data_5NEF # _model_server_result.job_id TPi0Bmux-GNM0VOWnPV0dw _model_server_result.datetime_utc '2024-11-12 20:57:49' _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 5nef # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":104}' # _entry.id 5NEF # _exptl.entry_id 5NEF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _entity.pdbx_number_of_molecules 6 _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 120 _cell.entry_id 5NEF _cell.length_a 55.7 _cell.length_b 55.7 _cell.length_c 132.56 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NEF _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 6_555 -x,-x+y,-z -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 D N N ? 4 E N N ? 4 F N N ? 4 G N N ? 4 H N N ? 4 I N 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 A O3' A 16 A A 16 1_555 A P CBV 17 A CBV 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.612 ? covale ? covale2 A O3' CBV 17 A CBV 17 1_555 A P C 18 A C 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? metalc ? metalc1 A O6 G 7 A G 7 1_555 G NA NA . A NA 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? metalc ? metalc2 A OP1 A 8 A A 8 1_555 H NA NA . A NA 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.886 ? metalc ? metalc3 A OP2 G 10 A G 10 1_555 G NA NA . A NA 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.851 ? metalc ? metalc4 A OP2 C 18 A C 18 1_555 D NA NA . A NA 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.604 ? metalc ? metalc5 C O1 SO4 . A SO4 102 1_555 I NA NA . A NA 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.187 ? metalc ? metalc6 C O4 SO4 . A SO4 102 1_555 I NA NA . A NA 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.068 ? metalc ? metalc7 D NA NA . A NA 103 1_555 J O HOH . A HOH 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.614 ? metalc ? metalc8 D NA NA . A NA 103 1_555 J O HOH . A HOH 225 6_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.198 ? metalc ? metalc9 E NA NA . A NA 104 1_555 J O HOH . A HOH 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.864 ? hydrog WATSON-CRICK hydrog1 A N1 G 1 A G 1 1_555 A N3 C 18 A C 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 G 1 A G 1 1_555 A O2 C 18 A C 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 G 1 A G 1 1_555 A N4 C 18 A C 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 G 2 A G 2 1_555 A N3 CBV 17 A CBV 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N2 G 2 A G 2 1_555 A O2 CBV 17 A CBV 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O6 G 2 A G 2 1_555 A N4 CBV 17 A CBV 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N3 U 3 A U 3 1_555 A N1 A 16 A A 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O4 U 3 A U 3 1_555 A N6 A 16 A A 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N1 G 4 A G 4 1_555 A N3 C 15 A C 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N2 G 4 A G 4 1_555 A O2 C 15 A C 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A O6 G 4 A G 4 1_555 A N4 C 15 A C 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N1 G 5 A G 5 1_555 A N3 C 14 A C 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N2 G 5 A G 5 1_555 A O2 C 14 A C 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A O6 G 5 A G 5 1_555 A N4 C 14 A C 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N1 G 6 A G 6 1_555 A N3 C 13 A C 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N2 G 6 A G 6 1_555 A O2 C 13 A C 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A O6 G 6 A G 6 1_555 A N4 C 13 A C 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N1 G 7 A G 7 1_555 A N3 C 12 A C 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N2 G 7 A G 7 1_555 A O2 C 12 A C 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A O6 G 7 A G 7 1_555 A N4 C 12 A C 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'Na 1' _chem_comp.formula_weight 22.99 _chem_comp.id NA _chem_comp.mon_nstd_flag . _chem_comp.name 'SODIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5NEF _atom_sites.fract_transf_matrix[1][1] 0.017953 _atom_sites.fract_transf_matrix[1][2] 0.010365 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020731 _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] 0.007544 _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 GAI A 1 101 1 GAI GAI . C 3 SO4 A 1 102 1 SO4 SO4 . D 4 NA A 1 103 1 NA NA . E 4 NA A 1 104 2 NA NA . F 4 NA A 1 105 3 NA NA . G 4 NA A 1 106 4 NA NA . H 4 NA A 1 107 5 NA NA . I 4 NA A 1 108 6 NA NA . J 5 HOH A 1 201 17 HOH HOH . J 5 HOH A 2 202 28 HOH HOH . J 5 HOH A 3 203 29 HOH HOH . J 5 HOH A 4 204 21 HOH HOH . J 5 HOH A 5 205 8 HOH HOH . J 5 HOH A 6 206 15 HOH HOH . J 5 HOH A 7 207 18 HOH HOH . J 5 HOH A 8 208 32 HOH HOH . J 5 HOH A 9 209 33 HOH HOH . J 5 HOH A 10 210 7 HOH HOH . J 5 HOH A 11 211 27 HOH HOH . J 5 HOH A 12 212 5 HOH HOH . J 5 HOH A 13 213 14 HOH HOH . J 5 HOH A 14 214 13 HOH HOH . J 5 HOH A 15 215 11 HOH HOH . J 5 HOH A 16 216 4 HOH HOH . J 5 HOH A 17 217 16 HOH HOH . J 5 HOH A 18 218 9 HOH HOH . J 5 HOH A 19 219 19 HOH HOH . J 5 HOH A 20 220 3 HOH HOH . J 5 HOH A 21 221 2 HOH HOH . J 5 HOH A 22 222 24 HOH HOH . J 5 HOH A 23 223 31 HOH HOH . J 5 HOH A 24 224 1 HOH HOH . J 5 HOH A 25 225 25 HOH HOH . J 5 HOH A 26 226 10 HOH HOH . J 5 HOH A 27 227 12 HOH HOH . J 5 HOH A 28 228 6 HOH HOH . J 5 HOH A 29 229 30 HOH HOH . J 5 HOH A 30 230 22 HOH HOH . J 5 HOH A 31 231 23 HOH HOH . J 5 HOH A 32 232 20 HOH HOH . J 5 HOH A 33 233 26 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NA _atom_site.label_atom_id NA _atom_site.label_comp_id NA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id E _atom_site.label_entity_id 4 _atom_site.Cartn_x -18.978 _atom_site.Cartn_y 31.857 _atom_site.Cartn_z 1.687 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 63.28 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 104 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #