data_8YR2 # _model_server_result.job_id lvGNfhKQbhPkg-wzQYsz6Q _model_server_result.datetime_utc '2025-03-03 20:15:59' _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 8yr2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":704}' # _entry.id 8YR2 # _exptl.entry_id 8YR2 _exptl.method 'ELECTRON MICROSCOPY' # _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 4 _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 8YR2 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YR2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _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,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA _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 ? 4 E N N ? 4 F N N ? 4 W N N ? 4 X 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 GLY 71 B GLY 71 1_555 F NA NA . B NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc2 A O ALA 73 B ALA 73 1_555 E NA NA . B NA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.904 ? metalc ? metalc3 A O VAL 74 B VAL 74 1_555 F NA NA . B NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc4 A OD1 ASN 78 B ASN 78 1_555 E NA NA . B NA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.621 ? metalc ? metalc5 A O SER 318 B SER 318 1_555 E NA NA . B NA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? metalc ? metalc6 A OD1 ASP 418 B ASP 418 1_555 F NA NA . B NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc7 A OD2 ASP 418 B ASP 418 1_555 F NA NA . B NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.177 ? metalc ? metalc8 A OG SER 419 B SER 419 1_555 F NA NA . B NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.895 ? metalc ? metalc9 B O GLY 71 A GLY 71 1_555 X NA NA . A NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc10 B O VAL 74 A VAL 74 1_555 X NA NA . A NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc11 B OD1 ASN 78 A ASN 78 1_555 W NA NA . A NA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.752 ? metalc ? metalc12 B O SER 318 A SER 318 1_555 W NA NA . A NA 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? metalc ? metalc13 B O LEU 415 A LEU 415 1_555 X NA NA . A NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.026 ? metalc ? metalc14 B OD2 ASP 418 A ASP 418 1_555 X NA NA . A NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.077 ? metalc ? metalc15 B OG SER 419 A SER 419 1_555 X NA NA . A NA 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? # _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 8YR2 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 C 2 41U B 1 701 701 41U 41U . D 3 PIO B 1 702 702 PIO PIO . E 4 NA B 1 703 12 NA NA . F 4 NA B 1 704 13 NA NA . G 5 CL B 1 705 6 CL CL . H 6 CLR B 1 706 704 CLR CLR . I 6 CLR B 1 707 706 CLR CLR . J 6 CLR B 1 708 709 CLR CLR . K 6 CLR B 1 709 710 CLR CLR . L 6 CLR B 1 710 712 CLR CLR . M 6 CLR B 1 711 713 CLR CLR . N 6 CLR B 1 712 714 CLR CLR . O 7 A1LX7 B 1 713 705 A1LX7 PI0 . P 7 A1LX7 B 1 714 716 A1LX7 PI0 . Q 6 CLR B 1 715 701 CLR CLR . R 6 CLR B 1 716 702 CLR CLR . S 6 CLR B 1 717 703 CLR CLR . T 6 CLR B 1 718 704 CLR CLR . U 2 41U A 1 701 701 41U 41U . V 3 PIO A 1 702 702 PIO PIO . W 4 NA A 1 703 10 NA NA . X 4 NA A 1 704 11 NA NA . Y 5 CL A 1 705 5 CL CL . Z 6 CLR A 1 706 707 CLR CLR . AA 6 CLR A 1 707 708 CLR CLR . BA 6 CLR A 1 708 711 CLR CLR . CA 6 CLR A 1 709 715 CLR CLR . DA 6 CLR A 1 710 718 CLR CLR . EA 7 A1LX7 A 1 711 712 A1LX7 PI0 . FA 7 A1LX7 A 1 712 713 A1LX7 PI0 . GA 6 CLR A 1 713 707 CLR CLR . HA 6 CLR A 1 714 708 CLR CLR . IA 6 CLR A 1 715 709 CLR CLR . JA 6 CLR A 1 716 713 CLR CLR . KA 8 HOH B 1 801 7 HOH HOH . KA 8 HOH B 2 802 6 HOH HOH . KA 8 HOH B 3 803 5 HOH HOH . LA 8 HOH A 1 801 4 HOH HOH . LA 8 HOH A 2 802 3 HOH HOH . LA 8 HOH A 3 803 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 F _atom_site.label_entity_id 4 _atom_site.Cartn_x 110.625 _atom_site.Cartn_y 116.332 _atom_site.Cartn_z 92.972 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 30 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 704 _atom_site.auth_asym_id B _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #