data_1D3Q # _model_server_result.job_id qLfLT61Xg5bXufxHzIqxfQ _model_server_result.datetime_utc '2024-12-27 02:38:16' _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 1d3q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":399}' # _entry.id 1D3Q # _exptl.entry_id 1D3Q _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 100.56 _cell.angle_gamma 90 _cell.entry_id 1D3Q _cell.length_a 71.15 _cell.length_b 71.73 _cell.length_c 73.1 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D3Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _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 _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 ? 5 E N N ? 5 F 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 disulf ? disulf1 A SG CYS 9 A CYS 9 1_555 B SG CYS 119 B CYS 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf2 B SG CYS 28 B CYS 64 1_555 B SG CYS 44 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 B SG CYS 173 B CYS 209 1_555 B SG CYS 187 B CYS 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 B SG CYS 201 B CYS 237 1_555 B SG CYS 231 B CYS 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 B ND2 ASN 53 B ASN 89 1_555 D C1 NAG . B NAG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale2 C C GLU 9 H GLU 308 1_555 C N TYS 10 H TYS 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.343 ? covale ? covale3 C C TYS 10 H TYS 309 1_555 C N LEU 11 H LEU 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.35 ? metalc ? metalc1 B O LYS 174 B LYS 210 1_555 E NA NA . B NA 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? metalc ? metalc2 B O THR 177 B THR 213 1_555 E NA NA . B NA 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? metalc ? metalc3 B O PHE 215 B PHE 251 4_446 E NA NA . B NA 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? metalc ? metalc4 B O ARG 233 B ARG 269 1_555 F NA NA . B NA 399 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc5 B O LYS 236 B LYS 272 1_555 F NA NA . B NA 399 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? # _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 1D3Q _atom_sites.fract_transf_matrix[1][1] 0.014055 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00262 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013941 _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] 0.013916 _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 4 NAG B 1 500 500 NAG NAG . E 5 NA B 1 398 398 NA NA . F 5 NA B 1 399 399 NA NA . G 6 BT2 B 1 400 400 BT2 BT2 . # _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 F _atom_site.label_entity_id 5 _atom_site.Cartn_x -29.387 _atom_site.Cartn_y -33.811 _atom_site.Cartn_z 30.279 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 20 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 399 _atom_site.auth_asym_id B _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 1 #