data_1BYJ # _model_server_result.job_id ZEVpFpfzeS_80zpiJSEykA _model_server_result.datetime_utc '2024-11-30 19:37:53' _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":"D","auth_seq_id":30}' # _entry.id 1BYJ # _exptl.entry_id 1BYJ _exptl.method 'SOLUTION NMR' # _entity.details ? _entity.formula_weight 177.198 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranose _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 4 _struct_asym.id D _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 'C7 H15 N O4' _chem_comp.formula_weight 177.198 _chem_comp.id GE3 _chem_comp.mon_nstd_flag . _chem_comp.name 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranose _chem_comp.type 'l-saccharide, beta linking' _chem_comp.pdbx_synonyms 5-METHYL-4-METHYLAMINO-TETRAHYDRO-PYRAN-2,3,5-TRIOL;3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinose;3-deoxy-4-C-methyl-3-(methylamino)-L-arabinose;3-deoxy-4-C-methyl-3-(methylamino)-arabinose # 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 C4 GE3 sing 163 n n C5 O5 GE3 sing 164 n n C5 H51 GE3 sing 165 n n C5 H52 GE3 sing 166 n n C4 O4 GE3 sing 167 n n C4 C3 GE3 sing 168 n n C4 C41 GE3 sing 169 n n O4 HO4 GE3 sing 170 n n C3 C2 GE3 sing 171 n n C3 N1 GE3 sing 172 n n C3 H3 GE3 sing 173 n n C2 C1 GE3 sing 174 n n C2 O2 GE3 sing 175 n n C2 H2 GE3 sing 176 n n C1 O1 GE3 sing 177 n n C1 O5 GE3 sing 178 n n C1 H1 GE3 sing 179 n n O1 HO1 GE3 sing 180 n n O2 HO2 GE3 sing 181 n n N1 C31 GE3 sing 182 n n N1 HN1 GE3 sing 183 n n C31 H311 GE3 sing 184 n n C31 H312 GE3 sing 185 n n C31 H313 GE3 sing 186 n n C41 H411 GE3 sing 187 n n C41 H412 GE3 sing 188 n n C41 H413 GE3 sing 189 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 GE3 . . . D 4 1.864 5.139 -1.932 1 0 ? C5 GE3 30 A 1 HETATM 2 C C4 GE3 . . . D 4 0.908 5.963 -1.025 1 0 ? C4 GE3 30 A 1 HETATM 3 O O4 GE3 . . . D 4 -0.366 5.997 -1.665 1 0 ? O4 GE3 30 A 1 HETATM 4 C C3 GE3 . . . D 4 1.497 7.417 -0.856 1 0 ? C3 GE3 30 A 1 HETATM 5 C C2 GE3 . . . D 4 1.736 8.066 -2.266 1 0 ? C2 GE3 30 A 1 HETATM 6 C C1 GE3 . . . D 4 2.694 7.18 -3.102 1 0 ? C1 GE3 30 A 1 HETATM 7 O O1 GE3 . . . D 4 4.031 7.244 -2.546 1 0 ? O1 GE3 30 A 1 HETATM 8 O O5 GE3 . . . D 4 2.173 5.818 -3.182 1 0 ? O5 GE3 30 A 1 HETATM 9 O O2 GE3 . . . D 4 2.286 9.375 -2.158 1 0 ? O2 GE3 30 A 1 HETATM 10 N N1 GE3 . . . D 4 0.751 8.31 0.096 1 0 ? N1 GE3 30 A 1 HETATM 11 C C31 GE3 . . . D 4 -0.576 8.828 -0.294 1 0 ? C31 GE3 30 A 1 HETATM 12 C C41 GE3 . . . D 4 0.734 5.199 0.307 1 0 ? C41 GE3 30 A 1 HETATM 13 H H51 GE3 . . . D 4 1.425 4.15 -2.166 1 0 ? H51 GE3 30 A 1 HETATM 14 H H52 GE3 . . . D 4 2.804 4.922 -1.392 1 0 ? H52 GE3 30 A 1 HETATM 15 H HO4 GE3 . . . D 4 -0.939 6.506 -1.086 1 0 ? HO4 GE3 30 A 1 HETATM 16 H H3 GE3 . . . D 4 2.494 7.294 -0.389 1 0 ? H3 GE3 30 A 1 HETATM 17 H H2 GE3 . . . D 4 0.777 8.134 -2.814 1 0 ? H2 GE3 30 A 1 HETATM 18 H H1 GE3 . . . D 4 2.751 7.561 -4.131 1 0 ? H1 GE3 30 A 1 HETATM 19 H HO2 GE3 . . . D 4 1.652 9.887 -1.649 1 0 ? HO2 GE3 30 A 1 HETATM 20 H HN1 GE3 . . . D 4 1.354 9.094 0.369 1 0 ? HN1 GE3 30 A 1 HETATM 21 H H311 GE3 . . . D 4 -0.49 9.538 -1.135 1 0 ? H311 GE3 30 A 1 HETATM 22 H H312 GE3 . . . D 4 -1.278 8.023 -0.568 1 0 ? H312 GE3 30 A 1 HETATM 23 H H313 GE3 . . . D 4 -1.026 9.376 0.552 1 0 ? H313 GE3 30 A 1 HETATM 24 H H411 GE3 . . . D 4 1.689 5.099 0.856 1 0 ? H411 GE3 30 A 1 HETATM 25 H H412 GE3 . . . D 4 0.028 5.712 0.985 1 0 ? H412 GE3 30 A 1 HETATM 26 H H413 GE3 . . . D 4 0.336 4.178 0.151 1 0 ? H413 GE3 30 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 40 _model_server_stats.query_time_ms 7533 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 26 #