data_8DW4 # _model_server_result.job_id hGYOPV4r0pKyBKLUN-TXKw _model_server_result.datetime_utc '2025-03-02 23:50:35' _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 8dw4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":403}' # _entry.id 8DW4 # _exptl.entry_id 8DW4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 6 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _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 8DW4 _cell.length_a 37.64 _cell.length_b 85.55 _cell.length_c 141.17 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DW4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 6 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 B O3' DC 5 B DC 5 1_555 B P 8OG 6 B 8OG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.601 ? covale ? covale2 B O3' 8OG 6 B 8OG 6 1_555 B P DT 7 B DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.601 ? covale ? covale3 C O3' DA 6 C DA 17 1_555 C P AAB 7 C AAB 18 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.608 ? covale ? covale4 C O3' AAB 7 C AAB 18 1_555 C P DG 8 C DG 19 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.611 ? covale ? covale5 C O3' AAB 7 C AAB 18 1_555 C P DG 8 C DG 19 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.607 ? metalc ? metalc1 A O SER 118 A SER 118 1_555 F NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? metalc ? metalc2 A O LEU 120 A LEU 120 1_555 F NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.854 ? metalc ? metalc3 A O VAL 123 A VAL 123 1_555 F NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.588 ? metalc ? metalc4 A SG CYS 198 A CYS 198 1_555 D FE3 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.668 ? metalc ? metalc5 A SG CYS 205 A CYS 205 1_555 D FE2 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc6 A SG CYS 208 A CYS 208 1_555 D FE1 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc7 A SG CYS 214 A CYS 214 1_555 D FE4 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc8 F NA NA . A NA 403 1_555 G O HOH . A HOH 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc9 F NA NA . A NA 403 1_555 C OP1 DC 10 C DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.91 ? metalc ? metalc10 F NA NA . A NA 403 1_555 I O HOH . C HOH 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? hydrog WATSON-CRICK hydrog1 B N1 DA 2 B DA 2 1_555 C N3 DT 11 C DT 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N6 DA 2 B DA 2 1_555 C O4 DT 11 C DT 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N1 DG 3 B DG 3 1_555 C N3 DC 10 C DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N2 DG 3 B DG 3 1_555 C O2 DC 10 C DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O6 DG 3 B DG 3 1_555 C N4 DC 10 C DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N1 DA 4 B DA 4 1_555 C N3 DT 9 C DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N6 DA 4 B DA 4 1_555 C O4 DT 9 C DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N3 DC 5 B DC 5 1_555 C N1 DG 8 C DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N4 DC 5 B DC 5 1_555 C O6 DG 8 C DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B O2 DC 5 B DC 5 1_555 C N2 DG 8 C DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N3 DT 7 B DT 7 1_555 C N1 DA 6 C DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B O4 DT 7 B DT 7 1_555 C N6 DA 6 C DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N1 DG 8 B DG 8 1_555 C N3 DC 5 C DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N2 DG 8 B DG 8 1_555 C O2 DC 5 C DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O6 DG 8 B DG 8 1_555 C N4 DC 5 C DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N1 DG 9 B DG 9 1_555 C N3 DC 4 C DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N2 DG 9 B DG 9 1_555 C O2 DC 4 C DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O6 DG 9 B DG 9 1_555 C N4 DC 4 C DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N1 DA 10 B DA 10 1_555 C N3 DT 3 C DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N6 DA 10 B DA 10 1_555 C O4 DT 3 C DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N3 DC 11 B DC 11 1_555 C N1 DG 2 C DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N4 DC 11 B DC 11 1_555 C O6 DG 2 C DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B O2 DC 11 B DC 11 1_555 C N2 DG 2 C DG 13 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 8DW4 _atom_sites.fract_transf_matrix[1][1] 0.026567 _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] 0.011689 _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] 0.007084 _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 SF4 A 1 401 401 SF4 SF4 . E 5 ACT A 1 402 501 ACT ACT . F 6 NA A 1 403 1 NA NA . G 7 HOH A 1 501 23 HOH HOH . G 7 HOH A 2 502 14 HOH HOH . G 7 HOH A 3 503 12 HOH HOH . G 7 HOH A 4 504 21 HOH HOH . G 7 HOH A 5 505 22 HOH HOH . G 7 HOH A 6 506 5 HOH HOH . G 7 HOH A 7 507 7 HOH HOH . G 7 HOH A 8 508 33 HOH HOH . G 7 HOH A 9 509 8 HOH HOH . G 7 HOH A 10 510 3 HOH HOH . G 7 HOH A 11 511 31 HOH HOH . G 7 HOH A 12 512 10 HOH HOH . G 7 HOH A 13 513 4 HOH HOH . G 7 HOH A 14 514 28 HOH HOH . G 7 HOH A 15 515 35 HOH HOH . G 7 HOH A 16 516 15 HOH HOH . G 7 HOH A 17 517 16 HOH HOH . G 7 HOH A 18 518 32 HOH HOH . H 7 HOH B 1 101 25 HOH HOH . H 7 HOH B 2 102 11 HOH HOH . H 7 HOH B 3 103 24 HOH HOH . H 7 HOH B 4 104 17 HOH HOH . I 7 HOH C 1 101 1 HOH HOH . I 7 HOH C 2 102 18 HOH HOH . I 7 HOH C 3 103 19 HOH HOH . I 7 HOH C 4 104 34 HOH HOH . I 7 HOH C 5 105 36 HOH HOH . I 7 HOH C 6 106 9 HOH HOH . I 7 HOH C 7 107 29 HOH HOH . I 7 HOH C 8 108 30 HOH HOH . I 7 HOH C 9 109 20 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 F _atom_site.label_entity_id 6 _atom_site.Cartn_x 25.724 _atom_site.Cartn_y 11.138 _atom_site.Cartn_z 4.901 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 42.63 _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 21 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 1 #