data_1Y4D # _model_server_result.job_id '_g1DBxz-pb_Y0bUh0b8w9w' _model_server_result.datetime_utc '2024-12-24 12:44:54' _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 1y4d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1002}' # _entry.id 1Y4D # _exptl.entry_id 1Y4D _exptl.method 'X-RAY DIFFRACTION' # _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 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 120 _cell.entry_id 1Y4D _cell.length_a 115.381 _cell.length_b 115.381 _cell.length_c 42.907 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Y4D _symmetry.cell_setting hexagonal _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _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 _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 4 _struct_asym.id D _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 metalc ? metalc1 A NE2 GLN 2 E GLN 2 1_555 C CA CA . E CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc2 A OD1 ASP 41 E ASP 41 1_555 C CA CA . E CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc3 A OD2 ASP 41 E ASP 41 1_555 C CA CA . E CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? metalc ? metalc4 A O LEU 75 E LEU 75 1_555 C CA CA . E CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc5 A OD1 ASN 77 E ASN 77 1_555 C CA CA . E CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? metalc ? metalc6 A O ILE 79 E ILE 79 1_555 C CA CA . E CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc7 A O VAL 81 E VAL 81 1_555 C CA CA . E CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc8 A O GLY 169 E GLY 169 1_555 D NA NA . E NA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.74 ? metalc ? metalc9 A O TYR 171 E TYR 171 1_555 D NA NA . E NA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.877 ? metalc ? metalc10 A O VAL 174 E VAL 174 1_555 D NA NA . E NA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.677 ? metalc ? metalc11 A OD2 ASP 197 E ASP 197 1_555 D NA NA . E NA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.669 ? metalc ? metalc12 D NA NA . E NA 1002 1_555 E O HOH . E HOH 1069 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.636 ? # _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 1Y4D _atom_sites.fract_transf_matrix[1][1] 0.008667 _atom_sites.fract_transf_matrix[1][2] 0.005004 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010008 _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] 0.023306 _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 3 CA E 1 1001 1001 CA CA . D 4 NA E 1 1002 1002 NA NA . E 5 HOH E 1 1003 1 HOH HOH . E 5 HOH E 2 1004 2 HOH HOH . E 5 HOH E 3 1005 3 HOH HOH . E 5 HOH E 4 1006 4 HOH HOH . E 5 HOH E 5 1007 5 HOH HOH . E 5 HOH E 6 1008 6 HOH HOH . E 5 HOH E 7 1009 7 HOH HOH . E 5 HOH E 8 1010 8 HOH HOH . E 5 HOH E 9 1011 9 HOH HOH . E 5 HOH E 10 1012 10 HOH HOH . E 5 HOH E 11 1013 11 HOH HOH . E 5 HOH E 12 1014 12 HOH HOH . E 5 HOH E 13 1015 14 HOH HOH . E 5 HOH E 14 1016 15 HOH HOH . E 5 HOH E 15 1017 16 HOH HOH . E 5 HOH E 16 1018 17 HOH HOH . E 5 HOH E 17 1019 19 HOH HOH . E 5 HOH E 18 1020 20 HOH HOH . E 5 HOH E 19 1021 21 HOH HOH . E 5 HOH E 20 1022 22 HOH HOH . E 5 HOH E 21 1023 23 HOH HOH . E 5 HOH E 22 1024 24 HOH HOH . E 5 HOH E 23 1025 25 HOH HOH . E 5 HOH E 24 1026 26 HOH HOH . E 5 HOH E 25 1027 27 HOH HOH . E 5 HOH E 26 1028 28 HOH HOH . E 5 HOH E 27 1029 29 HOH HOH . E 5 HOH E 28 1030 30 HOH HOH . E 5 HOH E 29 1031 31 HOH HOH . E 5 HOH E 30 1032 32 HOH HOH . E 5 HOH E 31 1033 34 HOH HOH . E 5 HOH E 32 1034 35 HOH HOH . E 5 HOH E 33 1035 36 HOH HOH . E 5 HOH E 34 1036 37 HOH HOH . E 5 HOH E 35 1037 38 HOH HOH . E 5 HOH E 36 1038 40 HOH HOH . E 5 HOH E 37 1039 41 HOH HOH . E 5 HOH E 38 1040 42 HOH HOH . E 5 HOH E 39 1041 44 HOH HOH . E 5 HOH E 40 1042 46 HOH HOH . E 5 HOH E 41 1043 47 HOH HOH . E 5 HOH E 42 1044 48 HOH HOH . E 5 HOH E 43 1045 50 HOH HOH . E 5 HOH E 44 1046 51 HOH HOH . E 5 HOH E 45 1047 52 HOH HOH . E 5 HOH E 46 1048 53 HOH HOH . E 5 HOH E 47 1049 54 HOH HOH . E 5 HOH E 48 1050 55 HOH HOH . E 5 HOH E 49 1051 56 HOH HOH . E 5 HOH E 50 1052 57 HOH HOH . E 5 HOH E 51 1053 58 HOH HOH . E 5 HOH E 52 1054 61 HOH HOH . E 5 HOH E 53 1055 62 HOH HOH . E 5 HOH E 54 1056 63 HOH HOH . E 5 HOH E 55 1057 65 HOH HOH . E 5 HOH E 56 1058 66 HOH HOH . E 5 HOH E 57 1059 67 HOH HOH . E 5 HOH E 58 1060 69 HOH HOH . E 5 HOH E 59 1061 70 HOH HOH . E 5 HOH E 60 1062 71 HOH HOH . E 5 HOH E 61 1063 72 HOH HOH . E 5 HOH E 62 1064 74 HOH HOH . E 5 HOH E 63 1065 75 HOH HOH . E 5 HOH E 64 1066 77 HOH HOH . E 5 HOH E 65 1067 78 HOH HOH . E 5 HOH E 66 1068 79 HOH HOH . E 5 HOH E 67 1069 81 HOH HOH . E 5 HOH E 68 1070 83 HOH HOH . E 5 HOH E 69 1071 85 HOH HOH . E 5 HOH E 70 1072 86 HOH HOH . E 5 HOH E 71 1073 87 HOH HOH . E 5 HOH E 72 1074 88 HOH HOH . E 5 HOH E 73 1075 89 HOH HOH . E 5 HOH E 74 1076 91 HOH HOH . E 5 HOH E 75 1077 94 HOH HOH . E 5 HOH E 76 1078 95 HOH HOH . E 5 HOH E 77 1079 96 HOH HOH . E 5 HOH E 78 1080 98 HOH HOH . E 5 HOH E 79 1081 99 HOH HOH . E 5 HOH E 80 1082 100 HOH HOH . E 5 HOH E 81 1083 101 HOH HOH . E 5 HOH E 82 1084 102 HOH HOH . E 5 HOH E 83 1085 103 HOH HOH . E 5 HOH E 84 1086 105 HOH HOH . E 5 HOH E 85 1087 106 HOH HOH . E 5 HOH E 86 1088 107 HOH HOH . E 5 HOH E 87 1089 108 HOH HOH . E 5 HOH E 88 1090 109 HOH HOH . E 5 HOH E 89 1091 110 HOH HOH . E 5 HOH E 90 1092 111 HOH HOH . E 5 HOH E 91 1093 112 HOH HOH . E 5 HOH E 92 1094 113 HOH HOH . F 5 HOH I 1 84 13 HOH HOH . F 5 HOH I 2 85 18 HOH HOH . F 5 HOH I 3 86 33 HOH HOH . F 5 HOH I 4 87 39 HOH HOH . F 5 HOH I 5 88 43 HOH HOH . F 5 HOH I 6 89 45 HOH HOH . F 5 HOH I 7 90 49 HOH HOH . F 5 HOH I 8 91 59 HOH HOH . F 5 HOH I 9 92 60 HOH HOH . F 5 HOH I 10 93 64 HOH HOH . F 5 HOH I 11 94 68 HOH HOH . F 5 HOH I 12 95 73 HOH HOH . F 5 HOH I 13 96 76 HOH HOH . F 5 HOH I 14 97 80 HOH HOH . F 5 HOH I 15 98 82 HOH HOH . F 5 HOH I 16 99 84 HOH HOH . F 5 HOH I 17 100 90 HOH HOH . F 5 HOH I 18 101 92 HOH HOH . F 5 HOH I 19 102 93 HOH HOH . F 5 HOH I 20 103 97 HOH HOH . F 5 HOH I 21 104 104 HOH HOH . F 5 HOH I 22 105 114 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 4 _atom_site.Cartn_x 12.635 _atom_site.Cartn_y 46.017 _atom_site.Cartn_z 1.446 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 12.99 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 1002 _atom_site.auth_asym_id E _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 1 #