6.952 40.433 1 0 ? HN12 CYY 102 A 1 HETATM 21 H HN31 CYY . . . D 4 -0.272 -2.895 45.689 1 0 ? HN31 CYY 102 A 1 HETATM 22 H HN32 CYY . . . D 4 -1.468 -2.846 44.576 1 0 ? HN32 CYY 102 A 1 HETATM 23 H HO6 CYY . . . D 4 2.53 -5.627 40.81 1 0 ? HO6 CYY 102 A 1 # _model_server_stats.io_time_ms 4 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 23 #