data_3DYQ # _model_server_result.job_id qYBs0AO-bfUzbPV46Xgm0w _model_server_result.datetime_utc '2024-10-25 20:34:20' _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 3dyq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":901}' # _entry.id 3DYQ # _exptl.entry_id 3DYQ _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 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 3DYQ _cell.length_a 103.65 _cell.length_b 103.65 _cell.length_c 270.041 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DYQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J 1 1 A,C,D,E,I 2 1 B,F,G,H,J 2 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_645 -y+3/2,x-1/2,z+1/4 0 -1 0 1 0 0 0 0 1 155.475 -51.825 67.51025 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N ? 2 F N N ? 2 G 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 I O HOH . A HOH 93 1_555 D NA NA . A NA 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc2 I O HOH . A HOH 95 1_555 D NA NA . A NA 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc3 A NE2 HIS 79 A HIS 256 1_555 C NA NA . A NA 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? metalc ? metalc4 A NE2 HIS 115 A HIS 292 1_555 C NA NA . A NA 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc5 A OD2 ASP 116 A ASP 293 1_555 C NA NA . A NA 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc6 A OD1 ASP 116 A ASP 293 1_555 D NA NA . A NA 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc7 A OD1 ASP 225 A ASP 402 1_555 C NA NA . A NA 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc8 E O1A PCG . A PCG 900 1_555 C NA NA . A NA 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? metalc ? metalc9 E O1A PCG . A PCG 900 1_555 D NA NA . A NA 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.918 ? metalc ? metalc10 B NE2 HIS 79 B HIS 256 1_555 F NA NA . B NA 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? metalc ? metalc11 B NE2 HIS 115 B HIS 292 1_555 F NA NA . B NA 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc12 B OD2 ASP 116 B ASP 293 1_555 F NA NA . B NA 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc13 B OD1 ASP 116 B ASP 293 1_555 G NA NA . B NA 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc14 B OD1 ASP 225 B ASP 402 1_555 F NA NA . B NA 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? # _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 3DYQ _atom_sites.fract_transf_matrix[1][1] 0.009648 _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] 0.009648 _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] 0.003703 _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 NA A 1 901 901 NA NA . D 2 NA A 1 902 902 NA NA . E 3 PCG A 1 900 900 PCG PCG . F 2 NA B 1 901 901 NA NA . G 2 NA B 1 902 902 NA NA . H 4 IBM B 1 900 900 IBM IBM . I 5 HOH A 1 5 5 HOH HOH . I 5 HOH A 2 7 7 HOH HOH . I 5 HOH A 3 9 9 HOH HOH . I 5 HOH A 4 11 11 HOH HOH . I 5 HOH A 5 12 12 HOH HOH . I 5 HOH A 6 13 13 HOH HOH . I 5 HOH A 7 15 15 HOH HOH . I 5 HOH A 8 18 18 HOH HOH . I 5 HOH A 9 20 20 HOH HOH . I 5 HOH A 10 21 21 HOH HOH . I 5 HOH A 11 22 22 HOH HOH . I 5 HOH A 12 23 23 HOH HOH . I 5 HOH A 13 24 24 HOH HOH . I 5 HOH A 14 26 26 HOH HOH . I 5 HOH A 15 27 27 HOH HOH . I 5 HOH A 16 28 28 HOH HOH . I 5 HOH A 17 29 29 HOH HOH . I 5 HOH A 18 31 31 HOH HOH . I 5 HOH A 19 32 32 HOH HOH . I 5 HOH A 20 33 33 HOH HOH . I 5 HOH A 21 36 36 HOH HOH . I 5 HOH A 22 38 38 HOH HOH . I 5 HOH A 23 39 39 HOH HOH . I 5 HOH A 24 41 41 HOH HOH . I 5 HOH A 25 42 42 HOH HOH . I 5 HOH A 26 45 45 HOH HOH . I 5 HOH A 27 46 46 HOH HOH . I 5 HOH A 28 48 48 HOH HOH . I 5 HOH A 29 50 50 HOH HOH . I 5 HOH A 30 52 52 HOH HOH . I 5 HOH A 31 55 55 HOH HOH . I 5 HOH A 32 56 56 HOH HOH . I 5 HOH A 33 57 57 HOH HOH . I 5 HOH A 34 60 60 HOH HOH . I 5 HOH A 35 64 64 HOH HOH . I 5 HOH A 36 67 67 HOH HOH . I 5 HOH A 37 68 68 HOH HOH . I 5 HOH A 38 69 69 HOH HOH . I 5 HOH A 39 71 71 HOH HOH . I 5 HOH A 40 72 72 HOH HOH . I 5 HOH A 41 74 74 HOH HOH . I 5 HOH A 42 75 75 HOH HOH . I 5 HOH A 43 76 76 HOH HOH . I 5 HOH A 44 78 78 HOH HOH . I 5 HOH A 45 79 79 HOH HOH . I 5 HOH A 46 83 83 HOH HOH . I 5 HOH A 47 87 87 HOH HOH . I 5 HOH A 48 88 88 HOH HOH . I 5 HOH A 49 89 89 HOH HOH . I 5 HOH A 50 92 92 HOH HOH . I 5 HOH A 51 93 93 HOH HOH . I 5 HOH A 52 95 95 HOH HOH . I 5 HOH A 53 1005 1005 HOH HOH . I 5 HOH A 54 1006 1006 HOH HOH . I 5 HOH A 55 1007 1007 HOH HOH . I 5 HOH A 56 1008 1008 HOH HOH . I 5 HOH A 57 1010 1010 HOH HOH . I 5 HOH A 58 1011 1011 HOH HOH . I 5 HOH A 59 1012 1012 HOH HOH . I 5 HOH A 60 1013 1013 HOH HOH . I 5 HOH A 61 1015 1015 HOH HOH . I 5 HOH A 62 1016 1016 HOH HOH . I 5 HOH A 63 1019 1019 HOH HOH . I 5 HOH A 64 1020 1020 HOH HOH . I 5 HOH A 65 1024 1024 HOH HOH . I 5 HOH A 66 1025 1025 HOH HOH . I 5 HOH A 67 1027 1027 HOH HOH . I 5 HOH A 68 1028 1028 HOH HOH . I 5 HOH A 69 1030 1030 HOH HOH . I 5 HOH A 70 1031 1031 HOH HOH . I 5 HOH A 71 1032 1032 HOH HOH . I 5 HOH A 72 1034 1034 HOH HOH . I 5 HOH A 73 1035 1035 HOH HOH . I 5 HOH A 74 1040 1040 HOH HOH . I 5 HOH A 75 1041 1041 HOH HOH . I 5 HOH A 76 1046 1046 HOH HOH . I 5 HOH A 77 1051 1051 HOH HOH . I 5 HOH A 78 1057 1057 HOH HOH . I 5 HOH A 79 1058 1058 HOH HOH . I 5 HOH A 80 1061 1061 HOH HOH . I 5 HOH A 81 1062 1062 HOH HOH . I 5 HOH A 82 1066 1066 HOH HOH . I 5 HOH A 83 1068 1068 HOH HOH . I 5 HOH A 84 1069 1069 HOH HOH . I 5 HOH A 85 1072 1072 HOH HOH . I 5 HOH A 86 1074 1074 HOH HOH . I 5 HOH A 87 1075 1075 HOH HOH . I 5 HOH A 88 1078 1078 HOH HOH . I 5 HOH A 89 1079 1079 HOH HOH . I 5 HOH A 90 1081 1081 HOH HOH . I 5 HOH A 91 1082 1082 HOH HOH . I 5 HOH A 92 1084 1084 HOH HOH . I 5 HOH A 93 1087 1087 HOH HOH . I 5 HOH A 94 1089 1089 HOH HOH . I 5 HOH A 95 1090 1090 HOH HOH . I 5 HOH A 96 1091 1091 HOH HOH . I 5 HOH A 97 1093 1093 HOH HOH . I 5 HOH A 98 1095 1095 HOH HOH . I 5 HOH A 99 1098 1098 HOH HOH . I 5 HOH A 100 1099 1099 HOH HOH . I 5 HOH A 101 1101 1101 HOH HOH . I 5 HOH A 102 1102 1102 HOH HOH . I 5 HOH A 103 1104 1104 HOH HOH . I 5 HOH A 104 1105 1105 HOH HOH . I 5 HOH A 105 1108 1108 HOH HOH . I 5 HOH A 106 1112 1112 HOH HOH . I 5 HOH A 107 1113 1113 HOH HOH . I 5 HOH A 108 1115 1115 HOH HOH . I 5 HOH A 109 1119 1119 HOH HOH . I 5 HOH A 110 1121 1121 HOH HOH . I 5 HOH A 111 1122 1122 HOH HOH . I 5 HOH A 112 1123 1123 HOH HOH . I 5 HOH A 113 1128 1128 HOH HOH . I 5 HOH A 114 1129 1129 HOH HOH . I 5 HOH A 115 1130 1130 HOH HOH . I 5 HOH A 116 1135 1135 HOH HOH . I 5 HOH A 117 1136 1136 HOH HOH . I 5 HOH A 118 1137 1137 HOH HOH . I 5 HOH A 119 1141 1141 HOH HOH . I 5 HOH A 120 1143 1143 HOH HOH . I 5 HOH A 121 1144 1144 HOH HOH . I 5 HOH A 122 1145 1145 HOH HOH . I 5 HOH A 123 1146 1146 HOH HOH . I 5 HOH A 124 1147 1147 HOH HOH . I 5 HOH A 125 1149 1149 HOH HOH . I 5 HOH A 126 1152 1152 HOH HOH . I 5 HOH A 127 1153 1153 HOH HOH . J 5 HOH B 1 1 1 HOH HOH . J 5 HOH B 2 2 2 HOH HOH . J 5 HOH B 3 3 3 HOH HOH . J 5 HOH B 4 4 4 HOH HOH . J 5 HOH B 5 6 6 HOH HOH . J 5 HOH B 6 8 8 HOH HOH . J 5 HOH B 7 10 10 HOH HOH . J 5 HOH B 8 14 14 HOH HOH . J 5 HOH B 9 16 16 HOH HOH . J 5 HOH B 10 17 17 HOH HOH . J 5 HOH B 11 19 19 HOH HOH . J 5 HOH B 12 25 25 HOH HOH . J 5 HOH B 13 30 30 HOH HOH . J 5 HOH B 14 35 35 HOH HOH . J 5 HOH B 15 37 37 HOH HOH . J 5 HOH B 16 40 40 HOH HOH . J 5 HOH B 17 43 43 HOH HOH . J 5 HOH B 18 44 44 HOH HOH . J 5 HOH B 19 47 47 HOH HOH . J 5 HOH B 20 49 49 HOH HOH . J 5 HOH B 21 51 51 HOH HOH . J 5 HOH B 22 53 53 HOH HOH . J 5 HOH B 23 54 54 HOH HOH . J 5 HOH B 24 58 58 HOH HOH . J 5 HOH B 25 61 61 HOH HOH . J 5 HOH B 26 62 62 HOH HOH . J 5 HOH B 27 63 63 HOH HOH . J 5 HOH B 28 65 65 HOH HOH . J 5 HOH B 29 66 66 HOH HOH . J 5 HOH B 30 70 70 HOH HOH . J 5 HOH B 31 73 73 HOH HOH . J 5 HOH B 32 77 77 HOH HOH . J 5 HOH B 33 81 81 HOH HOH . J 5 HOH B 34 82 82 HOH HOH . J 5 HOH B 35 84 84 HOH HOH . J 5 HOH B 36 85 85 HOH HOH . J 5 HOH B 37 86 86 HOH HOH . J 5 HOH B 38 90 90 HOH HOH . J 5 HOH B 39 91 91 HOH HOH . J 5 HOH B 40 1002 1002 HOH HOH . J 5 HOH B 41 1003 1003 HOH HOH . J 5 HOH B 42 1004 1004 HOH HOH . J 5 HOH B 43 1009 1009 HOH HOH . J 5 HOH B 44 1014 1014 HOH HOH . J 5 HOH B 45 1017 1017 HOH HOH . J 5 HOH B 46 1018 1018 HOH HOH . J 5 HOH B 47 1021 1021 HOH HOH . J 5 HOH B 48 1022 1022 HOH HOH . J 5 HOH B 49 1023 1023 HOH HOH . J 5 HOH B 50 1026 1026 HOH HOH . J 5 HOH B 51 1029 1029 HOH HOH . J 5 HOH B 52 1033 1033 HOH HOH . J 5 HOH B 53 1036 1036 HOH HOH . J 5 HOH B 54 1037 1037 HOH HOH . J 5 HOH B 55 1038 1038 HOH HOH . J 5 HOH B 56 1039 1039 HOH HOH . J 5 HOH B 57 1042 1042 HOH HOH . J 5 HOH B 58 1043 1043 HOH HOH . J 5 HOH B 59 1045 1045 HOH HOH . J 5 HOH B 60 1047 1047 HOH HOH . J 5 HOH B 61 1048 1048 HOH HOH . J 5 HOH B 62 1049 1049 HOH HOH . J 5 HOH B 63 1050 1050 HOH HOH . J 5 HOH B 64 1053 1053 HOH HOH . J 5 HOH B 65 1054 1054 HOH HOH . J 5 HOH B 66 1056 1056 HOH HOH . J 5 HOH B 67 1059 1059 HOH HOH . J 5 HOH B 68 1060 1060 HOH HOH . J 5 HOH B 69 1064 1064 HOH HOH . J 5 HOH B 70 1065 1065 HOH HOH . J 5 HOH B 71 1067 1067 HOH HOH . J 5 HOH B 72 1070 1070 HOH HOH . J 5 HOH B 73 1071 1071 HOH HOH . J 5 HOH B 74 1073 1073 HOH HOH . J 5 HOH B 75 1076 1076 HOH HOH . J 5 HOH B 76 1077 1077 HOH HOH . J 5 HOH B 77 1080 1080 HOH HOH . J 5 HOH B 78 1083 1083 HOH HOH . J 5 HOH B 79 1085 1085 HOH HOH . J 5 HOH B 80 1086 1086 HOH HOH . J 5 HOH B 81 1088 1088 HOH HOH . J 5 HOH B 82 1092 1092 HOH HOH . J 5 HOH B 83 1096 1096 HOH HOH . J 5 HOH B 84 1097 1097 HOH HOH . J 5 HOH B 85 1100 1100 HOH HOH . J 5 HOH B 86 1103 1103 HOH HOH . J 5 HOH B 87 1106 1106 HOH HOH . J 5 HOH B 88 1107 1107 HOH HOH . J 5 HOH B 89 1109 1109 HOH HOH . J 5 HOH B 90 1111 1111 HOH HOH . J 5 HOH B 91 1114 1114 HOH HOH . J 5 HOH B 92 1116 1116 HOH HOH . J 5 HOH B 93 1117 1117 HOH HOH . J 5 HOH B 94 1118 1118 HOH HOH . J 5 HOH B 95 1120 1120 HOH HOH . J 5 HOH B 96 1124 1124 HOH HOH . J 5 HOH B 97 1125 1125 HOH HOH . J 5 HOH B 98 1126 1126 HOH HOH . J 5 HOH B 99 1131 1131 HOH HOH . J 5 HOH B 100 1132 1132 HOH HOH . J 5 HOH B 101 1133 1133 HOH HOH . J 5 HOH B 102 1134 1134 HOH HOH . J 5 HOH B 103 1138 1138 HOH HOH . J 5 HOH B 104 1139 1139 HOH HOH . J 5 HOH B 105 1140 1140 HOH HOH . J 5 HOH B 106 1142 1142 HOH HOH . J 5 HOH B 107 1148 1148 HOH HOH . J 5 HOH B 108 1150 1150 HOH HOH . J 5 HOH B 109 1151 1151 HOH HOH . J 5 HOH B 110 1154 1154 HOH HOH . J 5 HOH B 111 1155 1155 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 2 _atom_site.Cartn_x 95.406 _atom_site.Cartn_y 31.665 _atom_site.Cartn_z 10.604 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 43.28 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 901 _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 22 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #