data_6XNF # _model_server_result.job_id IT52XK5mqL5X2Jg9hcuctA _model_server_result.datetime_utc '2025-02-23 15:19:57' _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 6xnf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":101}' # _entry.id 6XNF # _exptl.entry_id 6XNF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation N16A _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 100.647 _cell.angle_gamma 90 _cell.entry_id 6XNF _cell.length_a 59.65 _cell.length_b 35.19 _cell.length_c 47.02 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6XNF _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 # _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 E N N ? 3 F N N ? 3 G 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 C LYS 15 A LYS 15 1_555 A N V61 16 A V61 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 A C V61 16 A V61 16 1_555 A N TYR 17 A TYR 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? metalc ? metalc1 E NA NA . B NA 101 1_555 I O HOH . B HOH 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.791 ? metalc ? metalc2 I O HOH . B HOH 206 4_555 G NA NA . C NA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.641 ? # _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 6XNF _atom_sites.fract_transf_matrix[1][1] 0.016764 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003152 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.028417 _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] 0.02164 _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 D 3 NA A 1 101 17 NA NA . E 3 NA B 1 101 13 NA NA . F 3 NA B 1 102 19 NA NA . G 3 NA C 1 101 6 NA NA . H 4 HOH A 1 201 88 HOH HOH . H 4 HOH A 2 202 11 HOH HOH . H 4 HOH A 3 203 19 HOH HOH . H 4 HOH A 4 204 46 HOH HOH . H 4 HOH A 5 205 59 HOH HOH . H 4 HOH A 6 206 7 HOH HOH . H 4 HOH A 7 207 32 HOH HOH . H 4 HOH A 8 208 62 HOH HOH . H 4 HOH A 9 209 3 HOH HOH . H 4 HOH A 10 210 4 HOH HOH . H 4 HOH A 11 211 100 HOH HOH . H 4 HOH A 12 212 2 HOH HOH . H 4 HOH A 13 213 13 HOH HOH . H 4 HOH A 14 214 68 HOH HOH . H 4 HOH A 15 215 6 HOH HOH . H 4 HOH A 16 216 14 HOH HOH . H 4 HOH A 17 217 95 HOH HOH . H 4 HOH A 18 218 28 HOH HOH . H 4 HOH A 19 219 35 HOH HOH . H 4 HOH A 20 220 64 HOH HOH . H 4 HOH A 21 221 57 HOH HOH . H 4 HOH A 22 222 54 HOH HOH . H 4 HOH A 23 223 51 HOH HOH . H 4 HOH A 24 224 98 HOH HOH . H 4 HOH A 25 225 92 HOH HOH . H 4 HOH A 26 226 37 HOH HOH . I 4 HOH B 1 201 39 HOH HOH . I 4 HOH B 2 202 31 HOH HOH . I 4 HOH B 3 203 15 HOH HOH . I 4 HOH B 4 204 10 HOH HOH . I 4 HOH B 5 205 60 HOH HOH . I 4 HOH B 6 206 94 HOH HOH . I 4 HOH B 7 207 12 HOH HOH . I 4 HOH B 8 208 48 HOH HOH . I 4 HOH B 9 209 8 HOH HOH . I 4 HOH B 10 210 16 HOH HOH . I 4 HOH B 11 211 9 HOH HOH . I 4 HOH B 12 212 53 HOH HOH . I 4 HOH B 13 213 41 HOH HOH . I 4 HOH B 14 214 44 HOH HOH . I 4 HOH B 15 215 26 HOH HOH . I 4 HOH B 16 216 43 HOH HOH . I 4 HOH B 17 217 75 HOH HOH . I 4 HOH B 18 218 5 HOH HOH . I 4 HOH B 19 219 58 HOH HOH . I 4 HOH B 20 220 18 HOH HOH . I 4 HOH B 21 221 47 HOH HOH . I 4 HOH B 22 222 30 HOH HOH . I 4 HOH B 23 223 36 HOH HOH . I 4 HOH B 24 224 102 HOH HOH . I 4 HOH B 25 225 40 HOH HOH . J 4 HOH C 1 201 78 HOH HOH . J 4 HOH C 2 202 56 HOH HOH . J 4 HOH C 3 203 96 HOH HOH . J 4 HOH C 4 204 67 HOH HOH . J 4 HOH C 5 205 29 HOH HOH . J 4 HOH C 6 206 45 HOH HOH . J 4 HOH C 7 207 81 HOH HOH . J 4 HOH C 8 208 76 HOH HOH . J 4 HOH C 9 209 61 HOH HOH . J 4 HOH C 10 210 34 HOH HOH . J 4 HOH C 11 211 23 HOH HOH . J 4 HOH C 12 212 1 HOH HOH . J 4 HOH C 13 213 24 HOH HOH . J 4 HOH C 14 214 77 HOH HOH . J 4 HOH C 15 215 50 HOH HOH . J 4 HOH C 16 216 52 HOH HOH . J 4 HOH C 17 217 66 HOH HOH . J 4 HOH C 18 218 73 HOH HOH . J 4 HOH C 19 219 87 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 D _atom_site.label_entity_id 3 _atom_site.Cartn_x 20.891 _atom_site.Cartn_y 1.316 _atom_site.Cartn_z 12.124 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 63.03 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 101 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 490 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #