data_1BYJ # _model_server_result.job_id hWOj83sbomz0NwZIPbD6wg _model_server_result.datetime_utc '2024-11-27 22:54:17' _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 1byj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":28}' # _entry.id 1BYJ # _exptl.entry_id 1BYJ _exptl.method 'SOLUTION NMR' # _entity.details ? _entity.formula_weight 146.188 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranose _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 1BYJ _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1BYJ _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 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 covale ? covale1 B O1 GE1 . A GE1 28 1_555 C C4 GE2 . A GE2 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale2 C C2 GE2 . A GE2 29 1_555 D O1 GE3 . A GE3 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? 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 WATSON-CRICK hydrog13 A N3 C 6 A C 6 1_555 A N1 G 22 A G 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N4 C 6 A C 6 1_555 A O6 G 22 A G 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A O2 C 6 A C 6 1_555 A N2 G 22 A G 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N3 C 8 A C 8 1_555 A N1 G 19 A G 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N4 C 8 A C 8 1_555 A O6 G 19 A G 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O2 C 8 A C 8 1_555 A N2 G 19 A G 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-A MISPAIR' hydrog19 A O2 C 8 A C 8 1_555 A N6 A 21 A A 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N1 A 9 A A 9 1_555 A N3 U 18 A U 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N6 A 9 A A 9 1_555 A O4 U 18 A U 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N3 C 10 A C 10 1_555 A N1 G 17 A G 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N4 C 10 A C 10 1_555 A O6 G 17 A G 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A O2 C 10 A C 10 1_555 A N2 G 17 A G 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N3 C 11 A C 11 1_555 A N1 G 16 A G 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A N4 C 11 A C 11 1_555 A O6 G 16 A G 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A O2 C 11 A C 11 1_555 A N2 G 16 A G 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-G MISPAIR' hydrog28 A O2 U 12 A U 12 1_555 A N1 G 15 A G 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C6 H14 N2 O2' _chem_comp.formula_weight 146.188 _chem_comp.id GE1 _chem_comp.mon_nstd_flag . _chem_comp.name 2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranose _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms '3,4-DIDEOXY-2,6-AMINO-ALPHA-D GALACTOPYRANOSE;2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexose;2,6-diamino-2,3,4,6-tetradeoxy-D-erythro-hexose;2,6-diamino-2,3,4,6-tetradeoxy-erythro-hexose' # 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 O GE1 sing 116 n n C5 C4 GE1 sing 117 n n C5 C6 GE1 sing 118 n n C5 H5 GE1 sing 119 n n O C1 GE1 sing 120 n n C1 O1 GE1 sing 121 n n C1 C2 GE1 sing 122 n n C1 H1 GE1 sing 123 n n O1 HO1 GE1 sing 124 n n C2 N2 GE1 sing 125 n n C2 C3 GE1 sing 126 n n C2 H2 GE1 sing 127 n n N2 HN21 GE1 sing 128 n n N2 HN22 GE1 sing 129 n n C3 C4 GE1 sing 130 n n C3 H31 GE1 sing 131 n n C3 H32 GE1 sing 132 n n C4 H41 GE1 sing 133 n n C4 H42 GE1 sing 134 n n C6 N1 GE1 sing 135 n n C6 H61 GE1 sing 136 n n C6 H62 GE1 sing 137 n n N1 HN11 GE1 sing 138 n n N1 HN12 GE1 sing 139 n n # _atom_sites.entry_id 1BYJ _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 B 2 GE1 A 1 28 28 GE1 GE1 . C 3 GE2 A 1 29 29 GE2 GE2 . D 4 GE3 A 1 30 30 GE3 GE3 . # 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 GE1 . . . B 2 9.554 1.87 -2.768 1 0 ? C5 GE1 28 A 1 HETATM 2 O O GE1 . . . B 2 8.204 1.925 -3.336 1 0 ? O GE1 28 A 1 HETATM 3 C C1 GE1 . . . B 2 7.23 2.726 -2.597 1 0 ? C1 GE1 28 A 1 HETATM 4 O O1 GE1 . . . B 2 7.686 4.109 -2.508 1 0 ? O1 GE1 28 A 1 HETATM 5 C C2 GE1 . . . B 2 7.059 2.114 -1.178 1 0 ? C2 GE1 28 A 1 HETATM 6 N N2 GE1 . . . B 2 6.08 2.852 -0.354 1 0 ? N2 GE1 28 A 1 HETATM 7 C C3 GE1 . . . B 2 8.43 2.028 -0.455 1 0 ? C3 GE1 28 A 1 HETATM 8 C C4 GE1 . . . B 2 9.495 1.317 -1.318 1 0 ? C4 GE1 28 A 1 HETATM 9 C C6 GE1 . . . B 2 10.518 1.032 -3.633 1 0 ? C6 GE1 28 A 1 HETATM 10 N N1 GE1 . . . B 2 10.331 1.178 -5.086 1 0 ? N1 GE1 28 A 1 HETATM 11 H H5 GE1 . . . B 2 9.958 2.899 -2.742 1 0 ? H5 GE1 28 A 1 HETATM 12 H H1 GE1 . . . B 2 6.262 2.685 -3.14 1 0 ? H1 GE1 28 A 1 HETATM 13 H H2 GE1 . . . B 2 6.672 1.086 -1.302 1 0 ? H2 GE1 28 A 1 HETATM 14 H HN21 GE1 . . . B 2 5.16 2.839 -0.807 1 0 ? HN21 GE1 28 A 1 HETATM 15 H HN22 GE1 . . . B 2 5.951 2.38 0.548 1 0 ? HN22 GE1 28 A 1 HETATM 16 H H31 GE1 . . . B 2 8.794 3.04 -0.194 1 0 ? H31 GE1 28 A 1 HETATM 17 H H32 GE1 . . . B 2 8.328 1.493 0.51 1 0 ? H32 GE1 28 A 1 HETATM 18 H H41 GE1 . . . B 2 10.485 1.379 -0.83 1 0 ? H41 GE1 28 A 1 HETATM 19 H H42 GE1 . . . B 2 9.243 0.242 -1.348 1 0 ? H42 GE1 28 A 1 HETATM 20 H H61 GE1 . . . B 2 10.443 -0.038 -3.381 1 0 ? H61 GE1 28 A 1 HETATM 21 H H62 GE1 . . . B 2 11.553 1.314 -3.381 1 0 ? H62 GE1 28 A 1 HETATM 22 H HN11 GE1 . . . B 2 10.419 2.164 -5.355 1 0 ? HN11 GE1 28 A 1 HETATM 23 H HN12 GE1 . . . B 2 9.377 0.905 -5.347 1 0 ? HN12 GE1 28 A 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 50 _model_server_stats.query_time_ms 9447 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 23 #