data_1NEM # _model_server_result.job_id DGWKiojxJ6ZO3veHtMY9ug _model_server_result.datetime_utc '2025-03-06 03:30:05' _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":"D","auth_seq_id":28}' # _entry.id 1NEM # _exptl.entry_id 1NEM _exptl.method 'SOLUTION NMR' # _entity.details 'RING A OF NEOMYCIN B' _entity.formula_weight 163.195 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-DEOXY-D-STREPTAMINE _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 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 ? 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 H15 N2 O3 1' _chem_comp.formula_weight 163.195 _chem_comp.id NEB _chem_comp.mon_nstd_flag . _chem_comp.name 2-DEOXY-D-STREPTAMINE _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 N1 NEB sing 188 n n C1 C2 NEB sing 189 n n C1 C6 NEB sing 190 n n C1 H1 NEB sing 191 n n N1 H11 NEB sing 192 n n N1 H12 NEB sing 193 n n N1 H13 NEB sing 194 n n C2 C3 NEB sing 195 n n C2 H21 NEB sing 196 n n C2 H22 NEB sing 197 n n C3 N3 NEB sing 198 n n C3 C4 NEB sing 199 n n C3 H3 NEB sing 200 n n N3 H31 NEB sing 201 n n N3 H32 NEB sing 202 n n C4 O4 NEB sing 203 n n C4 C5 NEB sing 204 n n C4 H4 NEB sing 205 n n O4 HO4 NEB sing 206 n n C5 O5 NEB sing 207 n n C5 C6 NEB sing 208 n n C5 H5 NEB sing 209 n n O5 HO5 NEB sing 210 n n C6 O6 NEB sing 211 n n C6 H6 NEB sing 212 n n O6 HO6 NEB sing 213 n n # _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 C1 NEB . . . D 4 -2.783 1.981 -1.314 1 0.22 ? C1 NEB 28 A 1 HETATM 2 N N1 NEB . . . D 4 -3.009 3.432 -1.506 1 0.27 ? N1 NEB 28 A 1 HETATM 3 C C2 NEB . . . D 4 -3.942 1.372 -0.533 1 0.22 ? C2 NEB 28 A 1 HETATM 4 C C3 NEB . . . D 4 -3.722 -0.12 -0.326 1 0.18 ? C3 NEB 28 A 1 HETATM 5 N N3 NEB . . . D 4 -4.859 -0.639 0.421 1 0.2 ? N3 NEB 28 A 1 HETATM 6 C C4 NEB . . . D 4 -2.419 -0.35 0.436 1 0.16 ? C4 NEB 28 A 1 HETATM 7 O O4 NEB . . . D 4 -2.204 -1.765 0.603 1 0.15 ? O4 NEB 28 A 1 HETATM 8 C C5 NEB . . . D 4 -1.231 0.261 -0.32 1 0.17 ? C5 NEB 28 A 1 HETATM 9 O O5 NEB . . . D 4 -0.037 0.119 0.473 1 0.17 ? O5 NEB 28 A 1 HETATM 10 C C6 NEB . . . D 4 -1.452 1.745 -0.602 1 0.22 ? C6 NEB 28 A 1 HETATM 11 O O6 NEB . . . D 4 -0.39 2.238 -1.408 1 0.27 ? O6 NEB 28 A 1 HETATM 12 H H1 NEB . . . D 4 -2.669 1.521 -2.294 1 0.25 ? H1 NEB 28 A 1 HETATM 13 H H11 NEB . . . D 4 -2.173 3.827 -1.986 1 0.35 ? H11 NEB 28 A 1 HETATM 14 H H12 NEB . . . D 4 -3.849 3.555 -2.105 1 0.36 ? H12 NEB 28 A 1 HETATM 15 H H13 NEB . . . D 4 -3.142 3.914 -0.592 1 0.26 ? H13 NEB 28 A 1 HETATM 16 H H21 NEB . . . D 4 -4.881 1.546 -1.061 1 0.27 ? H21 NEB 28 A 1 HETATM 17 H H22 NEB . . . D 4 -4.026 1.863 0.448 1 0.25 ? H22 NEB 28 A 1 HETATM 18 H H3 NEB . . . D 4 -3.678 -0.655 -1.284 1 0.2 ? H3 NEB 28 A 1 HETATM 19 H H31 NEB . . . D 4 -5.691 -0.555 -0.133 1 0.27 ? H31 NEB 28 A 1 HETATM 20 H H32 NEB . . . D 4 -4.966 -0.09 1.248 1 0.25 ? H32 NEB 28 A 1 HETATM 21 H H4 NEB . . . D 4 -2.514 0.147 1.41 1 0.17 ? H4 NEB 28 A 1 HETATM 22 H H5 NEB . . . D 4 -1.18 -0.242 -1.3 1 0.17 ? H5 NEB 28 A 1 HETATM 23 H H6 NEB . . . D 4 -1.399 2.248 0.358 1 0.24 ? H6 NEB 28 A 1 HETATM 24 H HO6 NEB . . . D 4 0.457 2.054 -0.992 1 0.33 ? HO6 NEB 28 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 2667 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 24 #