data_5JDQ # _model_server_result.job_id LRI-5ENaNs8U0vrSvoAJNQ _model_server_result.datetime_utc '2024-11-23 02:47:35' _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 5jdq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 5JDQ # _exptl.entry_id 5JDQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _entity.pdbx_number_of_molecules 3 _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 5JDQ _cell.length_a 49.876 _cell.length_b 72.425 _cell.length_c 95.913 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JDQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,K,L,M,N,O,P _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 ? 2 B N N ? 2 C N N ? 2 D 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 metalc ? metalc1 A O ALA 47 A ALA 47 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc2 A OG1 THR 50 A THR 50 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc3 A O THR 50 A THR 50 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc4 A OG SER 51 A SER 51 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc5 A OE1 GLU 54 A GLU 54 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc6 A OE2 GLU 54 A GLU 54 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? metalc ? metalc7 A OE2 GLU 54 A GLU 54 1_555 D NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc8 A OG SER 77 A SER 77 1_555 D NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc9 A O ILE 118 A ILE 118 1_555 E SR SR . A SR 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? metalc ? metalc10 A OD1 ASP 121 A ASP 121 1_555 E SR SR . A SR 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? metalc ? metalc11 A O GLY 122 A GLY 122 1_555 E SR SR . A SR 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? metalc ? metalc12 A OD2 ASP 127 A ASP 127 1_555 E SR SR . A SR 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? metalc ? metalc13 A O ALA 206 A ALA 206 1_555 D NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.516 ? metalc ? metalc14 A O THR 209 A THR 209 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc15 A OG1 THR 209 A THR 209 1_555 D NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? metalc ? metalc16 A OG SER 210 A SER 210 1_555 D NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc17 A OE2 GLU 213 A GLU 213 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc18 A OE1 GLU 213 A GLU 213 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc19 A OE2 GLU 213 A GLU 213 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc20 A OG SER 236 A SER 236 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc21 E SR SR . A SR 404 1_555 P O HOH . A HOH 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.896 ? # _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 5JDQ _atom_sites.fract_transf_matrix[1][1] 0.02005 _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] 0.013807 _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] 0.010426 _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 NA A 1 401 1 NA NA . C 2 NA A 1 402 2 NA NA . D 2 NA A 1 403 4 NA NA . E 3 SR A 1 404 1 SR SR . F 4 CL A 1 405 1 CL CL . G 4 CL A 1 406 2 CL CL . H 5 OLC A 1 407 1 OLC MON . I 5 OLC A 1 408 2 OLC MON . J 6 MYS A 1 409 1 MYS FAT . K 6 MYS A 1 410 2 MYS FAT . L 6 MYS A 1 411 3 MYS FAT . M 6 MYS A 1 412 4 MYS FAT . N 6 MYS A 1 413 5 MYS FAT . O 7 1PE A 1 414 1 1PE PEG . P 8 HOH A 1 501 16 HOH HOH . P 8 HOH A 2 502 4 HOH HOH . P 8 HOH A 3 503 13 HOH HOH . P 8 HOH A 4 504 2 HOH HOH . P 8 HOH A 5 505 15 HOH HOH . P 8 HOH A 6 506 10 HOH HOH . P 8 HOH A 7 507 14 HOH HOH . P 8 HOH A 8 508 7 HOH HOH . P 8 HOH A 9 509 6 HOH HOH . P 8 HOH A 10 510 11 HOH HOH . P 8 HOH A 11 511 3 HOH HOH . P 8 HOH A 12 512 12 HOH HOH . P 8 HOH A 13 513 9 HOH HOH . P 8 HOH A 14 514 17 HOH HOH . P 8 HOH A 15 515 5 HOH HOH . P 8 HOH A 16 516 8 HOH HOH . P 8 HOH A 17 517 1 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 2 _atom_site.Cartn_x 4.807 _atom_site.Cartn_y 22.896 _atom_site.Cartn_z 25.792 _atom_site.occupancy 0.6 _atom_site.B_iso_or_equiv 55.18 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 403 _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 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 1 #